Nucleosomal DNA binding drives the recognition of H3K36-methylated nucleosomes by the PSIP1-PWWP domain

Rick Van Nuland,Edwin Cuppen,Sebastiaan Van Heesch,Hugo Van Ingen,Rolf Boelens,Ht Marc Timmers,Marieke Simonis,Frederik Ma Van Schaik

doi:10.1186/1756-8935-6-12

Abstract

BackgroundRecognition of histone modifications by specialized protein domains is a key step in the regulation of DNA-mediated processes like gene transcription. The structural basis of these interactions is usually studied using histone peptide models, neglecting the nucleosomal context. Here, we provide the structural and thermodynamic basis for the recognition of H3K36-methylated (H3K36me) nucleosomes by the PSIP1-PWWP domain, based on extensive mutational analysis, advanced nuclear magnetic resonance (NMR), and computational approaches.ResultsThe PSIP1-PWWP domain binds H3K36me3 peptide and DNA with low affinity, through distinct, adjacent binding surfaces. PWWP binding to H3K36me nucleosomes is enhanced approximately 10,000-fold compared to a methylated peptide. Based on mutational analyses and NMR data, we derive a structure of the complex showing that the PWWP domain is bound to H3K36me nucleosomes through simultaneous interactions with both methylated histone tail and nucleosomal DNA.ConclusionConcerted binding to the methylated histone tail and nucleosomal DNA underlies the high- affinity, specific recognition of H3K36me nucleosomes by the PSIP1-PWWP domain. We propose that this bipartite binding mechanism is a distinctive and general property in the recognition of histone modifications close to the nucleosome core.

Highlights

Recognition of histone modifications by specialized protein domains is a key step in the regulation of DNA-mediated processes like gene transcription
H3K36 methylation-dependent nucleosome binding by PSIP1-PWWP To characterize the interaction of the PSIP1-PWWP domain with H3K36me nucleosomes, binding assays with immobilized GST-PWWP and mono-nucleosomal fractions from wild type or mutant Saccharomyces cerevisiae were performed
Here we determined the molecular basis of H3K36me nucleosome recognition by the PSIP1-PWWP domain

Summary

Introduction

Recognition of histone modifications by specialized protein domains is a key step in the regulation of DNA-mediated processes like gene transcription. The structural basis of these interactions is usually studied using histone peptide models, neglecting the nucleosomal context. The complex of DNA and histone proteins that packages the eukaryotic genome, are key in the regulation of transcription, maintenance of genomic integrity, chromosome condensation and segregation [1]. Modifications such as acetylation or methylation of lysine residues of histone proteins can serve to recruit effector proteins to specific genomic sites [2]. PSIP1 is an essential subunit of the MLL complex in MLL oncogenic transformations via HOX gene regulation [21], and is implicated in the homologous recombination pathway for DNA repair [22]

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