Alternative splicing and allosteric regulation modulate the chromatin binding of UHRF1.

Maria Tauber,Wolfgang Fischle,Papita Mandal,Lorena V Cortés-Medina,Shili Duan,Bothayna Al-Gashgari,Abrar Aljahani,Cheryl H Arrowsmith,Lixin Fan,Sarah Kreuz,Alexander Lemak,Dulat Azhibek,Michelle S Ong,Scott Houliston,Alaguraj Veluchamy,Zhadyra Yerkesh

doi:10.1093/nar/gkaa520

Abstract

UHRF1 is an important epigenetic regulator associated with apoptosis and tumour development. It is a multidomain protein that integrates readout of different histone modification states and DNA methylation with enzymatic histone ubiquitylation activity. Emerging evidence indicates that the chromatin-binding and enzymatic modules of UHRF1 do not act in isolation but interplay in a coordinated and regulated manner. Here, we compared two splicing variants (V1, V2) of murine UHRF1 (mUHRF1) with human UHRF1 (hUHRF1). We show that insertion of nine amino acids in a linker region connecting the different TTD and PHD histone modification-binding domains causes distinct H3K9me3-binding behaviour of mUHRF1 V1. Structural analysis suggests that in mUHRF1 V1, in contrast to V2 and hUHRF1, the linker is anchored in a surface groove of the TTD domain, resulting in creation of a coupled TTD-PHD module. This establishes multivalent, synergistic H3-tail binding causing distinct cellular localization and enhanced H3K9me3-nucleosome ubiquitylation activity. In contrast to hUHRF1, H3K9me3-binding of the murine proteins is not allosterically regulated by phosphatidylinositol 5-phosphate that interacts with a separate less-conserved polybasic linker region of the protein. Our results highlight the importance of flexible linkers in regulating multidomain chromatin binding proteins and point to divergent evolution of their regulation.

Highlights

Various posttranslational modifications (PTM) of histone proteins establish binding sites for chromatin factors and serve as platforms for integrating different cellular processes [1]
While several studies show that both functional tandem tudor domain (TTD) and/or plant homeodomain (PHD) domains are required for chromatin binding, focal nuclear localization, and the DNA maintenance methylation function of human and mouse UHRF1 [7,28,30], it is still under debate which chromatin ligand is involved in UHRF1 recruitment: H3K9me2/3, TOP2A, ligase 1 (LIG1) or others [7,8,31,58]
According to NCBI nomenclature, we refer to murine UHRF1 (mUHRF1) V1 as the variant that has, to our knowledge, been used by all previous studies. mLinker 2 V1 has an insertion of nine amino acids in its centre compared to variant 2 (V2). mLinker 2 V2 is, in contrast, highly similar to hLinker 2 (Figure 1A)

Summary

Introduction

Various posttranslational modifications (PTM) of histone proteins establish binding sites for chromatin factors and serve as platforms for integrating different cellular processes [1]. A number of specialized domains that recognize specific histone PTMs have been characterized. Chromo, chromobarrel, tudor, MBT and PWWP domains bind to histone methylation marks, bromodomain [2] and tandem PHD domains [3,4] recognize acetylation marks and SH2, BRCT, WD40 and 14–3–3 domains interact with phosphorylation marks [5]. Many chromatin-binding proteins and chromatin-targeted complexes contain several domains and factors that recognize histone PTMs. The different domains either work individually/independently or in combination (bi-/multivalent or synergistic) with each other. Whether multivalent or synergistic engagement with specific modification sites on chromatin is constitutive or whether the usage of individual binding domains in composite proteins or complexes is regulated remains to be addressed

Methods

Results

Conclusion