Plant Homeodomain (PHD) Fingers of CHD4 Are Histone H3-binding Modules with Preference for Unmodified H3K4 and Methylated H3K9

Abstract

A major challenge in chromatin biology is to understand the mechanisms by which chromatin is remodeled into active or inactive states as required during development and cell differentiation. One complex implicated in these processes is the nucleosome remodeling and histone deacetylase (NuRD) complex, which contains both histone deacetylase and nucleosome remodeling activities and has been implicated in the silencing of subsets of genes involved in various stages of cellular development. Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a core component of the NuRD complex and contains a nucleosome remodeling ATPase domain along with two chromodomains and two plant homeodomain (PHD) fingers. We have previously demonstrated that the second PHD finger of CHD4 binds peptides corresponding to the N terminus of histone H3 methylated at Lys 9 . Here, we determine the solution structure of PHD2 in complex with H3K9me3, revealing the molecular basis of histone recognition, including a cation-recognition mechanism for methylated Lys 9. Additionally, we demonstrate that the first PHD finger also exhibits binding to the N terminus of H3, and we establish the histone-binding surface of this domain. This is the first instance where histone binding ability has been demonstrated for two separate PHD modules within the one protein. These findings suggest that CHD4 could bind to two H3 N-terminal tails on the same nucleosome or on two separate nucleosomes simultaneously, presenting exciting implications for the mechanism by which CHD4 and the NuRD complex could direct chromatin remodeling.The N-terminal tails of histones are subject to many reversible covalent modifications in vivo, and different modifications have often been associated with either active or repressed chromatin states. According to prevailing ideas, the status of the cell is translated to chromatin in the form of specific post-translational modification (PTM) 4 patterns on histone tails. This tagged chromatin is then recognized by effector proteins and complexes that regulate how the underlying genetic information is used (1). The complicated and intertwined processes of tagging the histone tails, recognizing the tags, remodeling chromatin into active (open) or repressed (compacted) states, and removing the tags requires the coordination of multiple protein functions.The nucleosome remodeling and histone deacetylase (NuRD) complex is unique among nucleosome remodeling complexes in that it couples histone deacetylase activity with nucleosome remodeling ATPase activity (although the purpose of this enzymatic combination is currently unclear). The NuRD complex has traditionally been considered a transcriptional corepressor complex, consistent with the repressive function of histone deacetylation (reviewed in Refs. 2, 3). Several key NuRD complex components have been shown to play a role in development and cell lineage commitment in multiple contexts. For example, in Caenorhabditis elegans, the CHD4 homologue let-418 is required for the repression of germ line ...

SHPRH regulates rRNA transcription by recognizing the histone code in an mTOR-dependent manner

“…are critical for its interaction with histones (40,41). To examine whether this requirement for a negatively charged amino acid in the PHD is conserved in SHPRH, we aligned the SHPRH PHD with other PHDs.…”

Bivalent recognition of nucleosomes by the tandem PHD fingers of the CHD4 ATPase is required for CHD4-mediated repression

“…2B). Association of PHD1/2 with the two peptides was modeled using NMR data and the structures of unbound PHD1 and of PHD2 in complex with a histone peptide (16,23). PHD1 and PHD2 were oriented in order for the C-terminal end of PHD1 to align with the N-terminal end of PHD2.…”

“…We introduced mutations in the PHD1 and PHD2 fingers of the full length protein that have been shown to significantly reduce binding of the individual PHD modules to histone H3 peptides (15,16). Additionally, PHD finger deletion mutants (ΔD365-C411, ΔPHD1 and ΔD443-C490, ΔPHD2) of CHD4 were generated.…”

“…Unlike other chromodomains that bind methylated histone marks enriched in heterochromatic regions (10)(11)(12)(13), the CHD4 chromodomains exhibit a preference for DNA (14). The individual PHD fingers of CHD4 (PHD1 and PHD2) have been shown to possess histone-binding activity (15,16); however, the target of the tandem PHD1/2 module and the functional consequences of its association with chromatin remain unclear.…”

Nucleosome Remodeling and Epigenetics

“…A PHD domain in the BPTF subunit of the NURF complex recognizes H3K4me3 and couples this modification to nucleosome remodeling (Hargreaves and Crabtree 2011). The CHD4 subunit of the NuRD complex contains two PHD domains, the second of which recognizes H3K9me3, and the first one interacts preferentially with the amino terminus of H3 if unmodified at K4 (Mansfield et al 2011). Remarkably, DPF3b, a factor associated with human BAF, recognizes H3K14 acetylation through tandem PHD fingers (Zeng et al 2010).…”