Conservation and Regulation of the Essential Epigenetic Regulator UHRF1 Across Vertebrata Orthologs

Abstract

UHRF1 is a critical epigenetic regulator which serves as a molecular model for understanding the crosstalk between histone modification and DNA methylation. It is integrated in the process of DNA maintenance methylation through its histone ubiquitylation activity, ultimately functioning as a recruiter of DNA methyltransferase 1 (DNMT1). As the faithful propagation of DNA methylation patterns during cell division is a common molecular phenomenon among vertebrates, understanding the underlying conserved mechanism of UHRF1 for executing such a key process is important. Here, I present a broad-range evolutionary comparison of UHRF1 binding behavior and enzymatic activity of six species spanning across the vertebrata subphylum. According to their distinct binding modes to differentially methylated histone H3, a pattern is emerging which separates between mammalian and nonmammalian orthologs. H. sapiens, P. troglodytes and M. musculus UHRF1 orthologs utilize the functionality of both TTD and PHD domains to interact with histone H3 peptides, while G. gallus, X. laevis, and D. rerio employ either TTD or PHD. Further, UHRF1 allosteric regulation by 16:0 PI5P is a unique case to primate orthologs where H3K9me3 peptide binding is enhanced upon hUHRF1 and pUHRF1 interacting with 16:0 PI5P. This is due to their closed and autoinhibited conformation wherein TTD is blocked by the PBR region in linker 4. 16:0 PI5P outcompetes TTD for PBR binding resulting in a release of TTD blockage, hence, enhanced H3K9me3 binding. However, owing to the lack of phosphatidylinositol binding specificity and reduced sequence conservation of linker 4, the regulatory impact of 16:0 PI5P in avian and lower vertebrate orthologs could not be detected. Additionally, all UHRF1 orthologs exert their ubiquitylation enzymatic activity on histone H3 substrates, supporting the notion that the overall functionality of UHRF1 orthologs is conserved, despite their divergent molecular approaches. Taken together, my findings suggest that UHRF1 orthologs adopt distinct conformational states with a differential response to the allosteric regulators 16:0 PI5P and hemi-methylated DNA.