The Tandem PHD Fingers of Chd4 Bind Synergistically to Histone H3

Abstract

CHD4 is an ATPase dependent chromatin remodeler and a major subunit of the NuRD (nucleosome remodeling and deacetylase) complex, which is involved in transcriptional regulation and development. CHD4 contains a tandem of plant homeodomain (PHD) fingers, two chromodomains and an ATPase module. The PHD construct is found in many chromatin remodeling complexes and transcription factors, and is often found to be important for the targeting of these complexes to chromatin. Here we determine the specificity of the individual PHD domains of CHD4 for the unmodified tail of histone H3. We use NMR, mutational analysis and modeling to characterize the molecular basis of the interactions, revealing that both domains have an almost identical mode of interaction with the H3 tail. Analysis of the tandem PHD construct reveals that, when linked, each domain retains a distinct binding mode, however we find a synergistic effect on the binding affinities. Together our data reveal a unique mechanism of cooperative binding by multiple effector modules and suggest a multivalent targeting of CHD4 to chromatin that could manifest as either intra- or inter- nucleosomal.