Taxonomic distribution of proteins containing ARID domains

The tree below includes only several representative species and genera. The complete taxonomic breakdown of all proteins containing ARID domains can be accessed here. Click the counts or percentage values to display the corresponding proteins.

A novel DNA-binding motif shares structural homology to DNA replicationand repair nucleases and polymerases.

Yuan YC, Whitson RH, Liu Q, Itakura K, Chen Y
Nat Struct Biol. 1998; 5: 959-64

A novel class of DNA-binding domains has been established from at leastsixteen recently identified DNA-binding proteins. The three-dimensionalstructure of one of these domains, Mrf-2, has been solved using NMRmethods. This structure is significantly different from known DNA-bindingdomain structures. The mechanism of DNA recognition by this motif has beensuggested based on conserved residues, surface electrostatic potentialsand chemical shift changes. This new DNA-binding motif shares structuralhomology with T4 RNase H, E. coli endonuclease III and Bacillus subtilisDNA polymerase I. The structural homology suggests a mechanism forsubstrate recognition by these enzymes.

Characterization of the dead ringer gene identifies a novel, highlyconserved family of sequence-specific DNA-binding proteins.

Gregory SL, Kortschak RD, Kalionis B, Saint R
Mol Cell Biol. 1996; 16: 792-9

We reported the identification of a new family of DNA-binding proteinsfrom our characterization of the dead ringer (dri) gene of Drosophilamelanogaster. We show that dri encodes a nuclear protein that contains asequence-specific DNA-binding domain that bears no similarity to knownDNA-binding domains. A number of proteins were found to contain sequenceshomologous to this domain. Other proteins containing the conserved motifinclude yeast SWI1, two human retinoblastoma binding proteins, and othermammalian regulatory proteins. A mouse B-cell-specific regulator exhibits75% identity with DRI over the 137-amino-acid DNA-binding domains of theseproteins, indicating a high degree of conservation of this domain. Gelretardation and optimal binding site screens revealed that the in vitrosequence specificity of DRI is strikingly similar to that of manyhomeodomain proteins, although the sequence and predicted secondarystructure do not resemble a homeodomain. The early general expression ofdri and the similarity of DRI and homeodomain in vitro DNA-bindingspecificity compound the problem of understanding the in vivo specificityof action of these proteins. Maternally derived dri product is foundthroughout the embryo until germ band extension, when dri is expressed ina developmentally regulated set of tissues, including salivary glandducts, parts of the gut, and a subset of neural cells. The discovery ofthis new, conserved DNA-binding domain offers an explanation for theregulatory activity of several important members of this class andpredicts significant regulatory roles for the others.

The immunoglobulin heavy-chain matrix-associating regions are bound byBright: a B cell-specific trans-activator that describes a new DNA-bindingprotein family.

Herrscher RF, Kaplan MH, Lelsz DL, Das C, Scheuermann R, Tucker PW
Genes Dev. 1995; 9: 3067-82

B lymphocyte-restricted transcription of immunoglobulin heavy-chain (IgH)genes is specified by elements within the variable region (VH) promoterand the intronic enhancer (E mu). The gene encoding a protein that binds aVH promoter proximal site necessary for induced mu-heavy-chaintranscription has been cloned. This B-cell specific protein, termed Bright(B cell regulator of IgH transcription), is found in both soluble andmatrix insoluble nuclear fractions. Bright binds the minor groove of arestricted ATC sequence that is sufficient for nuclear matrix association.This sequence motif is present in previously described matrix-associatingregions (MARs) proximal to the promoter and flanking E mu. Bright canactivate E mu-driven transcription by binding these sites, but only whenthey occur in their natural context and in cell lines permissive for E muactivity. To bind DNA, Bright requires a novel tetramerization domain anda previously undescribed domain that shares identity with severalproteins, including SWI1, a component of the SWI/SNF complex.