The PHD and Chromo Domains Regulate the ATPase Activity of the Human Chromatin Remodeler CHD4

Abstract

The NuRD (nucleosome remodeling and deacetylase) complex serves as a crucial epigenetic regulator of cell differentiation, proliferation, and hematopoietic development by coupling the deacetylation and demethylation of histones, nucleosome mobilization, and the recruitment of transcription factors. The core nucleosome remodeling function of the mammalian NuRD complex is executed by the helicase-domain-containing ATPase CHD4 (Mi-2β) subunit, which also contains N-terminal plant homeodomain (PHD) and chromo domains. The mode of regulation of chromatin remodeling by CHD4 is not well understood, nor is the role of its PHD and chromo domains. Here, we use small-angle X-ray scattering, nucleosome binding ATPase and remodeling assays, limited proteolysis, cross-linking, and tandem mass spectrometry to propose a three-dimensional structural model describing the overall shape and domain interactions of CHD4 and discuss the relevance of these for regulating the remodeling of chromatin by the NuRD complex.

MBD2 and Multiple Domains of CHD4 Are Required for Transcriptional Repression by Mi-2/NuRD Complexes

“…These results reveal an exquisitely fine-tuned mechanism of chromatin remodeling in which the role of each domain in the central catalytic scaffold is crucial for function. Two studies recently used biophysical techniques to demonstrate that the PHD and chromodomains of CHD4 interact with the ATPase domain to regulate chromatin remodeling activity (32,48). These data support our findings that all of these domains are necessary for the transcriptional repressive function of CHD4 and, indeed, the entire NuRD complex.…”

“…maintain a condensed chromatin state. This model is supported by the structure of the chromo-and ATPase domains in CHD1 (11) and a recently published study employing small-angle X-ray scattering to generate a low-resolution structure of the PHD, chromo-, ATPase, and DUF1 domains of CHD4 (48). In contrast, the CHD4 CTD binds corepressor molecules or complexes necessary for NuRD repressive function, but it is not necessary for association of the complex with chromatin.…”

“…In our model, the PHD, chromo-, and ATPase domains interact to bind nucleosomal DNA (Fig. 7A), while the interaction between these domains stabilizes a structural unit that performs ATP hydrolysis to (28,34,48). In addition, the close interactions of CD1 and CD2 with the ATPase/helicase domain facilitate chromatin remodeling driven by ATP hydrolysis, which opposes the actions of activating chromatin remodeling complexes (CRCs) by maintaining the chromatin in a more condensed state.…”

“…The CHD1 CDs likely regulate the specificity of DNA binding of the ATPase domain, ensuring binding of nucleosomal rather than free DNA. Indeed, both PHD fingers, both chromodomains, and the N-terminal DUF domain interact to regulate the ATPase activity of CHD4 (48). In addition, the CTD of CHD4 (amino acids [aa] 1577 to 1912) interacts with pericentrin A (PCNA) (42).…”

Control of Histone H3 Lysine 9 (H3K9) Methylation State via Cooperative Two-step Demethylation by Jumonji Domain Containing 1A (JMJD1A) Homodimer

“…Because JMJD1A preferentially forms a stable homodimer, it is difficult to compare kinetic profiles between the dimer and monomer. To further support the channeling model, the detection of a monomethylated intermediate that binds to the inactive mutant in the WT/Mut heterodimer is important, for example, using cross-linking and tandem mass spectrometry (46). X-ray crystallography and high-resolution NMR spectroscopy (47) will provide data crucial in understanding the channeling mechanism in detail.…”