A mammalian DNA-binding protein that contains a chromodomain and an SNF2/SWI2-like helicase domain.

Abstract

Two overlapping cDNAs that encode a 197-kDa sequence-selective DNA-binding protein were isolated from libraries derived from mouse lymphoid cell mRNA. In addition to a DNA-binding domain, the protein contains both a chromodomain, which occurs in proteins that are implicated in chromatin compaction, and an SNF2/SWI2-like helicase domain, which occurs in proteins that are believed to activate transcription by counteracting the repressive effects of chromatin structure. A Southern blot analysis indicated that this protein, which we have named CHD-1, for chromodomainhelicase-DNA-binding protein, is present in most, if not all, mammalian species. A Northern blot analysis revealed multiple CHD mRNA components that differed both qualitatively and quantitatively among various cell types. The various mRNAs, which are probably produced by alternative RNA processing, could conceivably encode tissue-specific and developmental stage-specific isoforms of the protein. Based on its interesting combination of features, we suspect that CHD-1 plays an important role in gene regulation.In eukaryotic cells, selective transcription of discrete sets of genes is accomplished by a variety ofregulatory mechanisms. One major mechanism involves the concerted action of distinct combinations of proteins (transcription factors) that bind directly or indirectly to particular DNA sequences and act to stimulate or repress the basal transcriptional machinery (see ref. 1 for review). Another important mechanism regulates the accessibility of certain genes to the transcriptional apparatus by regional modifications of chromatin structure. Proteins participating in this type of mechanism could affect such processes as nucleosome packing, loop formation, DNA supercoiling, and attachment to the nuclear matrix (see ref Neither of these proteins has yet been found to possess DNA-binding capability.We report here on the isolation and characterization of cDNAs that encode a 197-kDa mouse protein with an SNF2 (Brm) pattern of helicase motifs in its central region and two other noteworthy features: a sequence-selective DNAbinding domain and a motif known as the chromodomain, which occurs in Pc and in HP1, a structural component of compacted chromatin (5, 21). The chromodomain is essential for the function of Pc, apparently being required for its assembly into chromatin as part of a multiprotein complex (5). Thus, the mouse protein, which we have termed CHD-1,t embodies within a single molecule characteristics of two functionally related proteins (Brm and Pc), as well as DNAbinding capability. This combination of features could endow CHD-1 with novel regulatory properties. MATERIALS AND METHODSIsolation of the KY3 and KY9 Clones and Plasmid Construction. Agtll phage from a mouse B-cell lymphoma (A20) cDNA expression library (Clontech) were screened with double-stranded oligonucleotide probes by the protocol of Vinson et al. (7) Isolation of Clone 3-3. A cDNA library was constructed from cytoplasmic poly(A)+ RNA of S194 plasmacytoma cells and the AZap...

Mechanisms of ATP dependent chromatin remodeling

“…CHD-1 (chromodomain-helicase DNA binding protein [103]) was first isolated from mouse as a protein which contains features of both the Swi2/Snf2 family of ATPases and the Polycomb/HP1 chromodomain family of proteins [104]. In contrast to polycomb/HP1, CHD1 is not localized to condensed chromatin but possesses a minor groove DNA binding motif found in H1, HMG I/Y, D1 and datin [105].…”

The Chd family of chromatin remodelers

“…The CHD family is characterized by two signature sequence motifs: tandem chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein structure [9,10]. The SNF2-like ATPase domain defines the ATPdependent chromatin remodeling proteins.…”

“…The INO80 member of the family is the only chromatin remodeling protein in which DNA helicase activity has been observed, and evidence indicates a role for this complex in the facilitation of DNA repair [7,8]. Lastly, the CHD family includes a number of proteins that are highly conserved from yeast to humans, though the function of many of these proteins remains unknown or poorly characterized [9,10] (Table 1). This review highlights the progress made in understanding the function of the CHD family of proteins.…”

Chromatin Remodeling and the Control of Gene Expression

“…A putative chromatin remodeling complex, CHD-1, was identified adventitiously as a mammalian DNA-binding protein, which contains three signature sequence motifs: the 52-amino acid chromodomain found in the heterochromatin protein HP-1 and the homeotic repressor Polycomb, the SNF2/SWI2 ATPase domain, and motifs characteristic of minor-groove binding proteins (99,100). CHD-1 shows a sequence-selective preference for binding to (A ϩ T)-rich tracts in vitro.…”