The Chd family of chromatin remodelers

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Abstract

Chromatin remodeling enzymes contribute to the dynamic changes that occur in chromatin structure during cellular processes such as transcription, recombination, repair, and replication. Members of the chromodomain helicase DNA-binding (Chd) family of enzymes belong to the SNF2 superfamily of ATP-dependent chromatin remodelers. The Chd proteins are distinguished by the presence of two N-terminal chromodomains that function as interaction surfaces for a variety of chromatin components. Genetic, biochemical, and structural studies demonstrate that Chd proteins are important regulators of transcription and play critical roles during developmental processes. Numerous Chd proteins are also implicated in human disease.

Introduction

The regulation of genes is a highly coordinated process that involves the ordered recruitment of transcriptional machinery components in concert with alterations in chromatin structure. Chromatin remodeling enzymes play critical roles in organizing genomic DNA within the native chromatin state. These highly conserved enzymes can be divided into two classes: those that mediate post-translational histone modifications and those that utilize energy derived from ATP hydrolysis to alter the histone-DNA contacts within the nucleosome. These modulators alter the chromatin structure by regulating the accessibility of nucleosomal DNA, shielding certain DNA regions while exposing others for interaction with the cell's regulatory machinery.

Targeted covalent modifications of specific histone residues specify particular events in multiple cellular processes, including transcriptional activation and silencing. Numerous chemical modifications of the histone proteins occur; these include acetylation, methylation, phosphorylation, ubiquitination, sumolation, and ADP-ribosylation [1]. These modifications affect local chromatin structure and also affect higher-order folding of the nucleosomal fiber. In contrast, multisubunit complexes that utilize energy derived from ATP hydrolysis alter chromatin structure by disrupting or mobilizing nucleosomes. Each of the identified ATP-dependent chromatin remodeling enzymes contains an ATPase subunit that belongs to the SNF2 superfamily of proteins [2], [3]. Based on the presence of other conserved domains, these enzymes are further classified into the SWI/SNF (mating type switching/sucrose non-fermenting), ISWI (imitation switch), INO80 (inositol), and CHD (chromodomain helicase DNA-binding) families.

The SWI/SNF family contains yeast SNF2 and STH1, Drosophila melanogaster brahma (BRM), and mammalian BRM and brahma-related gene 1 (BRG1). The distinguishing feature of these proteins is a bromodomain, which recognizes the acetylated lysine residues on the N-terminal tails of histones [4], [5]. The ISWI family comprises yeast homologues Isw1 and Isw2 and mammalian homologues SNF2H and SNF2L. These enzymes are characterized by a SANT domain, which functions as a histone-binding module [4], [6]. 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.

Section snippets

Signature motifs of the Chd proteins

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 ATP-dependent chromatin remodeling proteins. This domain contains a conserved set of amino acid motifs that has been found in proteins involved in a myriad of cellular processes including chromatin assembly, transcription regulation, DNA

Chd1Chd2 subfamily

The CHD family is divided into three subfamilies according to the presence or absence of additional domains. The first subfamily contains yeast Chd1 (ScChd1 or Chd1p), which is the only Chd family member present in yeast, and the Chd1 and Chd2 proteins from higher eukaryotes (Fig. 1). The Chd1 and Chd2 proteins contain a DNA-binding domain located in the C-terminal region [9], [10], [32]. Currently, mChd1 is the only family member with a functionally characterized DNA-binding domain, though the

Chd3Chd4 subfamily

The second subfamily, which lacks the DNA-binding domain, includes the proteins Chd3 and Chd4 (sometimes referred to as Mi-2α and Mi-2β, respectively) (Fig. 2). Additionally, the family includes D. melanogaster Mi-2 (dMi-2), a single gene encoding two transcripts [33]. These proteins harbor paired N-terminal PHD (plant homeo domain) Zn-finger-like domains that are not found in the Chd1–Chd2 subfamily [10]. The PHD Zn-finger-like domains are found in a number nuclear proteins implicated in

Chd5Chd9 subfamily

The third subfamily contains the proteins Chd5–Chd9, which were identified on the basis of structural and sequence conservation to known Chd proteins (Fig. 3). It should be noted that Chd9 is also referred to as CReMM (chromatin-related mesenchymal modulator) [39]. This subfamily is defined by additional functional motifs in the C-terminal region, including paired BRK (Brahma and Kismet) domains, a SANT-like (switching-defective protein 3, adaptor 2, nuclear receptor co-repressor, transcription

Localization properties and tissue expression patterns of Chd proteins

Studies of D. melanogaster Chd proteins (dChd) on polytene chromosomes also shed light on the function of Chd proteins. dChd1 was found to localize to regions of decondensed chromatin (interbands) and regions of high transcriptional activity (puffs) in polytene chromosomes by immunostaining [18], [46]. However, dChd1 did not stain all interbands and chromosome puffs. Furthermore, dChd1 signal was not detected in the chromocenter, a region that represents the heterochromatic

Chd protein function

Analyses of Chd proteins reveal a wide range of functions in vitro and in vivo. Table 1 provides a summary of these properties.

A role for Chd proteins in chromatin assembly and remodeling

ATPases of the SNF2 family have been broadly implicated in many cellular processes, including nucleosome assembly, disruption, and positioning. Biochemical analyses revealed that ScChd1 has an ATPase activity that affects DNA–histone interactions within the nucleosome in a manner that is distinct from the yeast SWI/SNF complex [54]. Additionally, a partial loss of chromatin assembly activity in vitro from crude DEAE fractions derived from deletion strains of ScChd1 was observed [55]. Recently,

Chd members form multisubunit complexes

Most SNF2-like ATPases are components of large multisubunit complexes. Yeast two-hybrid screens and immunocytochemical analyses showed an interaction between mChd1 and a nuclear protein, SSRP1 (structure-specific recognition protein 1), which is involved in transcription regulation [18]. Additionally, dChd1 was found to interact with human SSRP1 [18]. Moreover, mChd1 and SSRP1 copurified in fractionated nuclear extracts that corresponded to a complex of roughly Mr 700,000 [18]. Collectively,

Chd proteins and transcriptional elongation

The control of transcriptional elongation is a prominent mechanism of gene regulation. The activities of transcription elongation factors and their link to chromatin have been well established in yeast and mammalian systems [69]. Essential transcription elongation factors in yeast include Spt4–Spt5 and Spt16 and Pob3. In mammalian cells, the counterparts for these yeast factors are DSIF (DRB sensitivity inducing factor) and FACT (facilitates chromatin transcription), respectively [69].

Studies

Chd proteins in development and differentiation

Yeast strains bearing Chd1-null deletions were viable except when grown under suboptimal conditions, thereby suggesting a role for ScChd1 in regulating gene expression [10], [73]. Genetic analyses determined that ScChd1 interacts with SWI2 and that cells require one or the other for viability [54]. Similarly, ScChd1 also genetically interacts with ISWI1 and ISWI2 and a phenotypic survey of a triple mutant, iswi1 iswi2 chd1, indicated a moderate synthetic growth defect [73]. Together, this

A role for Chd in human disease

Mutations in genes encoding SNF2-like enzymes are known to cause a spectrum of disease phenotypes. The identification and characterization of these enzymes is critical for understanding the genetic events underlying the progression of disease. To date, hCHD3hCHD5 and hCHD7 have been implicated in human disease processes (Table 2).

hCHD3 and hCHD4 have been identified as autoantigens in patients with dermatomyositis, a connective-tissue disease characterized by inflammation of both muscles and

Conclusions and future directions

The hallmark of Chd proteins is their novel combination of structural domains. The signature motifs of this class of enzymes are paired chromodomains located in the N-terminal region and a SNF2-like ATPase domain located in the central region of the protein structure [9], [10]. Since the discovery of murine Chd1 in 1993, other Chd genes have been identified, yielding a total of nine highly conserved genes from diverse organisms [9], [10], [39], [40], [51]. The Chd family is divided into three

Acknowledgements

We apologize to our colleagues whose work we did not cite due to space limitations. Work in the authors’ lab is supported by grants from the NIH.

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