The PHD Finger of Human UHRF1 Reveals a New Subgroup of Unmethylated Histone H3 Tail Readers

Nada Lallous,Pierre Legrand,Santiago Ramón-Maiques,Jean-Pierre Samama,Catherine Birck,Alastair G Mcewen,Maria Gasset

doi:10.1371/journal.pone.0027599

Abstract

The human UHRF1 protein (ubiquitin-like containing PHD and RING finger domains 1) has emerged as a potential cancer target due to its implication in cell cycle regulation, maintenance of DNA methylation after replication and heterochromatin formation. UHRF1 functions as an adaptor protein that binds to histones and recruits histone modifying enzymes, like HDAC1 or G9a, which exert their action on chromatin. In this work, we show the binding specificity of the PHD finger of human UHRF1 (huUHRF1-PHD) towards unmodified histone H3 N-terminal tail using native gel electrophoresis and isothermal titration calorimetry. We report the molecular basis of this interaction by determining the crystal structure of huUHRF1-PHD in complex with the histone H3 N-terminal tail. The structure reveals a new mode of histone recognition involving an extra conserved zinc finger preceding the conventional PHD finger region. This additional zinc finger forms part of a large surface cavity that accommodates the side chain of the histone H3 lysine K4 (H3K4) regardless of its methylation state. Mutation of Q330, which specifically interacts with H3K4, to alanine has no effect on the binding, suggesting a loose interaction between huUHRF1-PHD and H3K4. On the other hand, the recognition appears to rely on histone H3R2, which fits snugly into a groove on the protein and makes tight interactions with the conserved aspartates D334 and D337. Indeed, a mutation of the former aspartate disrupts the formation of the complex, while mutating the latter decreases the binding affinity nine-fold.

Highlights

Human UHRF1, called ICBP90, is a multidomain nuclear protein associated with cellular proliferation and epigenetic regulation [1] (Fig. 1A)
Given the important differences with other PHD fingers, we explored the ability of huUHRF1-PHD to bind to histone H3 peptides
In this work we show that the PHD finger of human UHRF1

Summary

Introduction

Human UHRF1 (huUHRF1; ubiquitin-like containing PHD and RING finger domains 1), called ICBP90, is a multidomain nuclear protein associated with cellular proliferation and epigenetic regulation [1] (Fig. 1A). Through its Tudor domain, UHRF1 recognizes the histone silencing mark H3K9me (histone H3 trimethylated at lysine 9), and exhibits stronger cooperative binding to H3K9me3-modified nucleosomes in the presence of CpG methylation [11]. HuUHRF1-PHD was initially identified as a H3K9me binder [12], the crystal structure of the tandem tudor domain of this protein in complex with a histone H3K9me peptide and the recent characterization of the PHD finger showing no binding affinity for histones [15,16] questioned again the exact role of huUHRF1-PHD. Two distinct subclasses of PHD fingers have been identified, which can bind to either methylated (H3K4me, H3K9me) or unmethylated lysine residues on the histone H3 N-terminal tail with micromolar affinity. In most of the PHD finger structures recognizing unmodified or methylated H3K4, the arginine H3R2 fits snugly in a protein groove, where the positively charged guanidinium group forms a salt bridge with a conserved glutamate or aspartate

Methods

Results

Conclusion