Secondary literature sources for H4

The following references were automatically generated.

Sakaue T, Yoshikawa K, Yoshimura SH, Takeyasu K
Histone core slips along DNA and prefers positioning at the chain end.
Phys Rev Lett. 2001; 87: 78105-78105
Display abstract
We studied the stability and dynamics of a model of a nucleosome, the fundamental unit for the packing of long DNA in eukaryotes, using a Brownian dynamics simulation. For the proper folding of a stiff polymer on a core particle, moderate attractive interaction is shown to be essentially important, which explains the empirical experimental protocol for the reconstitution of nucleosomes. The effect of the chain end on the positioning of the core particle is examined and compared with the experimental data by atomic force microscopy measurement. It is also suggested that the core particle exhibits sliding motion along the chain as a manifestation of Brownian motion.

White CL, Suto RK, Luger K
Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions.
EMBO J. 2001; 20: 5207-18
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Chromatin is composed of nucleosomes, the universally repeating protein-DNA complex in eukaryotic cells. The crystal structure of the nucleosome core particle from Saccharomyces cerevisiae reveals that the structure and function of this fundamental complex is conserved between single-cell organisms and metazoans. Our results show that yeast nucleosomes are likely to be subtly destabilized as compared with nucleosomes from higher eukaryotes, consistent with the idea that much of the yeast genome remains constitutively open during much of its life cycle. Importantly, minor sequence variations lead to dramatic changes in the way in which nucleosomes pack against each other within the crystal lattice. This has important implications for our understanding of the formation of higher order chromatin structure and its modulation by post-translational modifications. Finally, the yeast nucleosome core particle provides a structural context by which to interpret genetic data obtained from yeast. Coordinates have been deposited with the Protein Data Bank under accession number 1ID3.

Fahrner RL, Cascio D, Lake JA, Slesarev A
An ancestral nuclear protein assembly: crystal structure of the Methanopyrus kandleri histone.
Protein Sci. 2001; 10: 2002-7
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Eukaryotic histone proteins condense DNA into compact structures called nucleosomes. Nucleosomes were viewed as a distinguishing feature of eukaryotes prior to identification of histone orthologs in methanogens. Although evolutionarily distinct from methanogens, the methane-producing hyperthermophile Methanopyrus kandleri produces a novel, 154-residue histone (HMk). Amino acid sequence comparisons show that HMk differs from both methanogenic and eukaryotic histones, in that it contains two histone-fold ms within a single chain. The two HMk histone-fold ms, N and C terminal, are 28% identical in amino acid sequence to each other and approximately 21% identical in amino acid sequence to other histone proteins. Here we present the 1.37-A-resolution crystal structure of HMk and report that the HMk monomer structure is homologous to the eukaryotic histone heterodimers. In the crystal, HMk forms a dimer homologous to [H3-H4](2) in the eukaryotic nucleosome. Based on the spatial similarities to structural ms found in the eukaryotic nucleosome that are important for DNA-binding, we infer that the Methanopyrus histone binds DNA in a manner similar to the eukaryotic histone tetramer [H3-H4](2).

Gangloff YG, Romier C, Thuault S, Werten S, Davidson I
The histone fold is a key structural motif of transcription factor TFIID.
Trends Biochem Sci. 2001; 26: 250-7
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Transcription factor TFIID is a multiprotein complex composed of the TATA binding protein and its associated factors, and is required for accurate and regulated initiation of transcription by RNA polymerase II. The subunit composition of this factor is highly conserved from yeast to mammals. X-ray crystallography and biochemical experiments have shown that the histone fold motif mediates many of the subunit interactions within this complex. These results, together with electron microscopy and yeast genetics, provide insights into the overall organization of this complex.

Duggan MM, Thomas JO
Two DNA-binding sites on the globular domain of histone H5 are required for binding to both bulk and 5 S reconstituted nucleosomes.
J Mol Biol. 2000; 304: 21-33
Display abstract
We have previously shown the existence of two DNA-binding sites on the globular domain of H5 (termed GH5), both of which are required for nucleosome organisation, as judged by the protection of a 166 bp chromatosome intermediate during micrococcal nuclease digestion of chromatin. This supports a model in which GH5 contacts two duplexes on the nucleosome. However, studies of a nucleosome assembled on the 5 S rRNA gene have argued against the requirement for two DNA-binding sites for chromatosome protection, which has implications for the role of linker histones. We have used this proposed difference in the requirement for a second site on the globular domain in the two models as a means of investigating whether bulk and reconstituted 5 S nucleosomes are indeed fundamentally different. GH5 protects a 166 bp chromatosome in both "bulk" and 5 S systems, and in both cases protection is abolished when all four basic residues in site II are replaced by alanine. Binding to four-way DNA junctions, which present a pair of juxtaposed duplexes, is also abolished. Single mutations of the basic residues did not abolish chromatosome protection in either system, or binding to four-way junctions, suggesting that the residues function as a cluster. Both bulk and 5 S nucleosomes thus require a functional second DNA-binding site on GH5 in order to bind properly to the nucleosome. This is likely to reflect a similar mode of binding in each case, in which two DNA duplexes are contacted in the nucleosome. There is no indication from these experiments that linker histones bind fundamentally differently to 5 S and bulk nucleosomes.

Polach KJ, Lowary PT, Widom J
Effects of core histone tail domains on the equilibrium constants for dynamic DNA site accessibility in nucleosomes.
J Mol Biol. 2000; 298: 211-23
Display abstract
The N and C-terminal tail domains of the core histones play important roles in gene regulation, but the mechanisms through which they act are not known. These tail domains are highly positively charged and are the sites of numerous post-translational modifications, including many sites for lysine acetylation. Nucleosomes in which these tail domains have been removed by trypsin remain otherwise intact, and are used by many laboratories as a model system for highly acetylated nucleosomes. Here, we test the hypothesis that one role of the tail domains is to directly regulate the accessibility of nucleosomal DNA to other DNA-binding proteins. Three assays are used: equilibrium binding by a site-specific, DNA-binding protein, and dynamic accessibility to restriction enzymes or to a non-specific exonuclease. The effects of removal of the tail domains as monitored by each of these assays can be understood within the framework of the site exposure model for the dynamic equilibrium accessibility of target sites located within the nucleosomal DNA. Removal of the tail domains leads to a 1.5 to 14-fold increase in position-dependent equilibrium constants for site exposure. The smallness of the effect weighs against models for gene activation in which histone acetylation is a mandatory initial event, required to facilitate subsequent access of regulatory proteins to nucleosomal DNA target sites. Alternative roles for histone acetylation in gene regulation are discussed.

Yoda K et al.
Human centromere protein A (CENP-A) can replace histone H3 in nucleosome reconstitution in vitro.
Proc Natl Acad Sci U S A. 2000; 97: 7266-71
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Centromere protein A (CENP-A) is a variant of histone H3 with more than 60% sequence identity at the C-terminal histone fold domain. CENP-A specifically locates to active centromeres of animal chromosomes and therefore is believed to be a component of the specialized centromeric nucleosomes on which the kinetochores are assembled. Here we report that CENP-A, highly purified from HeLa cells, can indeed replace histone H3 in a nucleosome reconstitution system mediated by nucleosome assembly protein-1 (NAP-1). The structure of the nucleosomes reconstituted with recombinant CENP-A, histones H2A, H2B, and H4, and closed circular DNAs had the following properties. By atomic force microscopy, "beads on a string" images were obtained that were similar to those obtained with nucleosomes reconstituted with four standard histones. DNA ladders with repeats of approximately 10 bp were produced by DNase I digestion, indicating that the DNA was wrapped round the protein complex. Mononucleosomes isolated by glycerol gradient sedimentation had a relative molecular mass of approximately 200 kDa and were composed of 120-150 bp of DNA and equimolar amounts of CENP-A, and histones H4, H2A, and H2B. Thus, we conclude that CENP-A forms an octameric complex with histones H4, H2A, and H2B in the presence of DNA.

Negri R, Buttinelli M, Panetta G, De Arcangelis V, Di Mauro E, Travers A
Helical repeat of DNA in the nucleosome core particle.
Biochem Soc Trans. 2000; 28: 373-6
Display abstract
Although the crystal structure of nucleosome core particle is essentially symmetrical in the vicinity of the dyad, the linker histone binds asymmetrically in this region to select a single high-affinity site from potentially two equivalent sites. To try to resolve this apparent paradox we mapped to base-pair resolution the dyads and rotational settings of nucleosome core particles reassembled on synthetic tandemly repeating 20 bp DNA sequences. In agreement with previous observations, we observed (1) that the helical repeat on each side of the dyad cluster is 10 bp maintaining register with the sequence repeat and (2) that this register changes by 2 bp in the vicinity of the dyad. The additional 2 bp required to effect the change in the rotational settings is accommodated by an adjustment immediately adjacent to the dyad. At the dyad the hydroxyl radical cleavage is asymmetric and we suggest that the inferred structural asymmetry could direct the binding of the linker histone to a single preferred site.

Suto RK, Clarkson MJ, Tremethick DJ, Luger K
Crystal structure of a nucleosome core particle containing the variant histone H2A.Z.
Nat Struct Biol. 2000; 7: 1121-4
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Activation of transcription within chromatin has been correlated with the incorporation of the essential histone variant H2A.Z into nucleosomes. H2A.Z and other histone variants may establish structurally distinct chromosomal domains; however, the molecular mechanism by which they function is largely unknown. Here we report the 2.6 A crystal structure of a nucleosome core particle containing the histone variant H2A.Z. The overall structure is similar to that of the previously reported 2.8 A nucleosome structure containing major histone proteins. However, distinct localized changes result in the subtle destabilization of the interaction between the (H2A.Z-H2B) dimer and the (H3-H4)(2) tetramer. Moreover, H2A.Z nucleosomes have an altered surface that includes a metal ion. This altered surface may lead to changes in higher order structure, and/or could result in the association of specific nuclear proteins with H2A.Z. Finally, incorporation of H2A.Z and H2A within the same nucleosome is unlikely, due to significant changes in the interface between the two H2A.Z-H2B dimers.

Vitolo JM, Thiriet C, Hayes JJ
The H3-H4 N-terminal tail domains are the primary mediators of transcription factor IIIA access to 5S DNA within a nucleosome.
Mol Cell Biol. 2000; 20: 2167-75
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Reconstitution of a DNA fragment containing a Xenopus borealis somatic type 5S rRNA gene into a nucleosome greatly restricts the binding of transcription factor IIIA (TFIIIA) to its cognate DNA sequence within the internal promoter of the gene. Removal of all core histone tail domains by limited trypsin proteolysis or acetylation of the core histone tails significantly relieves this inhibition and allows TFIIIA to exhibit high-affinity binding to nucleosomal DNA. Since only a single tail or a subset of tails may be primarily responsible for this effect, we determined whether removal of the individual tail domains of the H2A-H2B dimer or the H3-H4 tetramer affects TFIIIA binding to its cognate DNA site within the 5S nucleosome in vitro. The results show that the tail domains of H3 and H4, but not those of H2A and/or H2B, directly modulate the ability of TFIIIA to bind nucleosomal DNA. In vitro transcription assays carried out with nucleosomal templates lacking individual tail domains show that transcription efficiency parallels the binding of TFIIIA. In addition, we show that the stoichiometry of core histones within the 5S DNA-core histone-TFIIIA triple complex is not changed upon TFIIIA association. Thus, TFIIIA binding occurs by displacement of H2A-H2B-DNA contacts but without complete loss of the dimer from the nucleoprotein complex. These data, coupled with previous reports (M. Vettese-Dadey, P. A. Grant, T. R. Hebbes, C. Crane-Robinson, C. D. Allis, and J. L. Workman, EMBO J. 15:2508-2518, 1996; L. Howe, T. A. Ranalli, C. D. Allis, and J. Ausio, J. Biol. Chem. 273:20693-20696, 1998), suggest that the H3/H4 tails are the primary arbiters of transcription factor access to intranucleosomal DNA.

Shirakawa M
[Structures of proteins that regulate chromatin structures]
Tanpakushitsu Kakusan Koso. 2000; 45: 1658-70

Ahmad A, Takami Y, Nakayama T
Distinct regions of the chicken p46 polypeptide are required for its in vitro interaction with histones H2B and H4 and histone acetyltransferase-1.
Biochem Biophys Res Commun. 2000; 279: 95-102
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We cloned cDNA encoding the chicken p46 polypeptide, chp46, homologous to the p48 subunit of chicken chromatin assembly factor-1, chCAF-1p48. It comprises 424 amino acids including a putative initiation Met, is a member of the WD protein family, with seven WD repeat motifs, and exhibits 90.3% identity to chCAF-1p48 and 94.3% identity to the human and mouse p46 polypeptides (hup46 and mop46). The in vitro immunoprecipitation experiment established that chp46 interacts with histones H2B and H4 and chicken histone acetyltransferase-1, chHAT-1, whereas hup46 interacts with histones H2A and H4 and chHAT-1 and chCAF-1p48 with histone H4 and chHAT-1. The in vitro immunoprecipitation experiment, involving truncated mutants of chp46, revealed not only that two regions comprising amino acids 33-179 and 375-404 are necessary for its binding to H2B, but also that two regions comprising amino acids 1-32 and 405-424 are necessary for its binding to H4. Furthermore, the GST pulldown affinity assay, involving truncated mutants of chp46, revealed that a region comprising amino acids 359-404 (in fact, 375-404) binds to chHAT-1 in vitro. Taken together, these results indicate not only that chp46 should participate differentially in a number of DNA-utilizing processes through interactions of its distinct regions with chHAT-1 and histones H2B and H4, but also that the proper propeller structure of chp46 is not necessary for its interaction with chHAT-1.

Caretti G, Motta MC, Mantovani R
NF-Y associates with H3-H4 tetramers and octamers by multiple mechanisms.
Mol Cell Biol. 1999; 19: 8591-603
Display abstract
NF-Y is a CCAAT-binding trimer with two histonic subunits, NF-YB and NF-YC, resembling H2A-H2B. We previously showed that the short conserved domains of NF-Y efficiently bind to the major histocompatibility complex class II Ea Y box in DNA nucleosomized with purified chicken histones. Using wild-type NF-Y and recombinant histones, we find that NF-Y associates with H3-H4 early during nucleosome assembly, under conditions in which binding to naked DNA is not observed. In such assays, the NF-YB-NF-YC dimer forms complexes with H3-H4, for whose formation the CCAAT box is not required. We investigated whether they represent octamer-like structures, using DNase I, micrococcal nuclease, and exonuclease III, and found a highly positioned nucleosome on Ea, whose boundaries were mapped; addition of NF-YB-NF-YC does not lead to the formation of octameric structures, but changes in the digestion patterns are observed. NF-YA can bind to such preformed DNA complexes in a CCAAT-dependent way. In the absence of DNA, NF-YB-NF-YC subunits bind to H3-H4, but not to H2A-H2B, through the NF-YB histone fold. These results indicate that (i) the NF-Y histone fold dimer can efficiently associate DNA during nucleosome formation; (ii) it has an intrinsic affinity for H3-H4 but does not form octamers; and (iii) the interactions between NF-YA, NF-YB-NF-YC, and H3-H4 or nucleosomes are not mutually exclusive. Thus, NF-Y can intervene at different steps during nucleosome formation, and this scenario might be paradigmatic for other histone fold proteins involved in gene regulation.

Goldberg M et al.
The tail domain of lamin Dm0 binds histones H2A and H2B.
Proc Natl Acad Sci U S A. 1999; 96: 2852-7
Display abstract
In multicellular organisms, the higher order organization of chromatin during interphase and the reassembly of the nuclear envelope during mitosis are thought to involve an interaction between the nuclear lamina and chromatin. The nuclear distribution of lamins and of peripheral chromatin is highly correlated in vivo, and lamins bind specifically to chromatin in vitro. Deletion mutants of Drosophila lamin Dm0 were expressed to map regions of the protein that are required for its binding to chromosomes. The binding activity requires two regions in the lamin Dm0 tail domain. The apparent Kd of binding of the lamin Dm0 tail domain was found to be approximately 1 microM. Chromatin subfractions were examined to search for possible target molecules for the binding of lamin Dm0. Isolated polynucleosomes, nucleosomes, histone octamer, histone H2A/H2B dimer, and histones H2A or H2B displaced the binding of lamin Dm0 tail to chromosomes. This displacement was specific, because polyamines or proteins such as histones H1, H3, or H4 did not displace the binding of the lamin Dm0 tail to chromosomes. In addition, DNA sequences, including M/SARs, did not interfere with the binding of lamin Dm0 tail domain to chromosomes. Taken together, these results suggest that the interaction between the tail domain of lamin Dm0 and histones H2A and H2B may mediate the attachment of the nuclear lamina to chromosomes in vivo.

Travers A
The location of the linker histone on the nucleosome.
Trends Biochem Sci. 1999; 24: 4-7

Usachenko SI, Bradbury EM
Histone-DNA contacts in structure/function relationships of nucleosomes as revealed by crosslinking.
Genetica. 1999; 106: 103-15
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We describe studies of histone-DNA contacts in the nucleosome using the method of covalent zero length protein-DNA crosslinking. These studies show that in intact nuclei isolated from different sources the linear sequential arrangement of histone-DNA contacts in the nucleosomal core is essentially the same. However, the relative strength of certain contacts varies and correlates with the level of chromatin activity and condensation. These altered contacts are located in the sharply bent regions of the nucleosomal DNA and are supposed to be sensitive to the structural changes that may occur during nucleosome functions. Studies of the mechanism of these alterations revealed that the difference in strength of these contacts is attributed to the different conformational state of the nucleosomal core and is caused by stretching of the nucleosomal DNA upon chromatin decondensation during its activation. Histone-terminal domains may be involved in this process through posttranslational modifications affecting chromatin condensation. The described localization of the histone H2A C-terminal domain in the nucleosome by crosslinking demonstrates the ability of this methodology to determine the location of histone-terminal domains and thereby elucidate their role in nucleosome function. Results of the described experiments suggest that chromatin decondensation may alter the nucleosomal DNA conformation and affect the histone-DNA contacts resulting in a structural transition that may play a role in rendering the nucleosome competent for transcription and/or replication.

Usachenko SI, Bradbury EM
Localization of specific histone regions on nucleosomal DNA by cross-linking.
Methods Enzymol. 1999; 304: 264-78

Thomas JO
Histone H1: location and role.
Curr Opin Cell Biol. 1999; 11: 312-7
Display abstract
Recent experiments have shown directly that, in bulk chromatin, the globular domain of histone H1 is positioned close to the dyad axis and is asymmetrically disposed, consistent with a polar arrangement of H1 molecules along the nucleosome filament. In addition to a structural role, H1 may also have gene-specific effects on transcription. The positioning of a core particle relative to a transcription factor binding-site may favour either transcription factor binding or H1 binding, depending on the location of the site.

An W, Zlatanova J, Leuba SH, van Holde K
The site of binding of linker histone to the nucleosome does not depend upon the amino termini of core histones.
Biochimie. 1999; 81: 727-32
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Using nucleosomes reconstituted on a defined sequence of DNA, we have investigated the question as to whether the N-terminal tails of core histones play a role in determining the site of binding of a linker histone. Reconstitutes used histone cores of three types: intact, lacking the N-terminal H3 tails, or lacking all tails. In each case the same, single defined position for the histone core was observed, using high-resolution mapping. The affinity for binding of linker histone H1(o) was highest for the intact cores, lowest for the tailless cores. However, the location of the linker histone, as judged by micrococcal nuclease protection, was exactly the same in each case, an asymmetric site of about 17 bp to one side of the core particle DNA.

Zhou YB, Gerchman SE, Ramakrishnan V, Travers A, Muyldermans S
Position and orientation of the globular domain of linker histone H5 on the nucleosome.
Nature. 1998; 395: 402-5
Display abstract
It is essential to identify the exact location of the linker histone within nucleosomes, the fundamental packing units of chromatin, in order to understand how condensed, transcriptionally inactive chromatin forms. Here, using a site-specific protein-DNA photo-crosslinking method, we map the binding site and the orientation of the globular domain of linker histone H5 on mixed-sequence chicken nucleosomes. We show, in contrast to an earlier model, that the globular domain forms a bridge between one terminus of chromatosomal DNA and the DNA in the vicinity of the dyad axis of symmetry of the core particle. Helix III of the globular domain binds in the major groove of the first helical turn of the chromatosomal DNA, whereas the secondary DNA-binding site on the opposite face of the globular domain of histone H5 makes contact with the nucleosomal DNA close to its midpoint. We also infer that helix I and helix II of the globular domain of histone H5 probably face, respectively, the solvent and the nucleosome. This location places the basic carboxy-terminal region of the globular domain in a position from which it could simultaneously bind the nucleosome-linking DNA strands that exit and enter the nucleosome.

Hamiche A, Richard-Foy H
The switch in the helical handedness of the histone (H3-H4)2 tetramer within a nucleoprotein particle requires a reorientation of the H3-H3 interface.
J Biol Chem. 1998; 273: 9261-9
Display abstract
It has recently been proposed that the histone (H3-H4)2 tetramer undergoes structural changes, which allow the particle to accommodate both negatively and positively constrained DNA. To investigate this process, we modified histone H3 at the H3-H3 interface, within the histone (H2A-H2B-H3-H4)2 octamer or the histone (H3-H4)2 tetramer, by forming adducts on the single cysteine of duck histone H3. We used three sulfhydryl reagents, iodoacetamide, N-ethylmaleimide, and 5,5'-dithiobis(2-nitrobenzoic acid). Torsionally constrained DNA was assembled on the modified histones. The H3 adducts, which have no effect on the structure of the nucleosome, dramatically affected the structural transitions that the (H3-H4)2 tetrameric nucleoprotein particle can undergo. Iodoacetamide and N-ethylmaleimide treatment prevented the assembly of positively constrained DNA on the tetrameric particle, whereas 5, 5'-dithiobis(2-nitrobenzoic acid) treatment strongly favored it. Determination of DNA topoisomer equilibrium after relaxation of the tetrameric nucleoprotein particles with topoisomerase I demonstrated that the structural transition occurs without histone dissociation. Incorporation of H2A-H2B dimers into the tetrameric particle containing modified or unmodified cysteines allowed nucleosomes to reform and blocked the structural transition of the particle. We demonstrate the importance of the histone H3-H3 contact region in the conformational changes of the histone tetramer nucleoprotein particle and the role of H2A-H2B in preventing a structural transition of the nucleosome.

Verreault A, Kaufman PD, Kobayashi R, Stillman B
Nucleosomal DNA regulates the core-histone-binding subunit of the human Hat1 acetyltransferase.
Curr Biol. 1998; 8: 96-108
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BACKGROUND: In eukaryotic cells, newly synthesized histone H4 is acetylated at lysines 5 and 12, a transient modification erased by deacetylases shortly after deposition of histones into chromosomes. Genetic studies in Saccharomyces cerevisiae revealed that acetylation of newly synthesized histones H3 and H4 is likely to be important for maintaining cell viability; the precise biochemical function of this acetylation is not known, however. The identification of enzymes mediating site-specific acetylation of H4 at Lys5 and Lys12 may help explain the function of the acetylation of newly synthesized histones. RESULTS: A cDNA encoding the catalytic subunit of the human Hat1 acetyltransferase was cloned and, using specific antibodies, the Hat1 holoenzyme was purified from human 293 cells. The human enzyme acetylates soluble but not nucleosomal H4 at Lys5 and Lys12 and acetylates histone H2A at Lys5. Unexpectedly, we found Hat1 in the nucleus of S-phase cells. Like its yeast counterpart, the human holoenzyme consists of two subunits: a catalytic subunit, Hat1, and a subunit that binds core histones, p46, which greatly stimulates the acetyltransferase activity of Hat1. Both p46 and the highly related p48 polypeptide (the small subunit of human chromatin assembly factor 1; CAF-1) bind directly to helix 1 of histone H4, a region that is not accessible when H4 is in chromatin. CONCLUSIONS: We suggest that p46 and p48 are core-histone-binding subunits that target chromatin assembly factors, chromatin remodeling factors, histone acetyltransferases and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA.

Luger K, Richmond TJ
The histone tails of the nucleosome.
Curr Opin Genet Dev. 1998; 8: 140-6
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Reversible acetylation of core histone tails plays an important role in the regulation of eukaryotic transcription, in the formation of repressive chromatin complexes, and in the inactivation of whole chromosomes. The high-resolution X-ray structure of the nucleosome core particle, as well as earlier evidence, suggests that the histone tails are largely responsible for the assembly of nucleosomes into chromatin fibers and implies that the physiological effects of histone acetylation may be achieved by modulation of a dynamic inter-conversion between the fiber and a less condensed nucleofilament structure. In addition, the tails and adjacent regions serve as recognition sites for chromatin assembly and transcription remodeling machinery and the interactions that occur may also be responsive to histone acetylation.

An W, Leuba SH, van Holde K, Zlatanova J
Linker histone protects linker DNA on only one side of the core particle and in a sequence-dependent manner.
Proc Natl Acad Sci U S A. 1998; 95: 3396-401
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The protection against micrococcal nuclease digestion afforded to chromatosomal DNA by the presence of a linker histone (H1(o)) has been quantitatively measured in two reconstituted systems. We have used chromatosomes reconstituted at two distinct positions on a DNA fragment containing the 5S rRNA gene from Lytechinus variegatus and at a specific position on a sequence containing Gal4- and USF-binding sites. In all cases, we find asymmetric protection, with approximately 20 bp protected on one side of the core particle and no protection on the other. We demonstrated through crosslinking experiments that the result is not due to any sliding of the histone core caused by either linker histone addition or micrococcal nuclease cleavage. Because the core particle is itself a symmetric object, the preferred asymmetric location of a linker histone must be dictated by unknown elements in the DNA sequence.

Lee KM, Hayes JJ
Linker DNA and H1-dependent reorganization of histone-DNA interactions within the nucleosome.
Biochemistry. 1998; 37: 8622-8
Display abstract
We have employed a site-directed photochemical cross-linking procedure to precisely map interactions between nucleosomal DNA and the C-terminal tail of core histone H2A. We find that this tail has the potential to contact multiple sites within the nucleosome and that these contacts are dependent upon the configuration of the complex. This tail contacts DNA near the dyad axis within nucleosome core particles but rearranges to a site near the edge of the nucleosomal DNA when linker DNA is present. Moreover, in the presence of linker histone H1 the contacts near the edge of the nucleosome but not at the dyad are further rearranged. In addition, we present further evidence for the suggestion that the binding of linker histone causes a subtle but global change in core histone-DNA interactions within the nucleosome [Usachenko, S. I., Gavin, I. M., and Bavykin, S. G. (1996) J. Biol. Chem. 271, 3831-3836].

Cirillo LA et al.
Binding of the winged-helix transcription factor HNF3 to a linker histone site on the nucleosome.
EMBO J. 1998; 17: 244-54
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The transcription factor HNF3 and linker histones H1 and H5 possess winged-helix DNA-binding domains, yet HNF3 and other fork head-related proteins activate genes during development whereas linker histones compact DNA in chromatin and repress gene expression. We compared how the two classes of factors interact with chromatin templates and found that HNF3 binds DNA at the side of nucleosome cores, similarly to what has been reported for linker histone. A nucleosome structural binding site for HNF3 is occupied at the albumin transcriptional enhancer in active and potentially active chromatin, but not in inactive chromatin in vivo. While wild-type HNF3 protein does not compact DNA extending from the nucleosome, as does linker histone, site-directed mutants of HNF3 can compact nucleosomal DNA if they contain basic amino acids at positions previously shown to be essential for nucleosomal DNA compaction by linker histones. The results illustrate how transcription factors can possess special nucleosome-binding activities that are not predicted from studies of factor interactions with free DNA.

Pereira SL, Reeve JN
Histones and nucleosomes in Archaea and Eukarya: a comparative analysis.
Extremophiles. 1998; 2: 141-8
Display abstract
Archaeal histones from mesophilic, thermophilic, and hyperthermophilic members of the Euryarchaeota have primary sequences, the histone fold, tertiary structures, and dimer formation in common with the eukaryal nucleosome core histones H2A, H2B, H3, and H4. Archaeal histones form nucleoprotein complexes in vitro and in vivo, designated archaeal nucleosomes, that contain histone tetramers and protect approximately 60 base pairs of DNA from nuclease digestion. Based on the sequence and structural homologies and experimental data reviewed here, archaeal nucleosomes appear similar, and may be homologous in evolutionary terms and function, to the structure at the center of the eukaryal nucleosome formed by the histone (H3 + H4)2 tetramer.

Featherstone C
Researchers get their first good look at the nucleosome.
Science. 1997; 277: 1763-4

Moore SC, Ausio J
Major role of the histones H3-H4 in the folding of the chromatin fiber.
Biochem Biophys Res Commun. 1997; 230: 136-9
Display abstract
We have characterized the hydrodynamic behavior of nucleosome arrays in which the N- and C-terminal "tails" of the histone H2A-H2B and H3-H4 domains have been selectively removed by digestion with immobilized trypsin. The sedimentation coefficient of the polynucleosome fibers lacking the histone H2A-H2B tails exhibited a salt dependence close to that of the non-trypsinized nucleosome arrays. In contrast, the salt-dependent behavior of the H3-H4-trypsinized polynucleosome fibers was found to be closer to that observed for the nucleosome arrays on which all the histones were trypsinized. This indicates that the N- and C-terminal domains of histones H3-H4 play a major role in the folding of the chromatin fiber. Magnesium titration of the polynucleosome fibers consisting of these trypsinized histone octamer hybrids at low ionic strength indicates that the histone H3-H4 tails also play an important role in the association of the polynucleosome fibers. These findings suggest that, after linker histones (histones of the H1 family), the tails of the histone H3-H4 domains are the major players in the processes that lead to the intra-association (folding) and inter-association of the chromatin fiber.

Prunell A
Linker histones' role revisited.
Biophys J. 1997; 72: 983-4

Stemmer C, Briand JP, Muller S
Mapping of linear histone regions exposed at the surface of the nucleosome in solution.
J Mol Biol. 1997; 273: 52-60
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Antibodies directed against defined regions of histone molecules represent one of the most specific probes for studying the topography and conformational changes of nucleosomes and chromatin. We have developed an assay involving a series of monoclonal and polyclonal antibody probes specifically reacting with a complete set of 40 overlapping synthetic peptides (6 to 28 residues long) covering the whole sequence of the four core histones H2A, H2B, H3 and H4. In this assay, mono-, di- and trinucleosomes, as well as a long chain of chromatin containing 20 to 35 nucleosomes, were used in solution as competitors of the antibody reaction. At least 11 surface-oriented linear regions were characterized on the mononucleosome; namely, the N-terminal domains of H2A (residues 1 to 20), H2B (residues 1 to 25) and H3 (residues 1 to 30), the C-terminal domains of H2A (residues 116 to 129) and H4 (residues 85 to 102), and six domains located in internal segments in the primary structures of core histones (33 to 49 H2A, 65 to 85 H2A, 60 to 78 H2B, 50 to 70 H3, 111 to 130 H3 and 42 to 59 H4). Only a few changes in the nucleosome topography were observed when free oligo- and polynucleosome structure were comparatively studied.

Lee KM, Hayes JJ
The N-terminal tail of histone H2A binds to two distinct sites within the nucleosome core.
Proc Natl Acad Sci U S A. 1997; 94: 8959-64
Display abstract
Each of the core histone proteins within the nucleosome has a central "structured" domain that comprises the spool onto which the DNA superhelix is wrapped and an N-terminal "tail" domain in which the structure and molecular interactions have not been rigorously defined. Recent studies have shown that the N-terminal domains of core histones probably contact both DNA and proteins within the nucleus and that these interactions play key roles in the regulation of nuclear processes (such as transcription and replication) and are critical in the formation of the chromatin fiber. An understanding of these complex mechanisms awaits identification of the DNA or protein sites within chromatin contacted by the tail domains. To this end, we have developed a site-specific histone protein-DNA photocross-linking method to identify the DNA binding sites of the N-terminal domains within chromatin complexes. With this approach, we demonstrate that the N-terminal tail of H2A binds DNA at two defined locations within isolated nucleosome cores centered around a position approximately 40 bp from the nucleosomal dyad and that this tail probably adopts a defined structure when bound to DNA.

Baneres JL, Martin A, Parello J
The N tails of histones H3 and H4 adopt a highly structured conformation in the nucleosome.
J Mol Biol. 1997; 273: 503-8
Display abstract
The histone N tails correspond to conserved amino acid sequences that are peripherally located in the nucleosome and undergo a variety of post-synthetic modifications during cell cycle. These N tails have been recently recognized as directly interacting with transcription-related proteins. We show here, based on circular dichroic evidence, that the N tails of both tetrameric histones H3 and H4 are highly organized as DNA-bound polypeptide segments in the nucleosome core particle, with about half of their residues, taken together, being alpha-helical. In contrast, the N tails of both dimeric histones H2A and H2B are found essentially in a random-coil conformation. The implications of these findings on nucleosome structure and recognition are discussed.

Widom J
Chromatin: the nucleosome unwrapped.
Curr Biol. 1997; 7: 6535-6535
Display abstract
The structure of the nucleosome core particle has been determined by X-ray crystallography at 2.8 A resolution. The structure has several significant surprises, and provides important new insights into the structure and function of chromatin.

Khrapunov SN, Dragan AI, Sivolob AV, Zagariya AM
Mechanisms of stabilizing nucleosome structure. Study of dissociation of histone octamer from DNA.
Biochim Biophys Acta. 1997; 1351: 213-22
Display abstract
The influence of ionic strength on DNA-histone and histone-histone interactions in reconstituted nucleosomes was studied by measuring the parameters of histone tyrosine fluorescence: fluorescence intensity and lambda(max) position. The first parameter is sensitive to histone-DNA interactions. The changes of the second one accrue due to hydrogen bond formation/disruption between tyrosines in the histone H2A-H2B dimer and the (H3-H4)2 tetramer. The simultaneous measurement of these parameters permits the recording of both the dissociation of histone complexes from DNA, as well as changes in histone-histone interactions. As ionic strength is increased, the H2A-H2B histone dimer dissociated first, followed by dissociation of the (H3-H4)2 tetramer [Yager, T.G., McMurray, C.T. and Van Holde, K.E. (1989) Biochemistry 28, 2271-2276]. The H2A-H2B dimer is dissociated in two stages: first, the ionic bonds with DNA were disrupted, followed by the dissociation of the histone dimer from the tetramer. And secondly, the disruption of dimer-tetramer specific H-bonds. It was established that the energy of electrostatic interactions of the histone dimer with DNA within the nucleosome is much less than the energy of interaction of the histone dimer with the tetramer.

Dutnall RN, Ramakrishnan V
Twists and turns of the nucleosome: tails without ends.
Structure. 1997; 5: 1255-9
Display abstract
The high-resolution structure of a nucleosome core particle gives us our first detailed look at the primary level of eukaryotic DNA organization. The structure reveals the nature of histone-DNA contacts and provides some surprises regarding the histone tails and their possible involvement in higher levels of chromatin organization.

Rhodes D
Chromatin structure. The nucleosome core all wrapped up.
Nature. 1997; 389: 231233-231233

Ramakrishnan V
Histone structure and the organization of the nucleosome.
Annu Rev Biophys Biomol Struct. 1997; 26: 83-112
Display abstract
Chromatin structure is now believed to be dynamic and intimately related with cellular processes such as transcription. Over the past few years, high-resolution structures for the histones have become available. These structures and their implications for nucleosome organization are reviewed here.

Tse C, Hansen JC
Hybrid trypsinized nucleosomal arrays: identification of multiple functional roles of the H2A/H2B and H3/H4 N-termini in chromatin fiber compaction.
Biochemistry. 1997; 36: 11381-8
Display abstract
A defined 12-mer nucleosomal array in solution exists in a complex equilibrium between an unfolded 29S conformation, a 40S folding intermediate, an extensively folded 55S conformation, and soluble oligomeric states formed from cooperative intermolecular association of individual 12-mer arrays. Proteolytic removal of all of the core histone N-terminal tail domains previously has been shown to abolish both salt-dependent nucleosomal array folding and oligomerization. To elucidate the individual contributions of the H2A/H2B and H3/H4 tail domains to nucleosomal array condensation, "hybrid" trypsinized nucleosomal arrays have been assembled from tandemly repeated 5S rDNA and either trypsinized H3/H4 tetramers and intact H2A/H2B dimers or trypsinized H2A/H2B dimers and intact H3/H4 tetramers. Neither of the hybrid trypsinized arrays formed either the 40S or the 55S folded conformations in 2 mM MgCl2. In >/=4 mM MgCl2, however, both fully trypsinized arrays and each hybrid trypsinized array formed the 40S folding intermediate, but not the 55S conformation. In contrast to folding, each hybrid trypsinized nucleosomal array oligomerized completely in MgCl2. These studies have identified three mechanistically distinct functions performed by the core histone N-termini during salt-dependent condensation of nucleosomal arrays. The complexity of tail domain function in chromatin is discussed in the context of a competitive interaction model in which the core histone N-termini provide direct mechanistic links between the structure and function of the chromatin fiber.

Pruss D, Bavykin SG
Chromatin studies by DNA-protein cross-linking.
Methods. 1997; 12: 36-47
Display abstract
Our current level of understanding of chromatin structure was to a large extent achieved with the help of DNA-protein cross-linking. The versatile inventory of cross-linking techniques allows the identification of the contacts between DNA and proteins with a single nucleotide-single amino acid precision, to detect minor components of the complex nucleoprotein systems, to reveal the interactions of the flexible protein domains with DNA, and to assay for conformational changes in the nucleosomes.

Travers A, Drew H
DNA recognition and nucleosome organization.
Biopolymers. 1997; 44: 423-33
Display abstract
The affinity of a DNA sequence for the histone octamer in a core nucleosome depends on the intrinsic flexibility of the DNA. This parameter can be affected both by the sequence-dependent conformational preferences of individual base steps and by the nature and location of the exocyclic groups of the DNA bases. By adopting highly preferred conformations particular types of base step can influence the rotational positioning of the DNA on the surface of the histone octamer. The asymmetry of the next higher order of chromatin structure is determined in part by the asymmetric binding of the globular domain of histone H5 to the core nucleosome.

Zubrzycki IZ, Bohm L
Folding of the SPKK rich peptide in the presence of the octa-oligonucleotide.
Z Naturforsch [C]. 1997; 52: 77-81
Display abstract
The nucleosome contains of 200 base pairs of DNA complexed with four core histone complex: H2A, H2B, H3, and H4. The fifth histone species, the H1 histone, interacts with linker DNA connecting neighbouring nucleosomes. We have studied the influence of the phosphorylation on the interactions of a repeating unit 15 residues long, containing the SPKK motif, the motif thought to induce turn along peptides sequences, enclosed within the trout testis H1 C-terminal domain with octanucleotide by means of the thermal denaturation and CD technique. The results indicate that the peptide preferentially binds to a single stranded oligonucleotide. It has been shown further that there is no beta structure present but a distorted helical structure has been detected.

Kingston RE
A snapshot of a dynamic nuclear building block.
Nat Struct Biol. 1997; 4: 763-6

Ouzounis CA, Kyrpides NC
Parallel origins of the nucleosome core and eukaryotic transcription from Archaea.
J Mol Evol. 1996; 42: 234-9
Display abstract
Computational sequence analysis of 10 available archaean histone-like proteins has shown that this family is not only divergently related to the eukaryotic core histones H2A/B, H3, and H4, but also to the central domain of subunits A and C of the CCAAT-binding factor (CBF), a transcription factor associated with eukaryotic promoters. Despite the low sequence identity, it is unambiguously shown that the core histone fold shares a common evolutionary history. Archaean histones and the two CBF families show a remarkable variability in contrast to eukaryotic core histones. Conserved residues shared between families are identified, possibly being responsible for the functional versatility of the core histone fold. The H4 subfamily is most similar to archaean proteins and may be the progenitor of the other core histones in eukaryotes. While it is not clear whether archaean histones are more actively involved in transcription regulation, the present observations link two processes, nucleosomal packing and transcription in a unique way. Both these processes, evidently hybrid in Archaea, have originated before the ermergence of the eukaryotic cell.

Goytisolo FA et al.
Identification of two DNA-binding sites on the globular domain of histone H5.
EMBO J. 1996; 15: 3421-9
Display abstract
The nature of the complexes of histones H1 and H5 and their globular domains (GH1 and GH5) with DNA suggested two DNA-binding sites which are likely to be the basis of the preference of H1 and H5 for the nucleosome, compared with free DNA. More recently the X-ray and NMR structures of GH5 and GH1, respectively, have identified two basic clusters on opposite sides of the domains as candidates for these sites. Removal of the positive charge at either location by mutagenesis impairs or abolishes the ability of GH5 to assemble cooperatively in 'tramline' complexes containing two DNA duplexes, suggesting impairment or loss of its ability to bind two DNA duplexes. The mutant forms of GH5 also fail to protect the additional 20 bp of nucleosomal DNA that are characteristically protected by H1, H5 and wild-type recombinant GH5. They still bind to H1/H5-depleted chromatin, but evidently inappropriately. These results confirm the existence of, and identify the major components of, two DNA-binding sites on the globular domain of histone H5, and they strongly suggest that both binding sites are required to position the globular domain correctly on the nucleosome.

Suzuki M, Suckow J, Kisters-Woike B, Aramaki H, Makino K
Multi-helical DNA-binding domains: their structures and modes of DNA-binding.
Adv Biophys. 1996; 32: 31-52

Wolffe AP, Pruss D
Deviant nucleosomes: the functional specialization of chromatin.
Trends Genet. 1996; 12: 58-62
Display abstract
Regulatory proteins exist with strong sequence and structural similarities to the histone proteins. Molecular genetic and cell biological analyses suggest that these proteins are localized at particular sites within the chromosome. Their assembly into nucleosomal structures confers specialized functions to individual chromosomal domains.

Usachenko SI, Gavin IM, Bavykin SG
Alterations in nucleosome core structure in linker histone-depleted chromatin.
J Biol Chem. 1996; 271: 3831-6
Display abstract
We have previously shown that the sequential arrangement of histone-DNA contacts is essentially the same in the nucleosomal core of sea urchin sperm nuclei, where chromatin is highly condensed and repressed, and in nuclei from lily bud sepals or yeast, where chromatin is highly active in transcription and replication and is significantly or completely depleted of histone H1. However, the difference in the strength of some histone-DNA contacts has not been understood or discussed. In this work, we demonstrate that some of these differences are due to a conformational change in the nucleosomal core. We show that the nucleosomal core in linker histone-depleted chromatin is in a different conformational state compared with the nucleosomal core in folded chromatin or in isolated core nucleosomes. This conformational state is characterized by altered strengths in the histone H4 and H2A/H2B contacts with the regions of sharply bent nucleosomal DNA around sites +/-1 and +/-4 and site +/-5, respectively. We demonstrate that this conformation, which we call the "stretched nucleosome," is a general feature of unfolded linker histone-depleted chromatin and may occur during chromatin activation. Our results suggest that this nucleosome structural alteration does not depend on chromatin sources and histone variants studied in this work. In addition, we show that this alteration is reversible and is caused by the stretching of linker DNA during chromatin unfolding.

Blomquist P, Li Q, Wrange O
The affinity of nuclear factor 1 for its DNA site is drastically reduced by nucleosome organization irrespective of its rotational or translational position.
J Biol Chem. 1996; 271: 153-9
Display abstract
A DNA-bending sequence has been used for in vitro reconstitution of nucleosomes in order to direct a nuclear factor 1 (NF-1) binding site into different nucleosome positions. By this strategy nucleosomes were obtained that had one of two rotational positions of the NF-1 binding site, one oriented toward the periphery and the other toward the histone octamer, translationally positioned 50 and 45 base pairs, respectively, from the nucleosome dyad. The affinity of partially purified NF-1 for these nucleosomal targets was compared with its affinity for free DNA by dimethylsulfate methylation protection and DNase I footprinting assays. The binding affinity of NF-1 to all nucleosomal targets was reduced 100-300-fold compared with its affinity for free DNA. The two rotational settings of the NF-1 site showed the same binding affinity for NF-1 as did other nucleosome constructs in which the NF-1 binding site was translationally positioned from 10 to 40 base pairs from the nucleosome dyad. We conclude that the nucleosomal inhibition of NF-1 binding is an inherent characteristic of NF-1 since another transcription factor, the glucocorticoid receptor, is able to bind to its DNA site in a nucleosome.

Ballestar E, Abad C, Franco L
Core histones are glutaminyl substrates for tissue transglutaminase.
J Biol Chem. 1996; 271: 18817-24
Display abstract
Chicken erythrocyte core histones are glutaminyl substrates in the transglutaminase (TGase) reaction with monodansylcadaverine (DNC) as donor amine. The modification is very fast when compared with that of many native substrates of TGase. Out of the 18 glutamines of the four histones, nine (namely glutamine 95 of H2B; glutamines 5, 19, and 125 of H3; glutamines 27 and 93 of H4; and glutamines 24, 104, and 112 of H2A) are the amine acceptors in free histones. The use of Gln112 of H2A requires a temperature-dependent partial unfolding of the histone, showing that structural determinants are decisive for the glutamine specificity. The structures of H2A and H2B do not appreciably change upon modification with DNC as determined by circular dichroism, and core particles reconstituted from these DNC-modified histones are indistinguishable from native nucleosome cores. When the reaction is carried out with native nucleosomes, only glutamines 5 and 19 of H3, which are located in the N-terminal tail, and glutamine 22 of H2B, which is not labeled in free histone, are modified. Methylamine and putrescine also are incorporated into nucleosomes by the TGase reaction. Our results reveal several possibilities for the application of the TGase reaction in the chromatin field, and taking into account that histones are easily cross-linked or modified by polyamines in vitro, the possibility that they may be TGase substrates in vivo is discussed.

Wang ZF, Tisovec R, Debry RW, Frey MR, Matera AG, Marzluff WF
Characterization of the 55-kb mouse histone gene cluster on chromosome 3.
Genome Res. 1996; 6: 702-14
Display abstract
The histone gene cluster on mouse chromosome 3 has been isolated as a series of overlapping P1 clones, covering 110-120 kb, by probing with the histone H3-614 gene that had been mapped previously to mouse chromosome 3. There are genes for 10 core histone proteins present in a 55-kb cluster within this contig. There are three histone H3 genes, two of which are identical; four histone H2a genes, two of which are identical, one histone H4 gene; and two histone H2b genes. These histone H3 and H2a genes encode approximately 40% of the total H3 and H2a mRNA, whereas the histone H4 and histone H2b genes encode < 10% of the total H4 and H2b mRNA. There are no histone H1 genes present in this cluster. All of the histone H2a genes encode histone H2a.2 proteins (or variants of H2a.2), and account for all the H2a.2 genes in the mouse genome. All three histone H3 genes encode the histone H3.2 protein. A 21-kb region containing the adjacent H3-614 and H2a-614 genes has been duplicated and is present in an inverted repeat separated by 4.5 kb. The other two H2a genes are adjacent, with the 3' ends of their mRNAs separated by only 49 nucleotides in the DNA and the U7 snRNP binding sites separated by only 20 nucleotides. One of the histone H2b genes has lost the stem-loop sequence characteristic of the replication-dependent histone mRNAs and encodes only polyadenylated mRNAs.

Wolffe AP, Pruss D
Hanging on to histones. Chromatin.
Curr Biol. 1996; 6: 234-7
Display abstract
Transcriptional control at a number of promoters has been found to involve the highly selective recognition of individual core histones by regulatory proteins, showing how the eukaryotic transcriptional machinery is adapted to function in a chromosomal environment.

Verreault A, Kaufman PD, Kobayashi R, Stillman B
Nucleosome assembly by a complex of CAF-1 and acetylated histones H3/H4.
Cell. 1996; 87: 95-104
Display abstract
Chromatin assembly factor 1 (CAF-1) assembles nucleosomes in a replication-dependent manner. The small subunit of CAF-1 (p48) is a member of a highly conserved subfamily of WD-repeat proteins. There are at least two members of this subfamily in both human (p46 and p48) and yeast cells (Hat2p, a subunit of the B-type H4 acetyltransferase, and Msi1p). Human p48 can bind to histone H4 in the absence of CAF-1 p150 and p60. p48, also a known subunit of a histone deacetylase, copurifies with a chromatin assembly complex (CAC), which contains the three subunits of CAF-1 (p150, p60, p48) and H3 and H4, and promotes DNA replication-dependent chromatin assembly. CAC histone H4 exhibits a novel pattern of lysine acetylation that overlaps with, but is distinct from, that reported for newly synthesized H4 isolated from nascent chromatin. Our data suggest that CAC is a key intermediate of the de novo nucleosome assembly pathway and that the p48 subunit participates in other aspects of histone metabolism.

Pruss D et al.
An asymmetric model for the nucleosome: a binding site for linker histones inside the DNA gyres.
Science. 1996; 274: 614-7
Display abstract
Histone-DNA contacts within a nucleosome influence the function of trans-acting factors and the molecular machines required to activate the transcription process. The internal architecture of a positioned nucleosome has now been probed with the use of photoactivatable cross-linking reagents to determine the placement of histones along the DNA molecule. A model for the nucleosome is proposed in which the winged-helix domain of the linker histone is asymmetrically located inside the gyres of DNA that also wrap around the core histones. This domain extends the path of the protein superhelix to one side of the core particle.

Vettese-Dadey M, Grant PA, Hebbes TR, Crane- Robinson C, Allis CD, Workman JL
Acetylation of histone H4 plays a primary role in enhancing transcription factor binding to nucleosomal DNA in vitro.
EMBO J. 1996; 15: 2508-18
Display abstract
Core histones isolated from normal and butyrate-treated HeLa cells have been reconstituted into nucleosome cores in order to analyze the role of histone acetylation in enhancing transcription factor binding to recognition sites in nucleosomal DNA. Moderate stimulation of nucleosome binding was observed for the basic helix-loop-helix factor USF and the Zn cluster DNA binding domain factor GAL4-AH using heterogeneously acetylated histones. However, by coupling novel immunoblotting techniques to a gel retardation assay, we observed that nucleosome cores containing the most highly acetylated forms of histone H4 have the highest affinity for these two transcription factors. Western analysis of gel-purified USF-nucleosome and GAL4-AH-nucleosome complexes demonstrated the predominant presence of acetylated histone H4 relative to acetylated histone H3. Immunoprecipitation of USF-nucleosome complexes with anti-USF antibodies also demonstrated that these complexes were enriched preferentially in acetylated histone H4. These data show that USF and GAL4-AH preferentially interact with nucleosome cores containing highly acetylated histone H4. Acetylation of histone H4 thus appears to play a primary role in the structural changes that mediate enhanced binding of transcription factors to their recognition sites within nucleosomes.

Agarwal S, Behe MJ
Non-conservative mutations are well tolerated in the globular region of yeast histone H4.
J Mol Biol. 1996; 255: 401-11
Display abstract
Yeast histone H4 has been mutagenized at several positions which participate in the globular core of the nucleosome. The native protein contains residues at those positions which are invariant or highly conserved over all known H4 sequences, whether from yeast, Tetrahymena or higher eukaryotes. Nonetheless the protein is tolerant of non-conservative mutations. At the level of cell function the mutant proteins cause no significant change in length of the cell cycle of mating efficiency. At the level of chromatin structure no effect is observed on the internucleosomal spacing of chromatin or the pattern of hydroxyl radical cleavage of nucleosomal DNA.

Pennisi E
Linker histones, DNA's protein custodians, gain new respect.
Science. 1996; 274: 503-4

Godde JS, Nakatani Y, Wolffe AP
The amino-terminal tails of the core histones and the translational position of the TATA box determine TBP/TFIIA association with nucleosomal DNA.
Nucleic Acids Res. 1995; 23: 4557-64
Display abstract
We establish that the TATA binding protein (TBP) in the presence of TFIIA recognizes the TATA box in nucleosomal DNA dependent on the dissociation of the amino-terminal tails of the core histones from the nucleosome and the position of the TATA box within the nucleosome. We examine TBP/TFIIA access to the TATA box with this sequence placed in four distinct rotational frames with reference to the histone surface and at three distinct translational positions at the edge, side and dyad axis of the nucleosome. Under our experimental conditions, we find that the preferential translational position at which TBP/TFIIA can bind the TATA box is within linker DNA at the edge of the nucleosome and that binding is facilitated if contacts made by the amino-terminal tails of the histones with nucleosomal DNA are eliminated. TBP/TFIIA binding to DNA at the edge of the nucleosome occurs with the TATA box in all four rotational positions. This is indicative of TBP/TFIIA association directing the dissociation of the TATA box from the surface of the histone octamer.

Baxevanis AD, Arents G, Moudrianakis EN, Landsman D
A variety of DNA-binding and multimeric proteins contain the histone fold motif.
Nucleic Acids Res. 1995; 23: 2685-91
Display abstract
The histone fold motif has previously been identified as a structural feature common to all four core histones and is involved in both histone-histone and histone-DNA interactions. Through the use of a novel motif searching method, a group of proteins containing the histone fold motif has been established. The proteins in this group are involved in a wide variety of functions related mostly to DNA metabolism. Most of these proteins engage in protein-protein or protein-DNA interactions, as do their core histone counterparts. Among these, CCAAT-specific transcription factor CBF and its yeast homologue HAP are two examples of multimeric complexes with different component subunits that contain the histone fold motif. The histone fold proteins are distantly related, with a relatively small degree of absolute sequence similarity. It is proposed that these proteins may share a similar three-dimensional conformation despite the lack of significant sequence similarity.

Arents G, Moudrianakis EN
The histone fold: a ubiquitous architectural motif utilized in DNA compaction and protein dimerization.
Proc Natl Acad Sci U S A. 1995; 92: 11170-4
Display abstract
The histones of all eukaryotes show only a low degree of primary structure homology, but our earlier crystallographic results defined a three-dimensional structural motif, the histone fold, common to all core histones. We now examine the specific architectural patterns within the fold and analyze the nature of the amino acid residues within its functional segments. The histone fold emerges as a fundamental protein dimerization motif while the differentiations of the tips of the histone dimers appear to provide the rules of core octamer assembly and the basis for nucleosome regulation. We present evidence for the occurrence of the fold from archaebacteria to mammals and propose the use of this structural motif to define a distinct family of proteins, the histone fold superfamily. It appears that evolution has conserved the conformation of the fold even through variations in primary structure and among proteins with various functional roles.

Suzuki M, Gerstein M
Binding geometry of alpha-helices that recognize DNA.
Proteins. 1995; 23: 525-35
Display abstract
Many transcription factors have an alpha-helix that binds to DNA bases in a specific fashion. The DNA-binding geometry of these recognition helices varies substantially. We define a set of parameters to describe the binding geometry of recognition helices and analyze specific stereochemical elements that determine particular geometries. Because the convex surface of the helix must fit into the concave surface of the DNA major groove, the number of degrees of freedom of the recognition helix is reduced from a possible six to a single angle, which we call alpha. The chemically interacting DNA bases and amino acid residues must lie along a common line and have the same spacing along it. This pairing of base positions with residue positions seems to restrict the binding geometry further to a set of discrete values for alpha.

Ramakrishnan V
The histone fold: evolutionary questions.
Proc Natl Acad Sci U S A. 1995; 92: 11328-30

Furrer P, Bednar J, Dubochet J, Hamiche A, Prunell A
DNA at the entry-exit of the nucleosome observed by cryoelectron microscopy.
J Struct Biol. 1995; 114: 177-83
Display abstract
Whereas the DNA path inside the nucleosome is well established, it is essentially unknown in the "entry-exit" region, a missing piece in our understanding of the chromatin fiber's folding. The three-dimensional structure of "linker" DNA was investigated here on single nucleosomes reconstituted without H1 on a 256-bp DNA fragment. Cryoelectron microscopy and three-dimensional reconstruction of the DNA axis reveal these nucleosomes as 1.61 +/- 0.15 left-handed superhelical turn particles whose DNA arms bend away from the core particle, thus preventing the occurrence of a crossing in the entry-exit region.

Harp JM, Palmer EL, York MH, Gewiess A, Davis M, Bunick GJ
Preparative separation of nucleosome core particles containing defined-sequence DNA in multiple translational phases.
Electrophoresis. 1995; 16: 1861-4
Display abstract
The nucleosome core particle is composed of an octamer of core histone proteins and about 146 bp of DNA. When reconstituted from purified histone octamer and defined-sequence, nucleosome positioning DNA fragments, the DNA will bind to the histone core in a number of translational phases with respect to the dyad symmetry axis of the histone octamer. Only one of these phases contains symmetrically bound DNA, and it is this species which is required for crystallization and X-ray diffraction studies. We have developed a technique for separating nucleosome core particles, containing defined-sequence 146 bp DNA, which differ only in translational phasing of the DNA with respect to the histone octamer core.

Vettese-Dadey M, Walter P, Chen H, Juan LJ, Workman JL
Role of the histone amino termini in facilitated binding of a transcription factor, GAL4-AH, to nucleosome cores.
Mol Cell Biol. 1994; 14: 970-81
Display abstract
Facilitated, "cooperative" binding of GAL4-AH to nucleosomal DNA occurred in response to inhibition from the core histone amino termini. The binding of GAL4-AH (which contains the DNA-binding and dimerization domains of GAL4) to nucleosome cores containing multiple binding sites initiated at the end of a nucleosome core and proceeded in a cooperative manner until all sites were occupied. However, following tryptic removal of the core histone amino termini, GAL4-AH binding appeared to be noncooperative, similar to binding naked DNA. Binding of GAL4-AH to nucleosomes bearing a single GAL4 site at different positions indicated that inhibition of GAL4 binding was largely mediated by the histone amino termini and primarily occurred at sites well within the core and not near the end. When the histone amino termini were intact, binding of GAL4-AH to sites near the center of a nucleosome core was greatly enhanced by the presence of additional GAL4 dimers bound to more-accessible positions. These data illustrate that the binding of a factor to more-accessible sites, near the end of a nucleosome, allows facilitated binding of additional factors to the center of the nucleosome, thereby overcoming repression from the core histone amino termini. This mechanism may contribute to the binding of multiple factors to complex promoter and enhancer elements in cellular chromatin.

Usachenko SI, Bavykin SG, Gavin IM, Bradbury EM
Rearrangement of the histone H2A C-terminal domain in the nucleosome.
Proc Natl Acad Sci U S A. 1994; 91: 6845-9
Display abstract
Using zero-length covalent protein-DNA crosslinking, we have mapped the histone-DNA contacts in nucleosome core particles from which the C- and N-terminal domains of histone H2A were selectively trimmed by trypsin or clostripain. We found that the flexible trypsin-sensitive C-terminal domain of histone H2A contacts the dyad axis, whereas its globular domain contacts the end of DNA in the nucleosome core particle. The appearance of the histone H2A contact at the dyad axis occurs only in the absence of linker DNA and does not depend on the absence of linker histones. Our results show the ability of the histone H2A C-terminal domain to rearrange. This rearrangement might play a biological role in nucleosome disassembly and reassembly and the retention of the H2A-H2B dimer (or the whole octamer) during the passing of polymerases through the nucleosome.

Traub P, Shoeman RL
Intermediate filament and related proteins: potential activators of nucleosomes during transcription initiation and elongation?
Bioessays. 1994; 16: 349-55
Display abstract
Intermediate filament (IF) protein tetramers contain two DNA- and core-histone-binding motifs in rotational symmetry in one and the same structural entity. We propose that IF protein oligomers might displace histone octamers from nucleosomes in the process of transcription initiation and elongation, to deposit them transiently on their alpha-helical coiled-coil domains. We further propose that structurally related proteins of the karyoskeleton, constructed from an alpha-helical domain capable of coiled-coil formation and a basic DNA-binding region adjacent to it, may be similarly involved in nucleosome activation. These proteins would function as auxiliary factors that disrupt nucleosomal structure to permit transcription and other DNA-dependent processes to proceed expiditiously.

Alfonso PJ, Crippa MP, Hayes JJ, Bustin M
The footprint of chromosomal proteins HMG-14 and HMG-17 on chromatin subunits.
J Mol Biol. 1994; 236: 189-98
Display abstract
The position of chromosomal proteins HMG-14 and HMG-17 in nucleosome cores and in chromatosomes lacking linker histones has been mapped by hydroxyl radical footprinting. Both the nucleosome core and the H1/H5 depleted chromatosome can specifically bind two molecules of HMG-14/-17. The path of HMG-14 on the surface of chromatin subunits is indistinguishable from that of HMG-17. The bound HMGs protect the DNA from hydroxyl radical cleavage 25 base-pairs from the end of the DNA in nucleosome cores and in each of the two major grooves of the DNA flanking the nucleosomal dyad axis. Thus, in both cores and H1/H5-depleted chromatosomes the proteins bridge two adjacent DNA strands on the surface of the particles. The sites occupied by HMG near the end of the chromatosome-length particles are distinct from those occupied by the H1/H5 linker histones. In the region of the dyad axis the binding sites of HMGs overlap those of the linker histones. The placement of HMG-14/-17 near the nucleosomal dyad axis raises the possibility that interactions between histone H1 and HMGs may affect the transcriptional potential of chromatin.

Davies N, Lindsey GG
Histone H2B (and H2A) ubiquitination allows normal histone octamer and core particle reconstitution.
Biochim Biophys Acta. 1994; 1218: 187-93
Display abstract
146 bp core particles were assembled from reconstituted hybrid histone octamers where either histone H2A or H2B were replaced by their ubiquitinated counterparts uH2A and uH2B. No difference in the structure of the core particles was evident upon DNase 1 digestion suggesting that ubiquitination of these histones was not a barrier to normal core particle formation.

Richmond TJ, Rechsteiner T, Luger K
Studies of nucleosome structure.
Cold Spring Harb Symp Quant Biol. 1993; 58: 265-72

Samso M, Daban JR
Unfolded structure and reactivity of nucleosome core DNA-histone H2A,H2B complexes in solution as studied by synchrotron radiation X-ray scattering.
Biochemistry. 1993; 32: 4609-14
Display abstract
It has been previously found using different physicochemical techniques [Aragay, A., Diaz, P., & Daban, J.-R. (1988) J. Mol. Biol. 204, 141-154] that histones H2A,H2B in the absence of H3,H4 can associate with nucleosome core DNA (146 base pairs). Here we describe a synchrotron X-ray scattering study of core DNA-(H2A,H2B) complexes in solution. Our results obtained using different histone to DNA weight ratios and ionic conditions ranging from very low ionic strength to 0.2 M NaCl show that histones H2A,H2B are unable to fold core DNA. Model calculations indicate that histones H2A,H2B produce very elongated structures even when the reconstituted complexes are prepared at physiological ionic strength. In contrast, our scattering data indicate that the reconstituted complexes prepared at physiological salt concentration either with the four core histones or with histones H3,H4 without H2A,H2B are completely folded particles with a radius of gyration similar to that corresponding to the native nucleosome core (4.2 nm). Furthermore, our results show that the DNA of the extended complexes containing histones H2A,H2B becomes completely folded after the histone pair exchange reaction that occurs spontaneously between preformed DNA-(H2A,H2B) and DNA-(H3,H4) complexes. These observations, together with our previous studies, suggest that the open conformation of DNA-(H2A,H2B) complexes facilitates the involvement of this structure as a transient intermediate in the reaction of nucleosome formation at physiological ionic strength.

Pruss D, Wolffe AP
Histone-DNA contacts in a nucleosome core containing a Xenopus 5S rRNA gene.
Biochemistry. 1993; 32: 6810-4
Display abstract
We describe histone-DNA cross-linking in a nucleosome core containing a Xenopus borealis somatic 5S rRNA gene. Histones H3 and H4 are cross-linked to DNA within 30 bp to either side of the dyad axis. Histones H2A/H2B and H3 are cross-linked to DNA where it enters and exists, wrapping around the histone octamer. These latter interactions extend for 80 bp to one side of the dyad axis of the nucleosome core, including the entire binding site for transcription factor TFIIIA. These extensive interactions with linker DNA might account for inhibition of TFIIIA binding and also might assist in the folding of internucleosomal DNA within the chromatin fiber.

Moudrianakis EN, Arents G
Structure of the histone octamer core of the nucleosome and its potential interactions with DNA.
Cold Spring Harb Symp Quant Biol. 1993; 58: 273-9

Ramakrishnan V, Finch JT, Graziano V, Lee PL, Sweet RM
Crystal structure of globular domain of histone H5 and its implications for nucleosome binding.
Nature. 1993; 362: 219-23
Display abstract
The structure of GH5, the globular domain of the linker histone H5, has been solved to 2.5 A resolution by multiwavelength anomalous diffraction on crystals of the selenomethionyl protein. The structure shows a striking similarity to the DNA-binding domain of the catabolite gene activator protein CAP, thereby providing a possible model for the binding of GH5 to DNA.

Arents G, Moudrianakis EN
Topography of the histone octamer surface: repeating structural motifs utilized in the docking of nucleosomal DNA.
Proc Natl Acad Sci U S A. 1993; 90: 10489-93
Display abstract
The histone octamer core of the nucleosome is a protein superhelix of four spirally arrayed histone dimers. The cylindrical face of this superhelix is marked by intradimer and interdimer pseudodyad axes, which derive from the nature of the histone fold. The histone fold appears as the result of a tandem, parallel duplication of the "helix-strand-helix" motif. This motif, by its occurrence in the four dimers, gives rise to repetitive structural elements--i.e., the "parallel beta bridges" and the "paired ends of helix I" motifs. A preponderance of positive charges on the surface of the octamer appears as a left-handed spiral situated at the expected path of the DNA. We have matched a subset of DNA pseudodyads with the octamer pseudodyads and thus have built a model of the nucleosome. In it, the two DNA strands coincide with the path of the histone-positive charges, and the central 12 turns of the double helix contact the surface of the octamer at the repetitive structural motifs. The properties of these complementary contacts appear to explain the preference of histones for double-helical DNA and to suggest a possible basis for allosteric regulation of nucleosome function.

Hayes JJ, Bashkin J, Tullius TD, Wolffe AP
The histone core exerts a dominant constraint on the structure of DNA in a nucleosome.
Biochemistry. 1991; 30: 8434-40
Display abstract
We have examined the structures of unique sequence, A/T-rich DNAs that are predicted to be relatively rigid [oligo(dA).oligo(dT)], flexible [oligo[d(A-T)]], and curved, using the hydroxyl radical as a cleavage reagent. A 50-base-pair segment containing each of these distinct DNA sequences was placed adjacent to the T7 RNA polymerase promoter, a sequence that will strongly position nucleosomes. The final length of the DNA fragments was 142 bp, enough DNA to assemble a single nucleosome. Cleavage of DNA in solution, while bound to a calcium phosphate crystal, and after incorporation into a nucleosome is examined. We find that the distinct A/T-rich DNAs have very different structural features in solution and helical periodicities when bound to a calcium phosphate. In contrast, the organization of the different DNA sequences when associated with a histone octamer is very similar. We conclude that the histone core exerts a dominant constraint on the structure of DNA in a nucleosome and that inclusion of these various unique sequences has only a very small effect on overall nucleosome stability and structure.

Davies N, Lindsey GG
Histone-DNA contacts in the 167 bp 2-turn core particle.
Biochim Biophys Acta. 1991; 1129: 57-63
Display abstract
The histone-DNA contacts in the 167 bp 2-turn core particle have been compared with those in the 146 bp 1.75-turn core particle by the methodology developed by Mirzabekov and his colleagues. The contacts in the 167 bp 2-turn core particle retain the essential features of those in the 146 bp 1.75-turn core particle but contacts for histones H3 and H2A were found in the 10 bp extension that discriminates the two particles. In addition the contact for histone H2A near the dyad axis was far more pronounced in the case of the 146 bp core particle.

Gushchin DI, Ebralidze KK, Mirzabekov AD
[Structure of nucleosomes. Localization of the H2A and H2B histone segments interacting with DNA using DNA-protein crosslinking]
Mol Biol (Mosk). 1991; 25: 1400-11
Display abstract
Histones' H2A and H2B peptidic points which interact with nucleosomal DNA have been identified by using the methods of DNA--protein covalent cross-linking. H2B can be linked to DNA via its N-terminal tail and via several lysines contained within residues 24-34. The most prominent site of histone H2A covalent linking to DNA is His-123, the less prominent being Lys-119 and Lys-124.

Marky NL, Manning GS
The elastic resilience of DNA can induce all-or-none structural transitions in the nucleosome core particle.
Biopolymers. 1991; 31: 1543-57
Display abstract
DNA on the surface of the histone octamer in the native nucleosome core particle is modeled as a circumferentially wound elastic line on the surface of a cylinder. In a model for the radial transition, the line is allowed to straighten, and thus lose energy, by swinging off the surface, but it is impeded in such an excursion by a radial force field representing the attractive interaction between DNA and histone octamer. In a model for the axial transition, the line may straighten by becoming more parallel to a generator of the cylinder while remaining on the surface. In this mode of straightening, dimer-tetramer or tetramer-tetramer interfaces are disrupted, and the resulting energy gain impedes the transition. Both radial and axial transitions are predicted to occur in all-or-none fashion. We propose that these models are related to the abrupt transitions actually observed in the nucleosome core particle.

Hill CS, Thomas JO
Core histone-DNA interactions in sea urchin sperm chromatin. The N-terminal tail of H2B interacts with linker DNA.
Eur J Biochem. 1990; 187: 145-53
Display abstract
A three-stage chemical modification procedure [Lambert, S. F. & Thomas, J. O. (1986) Eur. J. Biochem. 160, 191-201; Thomas, J. O. & Wilson, C. M. (1986) EMBO J. 5, 3531-3537] for selectively radiolabelling lysine residues that interact with DNA has been used to investigate core histone--DNA interactions in sea urchin sperm chromatin, in particular to determine the binding site of the long N-terminal domain of sperm-specific H2B. Comparison of the patterns of radiolabelling of core histones from extended chromatin and nucleosome core particles (which lack linker DNA) reveals the regions of the histones involved in interactions with the linker. The results show that the N-terminal domain of H2B is bound to DNA outside the 146-bp nucleosome core, presumably to the linker DNA. H2A and H4 make no substantial contacts with the linker in extended chromatin; the N-terminal tail of H4 is bound within the core particle, but the N-terminal tail of H2A is not bound in core particles or in extended chromatin, and may therefore have a role in higher-order structure. H3, like H2B, makes contacts with DNA outside the 146-bp nucleosome core in its N-terminal region, as well as elsewhere, and probably interacts with the two 10-bp extensions that complete the two turns of DNA in the nucleosome and/or with the linker.

Perez JJ, Portugal J
Molecular modelling study of changes induced by netropsin binding to nucleosome core particles.
Nucleic Acids Res. 1990; 18: 3731-7
Display abstract
It is well known that certain sequence-dependent modulators in structure appear to determine the rotational positioning of DNA on the nucleosome core particle. That preference is rather weak and could be modified by some ligands as netropsin, a minor-groove binding antibiotic. We have undertaken a molecular modelling approach to calculate the relative energy of interaction between a DNA molecule and the protein core particle. The histones particle is considered as a distribution of positive charges on the protein surface that interacts with the DNA molecule. The molecular electrostatic potentials for the DNA, simulated as a discontinuous cylinder, were calculated using the values for all the base pairs. Computing these parameters, we calculated the relative energy of interaction and the more stable rotational setting of DNA. The binding of four molecules of netropsin to this model showed that a new minimum of energy is obtained when the DNA turns toward the protein surface by about 180 degrees, so a new energetically favoured structure appears where netropsin binding sites are located facing toward the histones surface. The effect of netropsin could be explained in terms of an induced change in the phasing of DNA on the core particle. The induced rotation is considered to optimize non-bonded contacts between the netropsin molecules and the DNA backbone.

Crane-Robinson C, Ptitsyn OB
Binding of the globular domain of linker histones H5/H1 to the nucleosome: a hypothesis.
Protein Eng. 1989; 2: 577-82
Display abstract
The amino acid sequence of the central globular domain of histone H1/H5 family members is highly homologous. Twenty-four such sequences have been compared to establish the conserved and variable residues. Fitting this to the tertiary structure of the H5 globular domain shows which of the conserved and variable residues are peripheral and which internal. Particular attention is paid to conserved basic residues on the surface, which we take to be DNA binding. Variable regions and conserved acidic residues are assumed not to be sites of contact with DNA. We conclude that one face of the domain, containing a cluster of basic residues, is the principal DNA binding site whilst two opposing faces, orthogonal to the principal site and also containing conserved basic residues, are subsidiary DNA binding sites. Since the DNA binding surface of the domain covers a full 180 degrees arc, we propose that it contacts a 'cage' of three DNA strands on the 2-fold axis of the chromatosome.

Uberbacher EC, Bunick GJ
Structure of the nucleosome core particle at 8 A resolution.
J Biomol Struct Dyn. 1989; 7: 1-18
Display abstract
The x-ray crystallographic structure of the nucleosome core particle has been determined using 8 A resolution diffraction data. The particle has a mean diameter of 106 A and a maximum thickness of 65 A in the superhelical axis direction. The longest chord through the histone core measures 85 A and is in a non-axial direction. The 1.87 turn superhelix consists of B-DNA with about 78 base pairs or 7.6 helical repeats per superhelical turn. The mean DNA helical repeat contains 10.2 +/- 0.05 base pairs and spans 35 A, slightly more than standard B-DNA. The superhelix varies several Angstroms in radius and pitch, and has three distinct domains of curvature (with radii of curvature of 60, 45 and 51 A). These regions are separated by localized sharper bends +/- 10 and +/- 40 base pairs from the center of the particle, resulting in an overall radius of curvature about 43 A. Compression of superhelical DNA grooves on the inner surface and expansion on the outer surface can be seen throughout the DNA electron density. This density has been fit with a double helical ribbon model providing groove width estimates of 12 +/- 1 A inside vs. 19 +/- 1 A outside for the major groove, and 8 +/- 1 A inside vs. 13 +/- 1 A outside for the minor groove. The histone core is primarily contained within the bounds defined by the superhelical DNA, contacting the DNA where the phosphate backbone faces in toward the core. Possible extensions of density between the gyres have been located, but these are below the significance level of the electron density map. In cross-section, a tripartite organization of the histone octamer is apparent, with the tetramer occupying the central region and the dimers at the extremes. Several extensions of histone density are present which form contacts between nucleosomes in the crystal, perhaps representing flexible or "tail" histone regions. The radius of gyration of the histone portion of the electron density is calculated to be 30.4 A (in reasonable agreement with solution scattering values), and the histone core volume in the map is 93% of its theoretical volume.

Aragay AM, Diaz P, Daban JR
Association of nucleosome core particle DNA with different histone oligomers. Transfer of histones between DNA-(H2A,H2B) and DNA-(H3,H4) complexes.
J Mol Biol. 1988; 204: 141-54
Display abstract
In non-denaturing low ionic strength gels, the titration of core DNA with H2A,H2B produces five well-defined bands. Quantitative densitometry and cross-linking experiments indicate that these bands are due to the successive binding of H2A,H2B dimers to core DNA. Only two bands are obtained with DNA-(H3,H4) samples. The slower of these bands is broad and presumably corresponds to two complexes containing one and two H3,H4 tetramers, respectively. In gels of higher ionic strength, DNA-(H2A,H2B) samples produce an ill-defined band, suggesting that the lifetime of the complexes containing H2A,H2B is relatively short. However, the low intensity of the free DNA band observed in these gels indicates that most of the DNA is associated with H2A,H2B. In agreement with this, our results obtained using different techniques (sedimentation, cross-linking, trypsin and nuclease digestions, and thermal denaturation) demonstrate that the association of H2A,H2B with core DNA occurs in free solution in both the absence and presence of NaCl (0.1 to 0.2 M). The low mobilities of DNA-(H2A,H2B) complexes, together with sedimentation and DNase I digestion results, indicate that the DNA in these complexes is not folded into the compact structure found in the core particle. Furthermore, non-denaturing gels have been used to study the dynamic properties of DNA-(H2A,H2B) and DNA-(H3,H4) complexes in 0.2 M-NaCl. Our results show that: (1) H2A,H2B and H3,H4 can associate, respectively, with DNA-(H3,H4) and DNA-(H2A,H2B) to produce complexes containing the four core histones; (2) DNA-(H2A,H2B) and DNA-(H3,H4) are able to transfer histones to free core DNA; (3) an exchange of histone pairs takes place between DNA-(H2A,H2B) and DNA-(H3,H4) and produces complexes with the same histone composition as that of the normal nucleosome core particle; and (4) although both histone pairs can exchange, histones H2A,H2B show a higher tendency than H3,H4 to migrate from one incomplete core particle to another. The complexes produced in these reactions have the same compact structure as reconstituted core particles containing the four core histones. Our kinetic results are consistent with a reaction mechanism in which the transfer of histones involves direct contacts between the reacting complexes. The possible participation of these spontaneous reactions on the mechanism of nucleosome assembly is discussed.

Travers AA, Klug A
The bending of DNA in nucleosomes and its wider implications.
Philos Trans R Soc Lond B Biol Sci. 1987; 317: 537-61
Display abstract
The DNA of a nucleosome core particle is wrapped tightly around a histone octamer with approximately 80 base pairs per superhelical turn. Studies of both naturally occurring and reconstituted systems have shown that DNA sequences very often adopt well-defined locations with respect to the octamer. Recent work in this laboratory has provided a structural explanation for this sequence-dependent positioning in terms of the differential flexibility of different sequences and of departures from smooth bending. The 'rules' that are emerging for DNA bendability and, from the results of other workers, on intrinsically bent DNA, are likely to be useful in considering looping and bending of DNA in other processes in which it is thought to be wrapped around a protein core.

Drew HR, Calladine CR
Sequence-specific positioning of core histones on an 860 base-pair DNA. Experiment and theory.
J Mol Biol. 1987; 195: 143-73
Display abstract
Previous experiments have shown that the locations of the histone octamer on DNA molecules of 140 to 240 base-pairs (bp) are influenced strongly by the nucleotide sequence. Here we have studied the locations of the histone octamer on a relatively long DNA molecule of 860 bp, using two different nucleases, micrococcal and DNAase I. Data were obtained from both the protein--DNA complexes and from the naked DNA at single-bond resolution, and then were analyzed by densitometry to yield plots of differential cleavage, which show clearly the changes in cutting due to the addition of protein. Our results show that the placement of core histones on the 860 bp molecule is definitely non-random. The digestion data provide evidence for five nucleosome cores, the centers of which lie in defined locations. In all but one of these protein--DNA complexes, the DNA adopts a unique, highly preferred rotational setting with respect to the protein surface. Another protein--DNA complex is unusual in that it protects 200 bp from digestion, yet is cut in its very center as if it were split into two parts. The apparent average twist of the DNA within all of these protein--DNA complexes is 10.2(+/- 0.1) bp, as measured by the periodicity of DNAase I digestion. This value is in excellent agreement with the twist of 10.21(+/- 0.05) bp deduced from the periodicity of sequence content in chicken nucleosome core DNA. In addition, we observe a discontinuity in the periodic cutting by DNAase I of about -1 to -3 bonds in going from any nucleosome core to the next. The most plausible interpretation of this discontinuity is that it reflects the angle by which adjacent protein--DNA complexes are aligned. Thus, any nucleosome may be related to its neighbor by a left-handed rotation in space of -1/10.2 to -3/10.2 helix turns, or -35 degrees to -105 degrees. Repeated many times, this operation would build a long, left-handed helix of nucleosomes similar to that described by many workers for the packing of nucleosomes in chromatin. In order to look for any long-range influences on the positioning of the histone octamer in the 860 bp molecule (as would be expected if the nucleosomes have to fit into some higher-order structure), we have examined the locations of the histone octamer on five different isolated short fragments of the 860-mer, all of nucleosomal length.(ABSTRACT TRUNCATED AT 400 WORDS)

Ebralidze KK, Mirzabekov AD
[One-domain interaction of histone H4 with DNA within the nucleosomal core particle]
Dokl Akad Nauk SSSR. 1986; 287: 241-4

Lambert SF, Thomas JO
Lysine-containing DNA-binding regions on the surface of the histone octamer in the nucleosome core particle.
Eur J Biochem. 1986; 160: 191-201
Display abstract
The DNA bound on the surface of the histone octamer in the nucleosome core particle partially protects the epsilon-amino side-chains of a subset of the lysine residues from reductive methylation. Most of the strongly protected lysines, which probably define the path of the DNA on the octamer surface, are in the globular ('structured') regions of the core histones rather than in the N-terminal or C-terminal 'tails'. Analysis of the protected peptides shows that the three strongest lysine-containing DNA-binding sites in the core histones contain the sequence-Lys/Arg-Lys-Thr/Ser-. On the assumption that the lysine-containing regions protected from chemical modification are also those found in lysine-DNA cross-links in another study [Mirzabekov et al. (1978) Proc. Natl Acad. Sci. USA 75, 4184-4188], particular DNA-protected peptides may be tentatively assigned to particular DNA contact points. This leads to a more detailed description of the DNA-binding regions on the octamer surface in the nucleosome core particle. Strong contacts, reflected in strongly protected lysines, may well contribute to the distortion of the DNA from smooth bending [Richmond et al. (1984) Nature (Lond.) 311, 532-537].

Dumuis-Kervabon A et al.
A chromatin core particle obtained by selective cleavage of histones by clostripain.
EMBO J. 1986; 5: 1735-42
Display abstract
Rat liver chromatin core particles digested with clostripain yield a structurally well-defined nucleoprotein particle with an octameric core made up of fragmented histone species (designated H'2A, H'2B, H'3 and H'4, respectively) after selective loss of a sequence segment located in the N-terminal region of each core histone. Sequential Edman degradation and carboxypeptidase digestion unambiguously establish that histones H2A, H2B, H3 and H4 are selectively cleaved at the carboxyl side of Arg 11, Lys 20, Arg 26 and Arg 19 respectively and that the C-terminal sequences remain unaffected. Despite the loss of the highly basic N-terminal regions, including approximately 17% of the total amino acids, the characteristic structural organization of the nucleosome core particle appears to be fully retained in the proteolyzed core particle, as judged by physicochemical and biochemical evidence. Binding of spermidine to native and proteolyzed core particles shows that DNA accessibility differs markedly in both structures. As expected the proteolyzed particle, which has lost all the in vivo acetylation sites, is not enzymatically acetylated, in contrast to the native particle. However, proteolyzed histones act as substrates of the acetyltransferase in the absence of DNA, as a consequence of the occurrence of potential acetylation sites in the core histones thus rendered accessible. The possible role of the histone N-terminal regions on chromatin structure and function is discussed in the light of the present observations with the new core particle obtained by clostripain proteolysis.

Ebralidse KK, Mirzabekov AD
One-domain interaction of histone H4 with nucleosomal core DNA is restricted to a narrow DNA segment.
FEBS Lett. 1986; 194: 69-72
Display abstract
The interaction of histone H4 with DNA in the nucleosomal core particle has been studied by crosslinking DNA to proteins through their lysine residues. We have compared the crosslinked peptides of H4 at the detected DNA-binding sites: H4(55), H4(65), H4(88), located, respectively, at about 55, 65 and 88 nucleotides from the core DNA termini. For all these binding sites, the patterns of crosslinked peptides were shown to be very similar. This suggests the presence of a single DNA-binding domain in the H4 molecule. The H4-binding sites are located within a narrow DNA segment close to one another on the complementary strands across the DNA grooves, overlap with sites +/- 1 of the DNA sharp bending [(1984) Nature 311, 532-537] and with the strong binding sites for histone H3: H3(75) and H3(85).

Uberbacher EC, Bunick GJ
X-ray structure of the nucleosome core particle.
J Biomol Struct Dyn. 1985; 2: 1033-55
Display abstract
Two monoclinic crystal forms (P2(1),C2) of chicken erythrocyte nucleosomes have been under study in this laboratory. The x-ray structure of the P2(1) crystal form has been solved to 15 A resolution. The B-DNA superhelix has a relatively uniform curvature, with only several local distortions observed in the superhelix. The individual histone domains have been localized and specific contacts between each histone and the DNA can be observed. Histone contacts to the inner surface of the DNA superhelix occur predominantly at the minor groove sites. Most of the histone core is contained within the inner surface of the superhelical DNA, except for part of H2A which extends between the DNA gyres near the terminus of the DNA. No part of H2A blocks the DNA terminus or would prevent a smooth exit of the DNA into the linker region. A similar extension of a portion of histone H4 between the DNA gyres occurs close to the dyad axis. Both unique nucleosomes in the P2(1) asymmetric unit demonstrate good dyad symmetry and are similar to each other throughout the histone core and DNA regions.

Schurr JM, Schurr RL
DNA motions in the nucleosome core particle: a reanalysis.
Biopolymers. 1985; 24: 1931-40

Jordano J, Nieto MA, Palacian E
Dissociation of nucleosomal particles by chemical modification. Equivalence of the two binding sites for H2A.H2B dimers.
J Biol Chem. 1985; 260: 9382-4
Display abstract
Treatment of nucleosomal particles with dimethylmaleic anhydride, a reagent for protein amino groups, is accompanied by a biphasic release of histones H2A plus H2B; one H2A.H2B dimer is more easily released than the other. This behavior allows the preparation of nucleosomal particles containing only one H2A.H2B dimer, which were complemented with 125I-labeled H2A.H2B. These reconstituted particles, which contain one labeled and one unlabeled H2A.H2B dimer, were treated with the amount of reagent needed to release one of the two H2A.H2B dimers. Radioactivity was equally distributed between residual particles and released proteins, which is consistent with equivalent binding sites in the nucleosomal particle for H2A.H2B dimers, rather than with intrinsically different sites. The asymmetric release of H2A.H2B dimers would be caused by a change in the binding site of one dimer following the release of the other. This behavior might be related to the structural dynamics of nucleosomes.

Bentley GA, Lewit-Bentley A, Finch JT, Podjarny AD, Roth M
Crystal structure of the nucleosome core particle at 16 A resolution.
J Mol Biol. 1984; 176: 55-75
Display abstract
The crystal structure of the nucleosome core particle has been studied by neutron diffraction to a resolution of 16 A. By using H2O/D2O solvent contrast variation, the structures of the DNA and histone core were analysed separately. The DNA, as seen at this resolution, forms a super-helix of pitch 25.8 A, radius 42.1 A and 1.8 turns in length. The histone core itself is approximately helical and follows the DNA along the inside of the super-helix, giving the nucleosome core particle an overall 2-fold axis of symmetry. Four regions can be distinguished in the protein density, which we interpret as dimers of histones within the octameric core. The dimers have been assigned on the basis of other evidence as being of two kinds, (H2A-H2B) and (H3-H4). Because solvent contrast variation can distinguish between hydrophobic and hydrophilic regions in the protein density, our results suggest that the interface between the monomers of each dimer is probably quite hydrophobic in character, while the interaction between dimers is weaker and/or more hydrophilic. The protein is in contact with most of the DNA and there are some regions where it may penetrate between the turns of the super-helix. In particular, the tetramer (H4-H3)-(H3-H4) is in close contact with the central part of the DNA, but significant contacts are seen also between the histones H3 and the extremities of the super-helix, thus explaining the stability of a nucleosome-like particle depleted of H2A and H2B. Significant departures from the molecular 2-fold axis of symmetry occur in the relative arrangements of the two (H2A-H2B) dimers.

Richmond TJ, Finch JT, Rushton B, Rhodes D, Klug A
Structure of the nucleosome core particle at 7 A resolution.
Nature. 1984; 311: 532-7
Display abstract
The crystal structure of the nucleosome core particle has been solved to 7 A resolution. The right-handed B-DNA superhelix on the outside contains several sharp bends and makes numerous interactions with the histone octamer within. The central turn of superhelix and H3 . H4 tetramer have dyad symmetry, but the H2A . H2B dimers show departures due to interparticle associations.

Khrapunov SN, Sivolob AV, Berdyshev GD
[Model of the packing of DNA and histone octamer in the structure of the nucleosome]
Biofizika. 1983; 28: 573-8
Display abstract
A model is proposed which describes the packing of polypeptide chains of histone molecules in the octamer (H3--H4--H2A--H2B)2, and interlocation of DNA and octamer in the nucleosome. DNA packing in the nucleosome is provided for by electrostatic interactions between DNA phosphates and cationic groups located on the globular part surface of histones octamer. The cationic groups of N- and C-end regions of the histone molecules (histones H3 and H4 in particular) additionally stabilize the nucleosome structure.

Mengeritsky G, Trifonov EN
Nucleotide sequence-directed mapping of the nucleosomes.
Nucleic Acids Res. 1983; 11: 3833-51
Display abstract
The concept of sequence-dependent deformational anisotropy of DNA proposed earlier is further elaborated and a computational procedure is developed for the sequence-directed mapping of the nucleosomes along chromatin DNA nucleotide sequences. The deformational anisotropy is found to be nonuniform along the molecule of the nucleosomal DNA, suggesting that the DNA superhelix in the nucleosome is slightly oval rather than circular in projection. The number of superhelical turns in the nucleosome core particle is estimated to be 2.0 +/- 0.2. Preliminary mapping of the nucleosomes in various chromatin DNA sequences yields the distribution of linker lengths which shows several minima separated by about 10 base-pairs. This is explained by sterical exclusion effects due to overlapping of the nucleosomes in space when some specific linker lengths are chosen. The mapping procedure described is tested by comparing its results with all the most accurate experimental mapping data reported so far. The comparison demonstrates that the exact positions of all the nucleosomes appear to be determined exclusively by the nucleotide sequences.

Wang JC
The path of DNA in the nucleosome.
Cell. 1982; 29: 724-6

Hayashi T, Ohe Y, Hayashi H, Iwai K
Human spleen histone H4. Isolation and amino acid sequence.
J Biochem (Tokyo). 1982; 92: 1995-2000
Display abstract
The amino acid sequence of human spleen histone H4 was investigated as part of a study on histone evolution, following previous investigations of human spleen histones H2B (J. Biochem. 85, 615-624), H2A (J. Biochem. 88, 27-34), and H3 (J. Biochem. 90, 1205-1211). The H4 fraction was obtained as described previously and further purified by Bio-Gel P-60 chromatography. The purified H4 was digested with trypsin and the peptides were fractionated by repeated column chromatographies with reasonable recoveries. Certain peptides were sequenced, and three modified residues (alpha-N-Ac-Ser-1, epsilon-N-Ac-Lys-16, and epsilon-N-Me-Lys-20) and one heterogeneous residue (Asn/Asp-25), which is probably a result of postsynthetic deamidation, were found. Thus, the human H4 was deduced to have a sequence of 102 amino acid residues completely identical with that of calf thymus H4, including the presence of three modified residues and the absence of any variant sequence. It is concluded that the animal H4 sequences and their postsynthetic modifications have been strongly conserved during the evolutionary process leading to man, as strongly as or more strongly than the H3 sequence, and much more strongly than the H2A and H2B sequences.

Chan DC, Piette LH
Effect of Tyrosyl modifications on nucleosome reconstitution: a spin-labeling study.
Biochemistry. 1982; 21: 3028-35
Display abstract
An imidazole spin-label was used to study the role of tyrosyl residues in the reassociation process for the nucleosome core particle. The nucleosome core particle, containing 145 base pairs of DNA and a histone core (two each of the four histones H2S, H2B, H3, and H4), was isolated from chicken erythrocytes. Native particles were first dissociated in 2 M NaCl and labeled with varying concentrations of imidazole spin-label. The labeled histone core and endogenous DNA were then reassociated back by salt step dialysis. Reconstituted spin-labeled complexes, purified by an isokinetic sucrose gradient, were found to have physical properties identical with those of unlabeled native particles. Spin-labeling the surface tyrosines of the histone core did not interfere with proper reassociation of the nucleosome core complex. ESR spectra of the reconstituted nucleosomes core complex are not the strongly anisotropic type, suggesting that labeled surface tyrosines in the histone core are not involved in specific DNA-histone interaction nor does wrapping of DNA on the histone core involve very close contact with the label. When labeling was carried out under denaturing conditions following exposure of the histone core to urea, additional histone tyrosine residues were spin-labeled. The resulting histone-DNA complexes that formed after reassociation had physical properties different from those of the native nucleosomes core. This result suggested that some of the "buried" tyrosines are essential for specific histone-histone interactions that lead to stable histone core structures. Spin-labeling the buried tyrosines prevented to compact supercoiling of DNA into nucleosome core particle.

Kornberg RD, Klug A
The nucleosome.
Sci Am. 1981; 244: 52-64

Allan J, Hartman PG, Crane-Robinson C, Aviles FX
The structure of histone H1 and its location in chromatin.
Nature. 1980; 288: 675-9
Display abstract
On the basis of their primary structure, the lysine-rich histones are a unified family of proteins. Each has an amino acid chain which falls into three distinct domains. Only the central domain (approximately 80 residues) is in a folded conformation. It is protected from trypsin digestion in chromatin and corresponds to the segment of highest sequence conservation. Without the flanking domains it is able to close two full turns of DNA in the nucleosome and can thus locate the H1 molecule.

Khachatrian HT, Pospelov VA
Spatial organization of histones and DNA in the nucleosome core particle: a model.
Mol Biol Rep. 1980; 6: 219-23
Display abstract
We present here an attempt to build up a space-filling model of the nucleosome core particle based on the chemical crosslinking data of Mirzabekov and co-workers (23). It is shown that the models proposed earlier are inconsistent with the results of these authors. The main characteristics of our model are as follows: a) the DNA superhelix contains at least 90 base pairs (bp) per turn; b) the particle has a dyad axis of symmetry; c) the histone octamer may be regarded as consisting of two heterotypic tetramers. The possible shape and function of core histones are discussed in the light of the model.

Klug A, Rhodes D, Smith J, Finch JT, Thomas JO
A low resolution structure for the histone core of the nucleosome.
Nature. 1980; 287: 509-16
Display abstract
Image reconstruction to 22 A resolution of the histone octamer (H3)2(H4)2(H2A)2(H2B)2 shows it to have a 2-fold axis of symmetry, and the overall shape of the left-handed helical spool on which to wind about two turns of a flat superhelix of DNA in the nucleosome. From this structure and the results of various cross-linking studies, we have deduced the arrangement of the individual histones. We propose that the (H3)2(H4)2 tetramer forms a dislocated disk which defines the central turn of DNA, while the two H2A-H2B dimers lie one on each face, each associated with about one half a turn.

Philip M, Jamaluddin M, Chandra HS
Nucleosome core protein: asymmetric dissociation of the octamer.
Biochim Biophys Acta. 1980; 607: 480-9
Display abstract
The octameric nucleosomal core-histone complex, (H2A)2-(H2B)2-(H3)2-(H4)2, isolated from rat liver, undergoes dissociation during gel exclusion chromatography as a result of dilution occurring in the columns. The elution pattern at pH 7.0 and 4 degree C showed a sharp leading peak containing all four histones but predominantly H3 and H4, and a trailing peak containing equal amounts of histones H2A and H2B. As column length was increased the area under the leading peak decreased and that under the trailing peak increased. In addition the relative positions of the two peaks varied with column length. From an analysis of the data on increase in elution volume of the leading peak in relation to column length an apparent molecular weight of 86 000 was calculated for the undissociated molecule. Its apparent molecular weight, histone composition and pattern of further dissociation in relation to column length suggest that this species is the hexamer, (H2A-H2B)-(H3)2-(H4)2. At pH 7.0 and 4 degrees C the dissociation of the core complex appears to be as follows: (H2A)2-(H2B)2-(H3)2-(H4)2 leads to (H2A-H2B)+(H2A-H2B)-(H3)2-(H4)2 leads to 2(H2A-H2B+(H3)2-(H4)2 This dissociation was accelerated by an increase in temperature or decrease in pH and was accompanied by marked conformational changes as judged by circular dichroism measurements.

Smythies JR
On the molecular structure of the nucleosome core particle of chromatin.
Ala J Med Sci. 1979; 16: 10-20

Mirzabekov AD, Shick VV, Belyavsky AV, Bavykin SG
Primary organization of nucleosome core particle of chromatin: sequence of histone arrangement along DNA.
Proc Natl Acad Sci U S A. 1978; 75: 4184-8
Display abstract
A high-resolution map for the arrangement of histones along DNA in the nucleosome core particle has been determined by a sequencing procedure based on crosslinking histones to the 5'-terminal DNA fragments produced by scission of one DNA strand at the point of crosslinking. The position of histones on DNA has been identified by measuring the length of crosslinked DNA fragments. The results demonstrate that each of the histones is arranged within several adjacent or dispersed DNA segments of a little less than 10 nucleotides in length. Histone-free intervals are located between these segments at the regular distances of about (10)n nucleotides from the 5' end of the DNA and are likely to face one side of the DNA helix. Histones appear to be arranged in a similar manner on both DNA strands and do not form "locks" around DNA. A linearized model of the core particle is proposed.

Spadafora C, Oudet P, Chambon P
The same amount of DNA is organized in in vitro-assembled nucleosomes irrespective of the origin of the histones.
Nucleic Acids Res. 1978; 5: 3479-89
Display abstract
The four histones H2A, H2B, H3 and H4 from calf thymus, CHO and sea urchin gastrula cells were associated by stepwise dialysis from 2 M NaCl with SV40 DNA Form I. The in vitro-assembled chromatins were visualized by electron microscopy and the size of the DNA fragments generated by digestion with DNase II was determined. Irrespective of the origin of the histones, the size of the smallest DNA band generated at early times of digestion was about 190 base pairs, whereas oligomeric DNA bands were multiples of 140 bp. These results support our previous proposal that the four histones H2A, H2B, H3 and H4 are able to organize more than 140 bp of DNA, but do not provide any evidence that the variability of histones H2A and H2B plays a role in the variability of the DNA repeat length of native chromatins.

Carter CW Jr
Histone packing in the nucleosome core particle of chromatin.
Proc Natl Acad Sci U S A. 1978; 75: 3649-53

Smythies JR, Benington F, Morin RD
A mechanism for the interaction of a histone and DNA.
J Theor Biol. 1972; 37: 151-8