Alternative splicing and allosteric regulation modulate the chromatin binding of UHRF1

Abstract

<jats:title>Abstract</jats:title> <jats:p>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.</jats:p>

The interplay between DNA and histone methylation: molecular mechanisms and disease implications

“…Indeed, point mutations in either the TTD, PHD, or linker regions reduce UHRF1's association with chromatin in cells and compromise UHRF1's ability to maintain DNA methylation (Rothbart et al, 2013). This is further illustrated by a recent study that identified a splicing variant of mouse UHRF1, which has additional 9 amino acids inserted in the TTD-PHD finger linker region compared to canonical mouse and human UHRF1 (Tauber et al, 2020). As a result, the variant UHRF1 had distinct H3K9me3 binding profiles and displayed enhanced ubiquitination activity toward H3K9me3-modified nucleosomes.…”

Molecular basis of UHRF1 allosteric activation for synergistic histone modification binding by PI5P

“…Different reader domains of composite proteins or complexes can either work individually/independently or in combination (multivalent and/ or synergistic) with each other 26,39,40 . The overall binding strength is higher in multivalent, synergistic interactions compared to independent multivalent binding (reflecting only the sum of the individual domain binding strength).…”

“…Region I maps to the TTD surface groove (aka acidic patch or R pocket) 3,26 that shares binding interface with either Linker 4/ PBR 3,27 or with Linker 2 41 . Like Linker 4, Linker 2 is enriched in positively charged amino acids (RRK motifs, see Fig.…”

“…Allosteric binding of PI5P releases the PBR from the TTD enabling its H3K9me recognition 3 . Other work unveiled that differential splicing in the flexible linker regions affects the overall regulation of human and mouse UHRF1 26 . The complex regulation of UHRF1 has made this factor an attractive model to study how a multidomain chromatin protein is conformationally and functionally controlled.Here, we set out to delineate the molecular details of PI5P-mediated allosteric activation of human UHRF1 (hUHRF1).…”

Staying true to yourself: mechanisms of DNA methylation maintenance in mammals

“…Also, oocytes exemplify the existence of splicing variants of DNMT1. Splicing variants of UHRF1 also exist in the mouse and modify the localization and binding behavior of UHRF1 ( 108 ), however the physiological role of these variants remains to be discovered.…”