Molecular basis of hUHRF1 allosteric activation for synergistic histone modification binding by PI5P

Abstract

Chromatin marks are recognized by distinct binding modules, many of which are embedded in multidomain proteins. How the different functionalities of such complex chromatin modulators are regulated is often unclear. Here, we delineated the interplay of the H3 amino terminus– and K9me-binding activities of the multidomain hUHRF1 protein. We show that the phosphoinositide PI5P interacts simultaneously with two distant flexible linker regions connecting distinct domains of hUHRF1. The binding is dependent on both, the polar head group, and the acyl part of the phospholipid and induces a conformational rearrangement juxtaposing the H3 amino terminus and K9me3 recognition modules of the protein. In consequence, the two features of the H3 tail are bound in a multivalent, synergistic manner. Our work highlights a previously unidentified molecular function for PI5P outside of the context of lipid mono- or bilayers and establishes a molecular paradigm for the allosteric regulation of complex, multidomain chromatin modulators by small cellular molecules.

Nuclear Phosphoinositides as Key Determinants of Nuclear Functions

“…UHRF1 acts to safeguard the genome by maintaining global DNA methylation profiles, silencing repetitive elements, and protecting chromatin from DNA damaging agents [168]. PtdIns5P interacts with a polybasic region (PBR) in the C-terminus of UHRF1 to induce a conformational change and rearrangement of its domains, allowing the tandem Tudor domain (TTD) in the N-terminus to bind more strongly to H3K9me3 [168,180]. Although the exact consequences of PtdIns5P interaction with UHRF1 in vivo are not clear, UHRF1 is often upregulated in tumour cells, and targeting the allosteric PtdIns5P interaction site may have therapeutic value.…”

25 Years of PI5P

“…Increased PI5P in the nucleus was shown to activate transcription through direct binding to the transcription factor TAF3 ( Stijf-Bultsma et al, 2015 ). Work from the lab of Wolfgang Fischle suggested PI5P allosterically activates the epigenetic regulator UHRF1, with PI5P inducing a state in UHRF1 that interacts more with methylated histones (H3K9me3) ( Gelato et al, 2014 ; Mandal et al, 2022 ). More recently, PI5P exogenously added to cells was shown to promote the degradation of UHRF1 ( Poli et al, 2023 ).…”