NORMAL GENOMIC

• Vicent GP et al.
• Two chromatin remodeling activities cooperate during activation of hormoneresponsive promoters.
• PLoS Genet. 2009; 5: 1000567-1000567
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• Steroid hormones regulate gene expression by interaction of theirreceptors with hormone responsive elements (HREs) and recruitment ofkinases, chromatin remodeling complexes, and coregulators to their targetpromoters. Here we show that in breast cancer cells the BAF, but not theclosely related PBAF complex, is required for progesterone induction ofseveral target genes including MMTV, where it catalyzes localizeddisplacement of histones H2A and H2B and subsequent NF1 binding. PCAF isalso needed for induction of progesterone target genes and acetylateshistone H3 at K14, an epigenetic mark that interacts with the BAF subunitsby anchoring the complex to chromatin. In the absence of PCAF, fullloading of target promoters with hormone receptors and BAF is precluded,and induction is compromised. Thus, activation of hormone-responsivepromoters requires cooperation of at least two chromatin remodelingactivities, BAF and PCAF.

• Zhou C, Miki B, Wu K
• CHB2, a member of the SWI3 gene family, is a global regulator inArabidopsis.
• Plant Mol Biol. 2003; 52: 1125-34
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• The SWI/SNF complex is an ATP-dependent chromatin remodeling complex thatplays an important role in the regulation of eukaryotic gene expression.Very little is known about the function of SWI/SNF complex in plantscompared with animals and yeast. SWI3 is one of the core components of theSWI/SNF chromatin remodeling complexes in yeast. We have identified aputative SWI3-like cDNA clone, CHB2 (AtSWI3B), from Arabidopsis thalianaby screening the expressed sequence tag database. CHB2 encodes a putativeprotein of 469 amino acids and shares 23% amino acid sequence identity and64% similarity with the yeast SWI3. The Arabidopsis genome contains fourSWI3-like genes, namely CHB1 (AtSWI3A), CHB2 (AtSWI3B), CHB3 (AtSWI3C) andCHB4 (AtSWI3D). The expression of CHB2, CHB3 and CHB4 mRNA was detected inall tissues analyzed by RT-PCR. The expression of CHB1 mRNA, however,could not be detected in the siliques, suggesting that there isdifferential expression among CHB genes in different Arabidopsis tissues.To investigate the role of CHB2 in plants, Arabidopsis plants weretransformed with a gene construct comprising a CHB2 cDNA in the antisenseorientation driven by the CaMV 35S promoter. Repression of CHB2 expressionresulted in pleiotropic developmental abnormalities including abnormalseedling and leaf phenotypes, dwarfism, delayed flowering and no apicaldominance, suggesting a global role for CHB2 in the regulation of geneexpression. Our results indicate that CHB2 plays an essential role inplant growth and development.

• Liu D, Rudland PS, Sibson DR, Barraclough R
• Identification of mRNAs differentially-expressed between benign andmalignant breast tumour cells.
• Br J Cancer. 2002; 87: 423-31
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• Two suppression subtracted cDNA libraries have been constructed, onecontaining cDNAs to mRNAs present at a higher level in a benign humanbreast tumour-derived cell line relative to the malignant mammary cellline, MCF-7, and the other containing cDNAs present at a higher level inthe MCF-7 cells relative to the benign cells. Randomly-picked cloned DNAshave been sequenced yielding 29 and 128 different cDNAs from the benignand malignant libraries, respectively. Using reverse Northernhybridisation, 76% and 83% of the cDNAs were differentially expressed bygreater than two-fold, whilst 14% and 11% of cDNAs in the respectivelibraries were differentially expressed by more than 15-fold. Amongstthese were oestrogen-responsive cDNAs and expressed sequence tags. Onesuch oestrogen-responsive expressed sequence tag, M41, is transcribed froma gene located on chromosome 21q22.3, within an intron of a larger gene.The M41 gene contains oestrogen response elements, one of which isassociated with alu repeats. M41 mRNA is expressed at a statisticallysignificantly higher level in human breast cancer specimens than in normalhuman breast and benign lesions. In carcinomas, its up-regulation isassociated with the development of the malignant cell.

• Roth SM, Ferrell RE, Peters DG, Metter EJ, Hurley BF, Rogers MA
• Influence of age, sex, and strength training on human muscle geneexpression determined by microarray.
• Physiol Genomics. 2002; 10: 181-90
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• The purpose of this study was to determine the influence of age, sex, andstrength training (ST) on large-scale gene expression patterns in vastuslateralis muscle biopsies using high-density cDNA microarrays andquantitative PCR. Muscle samples from sedentary young (20-30 yr) and older(65-75 yr) men and women (5 per group) were obtained before and after a9-wk unilateral heavy resistance ST program. RNA was hybridized to cDNAfilter microarrays representing approximately 4,000 known human genes andcomparisons were made among arrays to determine differential geneexpression as a result of age and sex differences, and/or response to ST.Sex had the strongest influence on muscle gene expression, withdifferential expression (>1.7-fold) observed for approximately 200 genesbetween men and women (approximately 75% with higher expression in men).Age contributed to differential expression as well, as approximately 50genes were identified as differentially expressed (>1.7-fold) in relationto age, representing structural, metabolic, and regulatory gene classes.Sixty-nine genes were identified as being differentially expressed(>1.7-fold) in all groups in response to ST, and the majority of thesewere downregulated. Quantitative PCR was employed to validate expressionlevels for caldesmon, SWI/SNF (BAF60b), and four-and-a-half LIM domains 1.These significant differences suggest that in the analysis of skeletalmuscle gene expression issues of sex, age, and habitual physical activitymust be addressed, with sex being the most critical variable.

• Papoulas O, Daubresse G, Armstrong JA, Jin J, Scott MP, Tamkun JW
• The HMG-domain protein BAP111 is important for the function of the BRMchromatin-remodeling complex in vivo.
• Proc Natl Acad Sci U S A. 2001; 98: 5728-33
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• The Drosophila trithorax group gene brahma (brm) encodes the ATPasesubunit of a SWI/SNF-like chromatin-remodeling complex. A key questionabout chromatin-remodeling complexes is how they interact with DNA,particularly in the large genomes of higher eukaryotes. Here, we reportthe characterization of BAP111, a BRM-associated protein that contains ahigh mobility group (HMG) domain predicted to bind distorted or bent DNA.The presence of an HMG domain in BAP111 suggests that it may modulateinteractions between the BRM complex and chromatin. BAP111 is an abundantnuclear protein that is present in all cells throughout development. Byusing gel filtration chromatography and immunoprecipitation assays, wefound that the majority of BAP111 protein in embryos is associated withthe BRM complex. Furthermore, heterozygosity for BAP111 enhanced thephenotypes resulting from a partial loss of brm function. These datademonstrate that the BAP111 subunit is important for BRM complex functionin vivo.

• Kadam S, McAlpine GS, Phelan ML, Kingston RE, Jones KA, Emerson BM
• Functional selectivity of recombinant mammalian SWI/SNF subunits.
• Genes Dev. 2000; 14: 2441-51
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• The SWI/SNF family of chromatin-remodeling complexes plays a key role infacilitating the binding of specific transcription factors to nucleosomalDNA in diverse organisms from yeast to man. Yet the process by whichSWI/SNF and other chromatin-remodeling complexes activate specific subsetsof genes is poorly understood. We show that mammalian SWI/SNF regulatestranscription from chromatin-assembled genes in a factor-specific mannerin vitro. The DNA-binding domains (DBDs) of several zinc finger proteins,including EKLF, interact directly with SWI/SNF to generate DNase Ihypersensitivity within the chromatin-assembled beta-globin promoter.Interestingly, we find that two SWI/SNF subunits (BRG1 and BAF155) arenecessary and sufficient for targeted chromatin remodeling andtranscriptional activation by EKLF in vitro. Remodeling is achieved withonly the BRG1-BAF155 minimal complex and the EKLF zinc finger DBD, whereastranscription requires, in addition, an activation domain. In contrast,the BRG1-BAF155 complex does not interact or function with two unrelatedtranscription factors, TFE3 and NF-kappaB. We conclude that specificdomains of certain transcription factors differentially target SWI/SNFcomplexes to chromatin in a gene-selective manner and that individualSWI/SNF subunits play unique roles in transcription factor-directednucleosome remodeling.

• Cote J, Peterson CL, Workman JL
• Perturbation of nucleosome core structure by the SWI/SNF complex persistsafter its detachment, enhancing subsequent transcription factor binding.
• Proc Natl Acad Sci U S A. 1998; 95: 4947-52
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• To investigate the mechanism of SWI/SNF action, we have analyzed thepathway by which SWI/SNF stimulates formation of transcriptionfactor-bound nucleosome core complexes. We report here that the SWI/SNFcomplex binds directly to nucleosome cores and uses the energy of ATPhydrolysis to disrupt histone/DNA interactions, altering the preferredpath of DNA bending around the histone octamer. This disruption occurswithout dissociating the DNA from the surface of the histone octamer.ATP-dependent disruption of nucleosomal DNA by SWI/SNF generates analtered nucleosome core conformation that can persist for an extendedperiod after detachment of the SWI/SNF complex. This disruptedconformation retains an enhanced affinity for the transcription factorGAL4-AH. Thus, ATP-dependent nucleosome core disruption and enhancedbinding of the transcription factor can be temporally separated. Theseresults indicate that SWI/SNF can act transiently in the remodeling ofchromatin structure, even before interactions of transcription factors.

• Nomoto K, Nakazato S, Kazahari K, Ono M
• Gene structure of rat BAF60b, a component of mammalian SW1/SNF complexes,and its physical linkage to the growth hormone gene and transcriptionfactor SUG/proteasome p45 gene.
• Gene. 1997; 202: 157-65
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• In the +27.6 to +36.7 kb downstream region from the transcriptional startsite of the rat growth hormone (GH) gene, a gene encoding BAF60b, acomponent of mammalian SWI/SNF complexes, was found to have the sametranscriptional orientation as the GH gene. The 5' end of the BAF60b genewas heterogeneous and the longest gene was 9060 bp long with 13 exons. Thelargest of all exons was estimated to be 2774 bases. Deduced rat BAF60bprotein was made of 531 amino acids and its amino acid sequence was 97%identical with the human counterpart. No TATA box was found up to the -100bp region but five GC boxes corresponding to the Sp1 binding site wereobserved up to 640 bp upstream from the transcriptional start site.Sixty-three bases downstream from the BAF60b gene, the polyadenylationsite of the gene encoding transcription factor SUG/proteasome p45, whoseexpression is constant in many tissues, was identified. The BAF60b genewas expressed as 3.0 kb poly(A)-rich RNA in seven tissues and one cellline from rat but its expression varied considerably according to thetissue.

• Lohning C, Rosenbaum C, Ciriacy M
• Isolation of the TYE2 gene reveals its identity to SWI3 encoding a generaltranscription factor in Saccharomyces cerevisiae.
• Curr Genet. 1993; 24: 193-9
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• The TYE2 gene was identified by recessive mutations which result in asignificant reduction of Ty-mediated ADH2 expression. We cloned the TYE2gene and analyzed its sequence. A large open reading frame of 825 codonswas found encoding a rather hydrophilic, 93-kilodalton protein whichcontains a highly acidic region at its N-terminus. By sequence comparisonwe found that TYE2 is identical to gene SWI3 which has recently been shownto encode a nuclear protein which may function as a global transcriptionactivation factor. The TYE2/SWI3 protein is necessary for the initiationof Ty1 transcription at its major initiation site in the delta element.Furthermore TYE2 function seems to be important for the expression of avariety of Ty-unrelated functions such as ADH1 expression, sporulation,growth on maltose, galactose, raffinose, and on non-fermentable carbonsources.