The chromatin remodeler LSH controls genome-wide cytosine hydroxymethylation

Abstract

TET proteins convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), leading to a dynamic epigenetic state of DNA that can influence transcription. While TET proteins have been associated with either epigenetic repression or activation complexes, the overall understanding of the molecular mechanisms involved in TETmediated regulation of gene transcription still remains limited. Here, we show that TET proteins interact with lymphoid-specific helicase (LSH), a chromatin remodeling factor belonging to the SNF2 super family. Lsh knock-out leads to a significant reduction of 5-hydroxymethylation global level in mouse embryonic fibroblasts (MEFs) and in embryonic stem cells (ESC). Whole genome sequencing of 5hmC in wild-type versus Lsh knock-out MEFs and ESCs showed that in absence of Lsh, some regions of the genome gain 5hmC while others lose it, with not much effect on gene expression. We further show that 5hmC modifications upon Lsh loss is not a direct consequence of 5mC decrease, as differentially hydroxymethylated regions (DhMR) did not overlap with DMR (differentially methylated regions), underlying that these modifications occurred at different genomic loci. Altogether, our results suggest that LSH is a key regulator of 5hmC in both MEFs and ESC and that TET proteins rely on specific factors to establish genome-wide 5hmC patterns.

PRDM9 activity depends on HELLS and promotes local 5-hydroxymethylcytosine enrichment

“…Recently, it was shown that HELLS interacts with all three TET methylcytosine dioxygenases ( de Dieuleveult et al, 2020 ; Jia et al, 2017 ). Upon oxidation, the activity of TET enzymes on methylated cytosines (5mC) leads to a first product, 5-hydroxymethylcytosine (5hmC).…”

“…One possible scenario could be that TET recruitment involves HELLS. Indeed, HELLS can interact with one, two, or all three TET enzymes, depending on the cell type (MCF-7 cells, HEK293T, mouse embryonic stem cells) ( de Dieuleveult et al, 2020 ; Jia et al, 2017 ), and co-localize with 5hmC when stably expressed in HK1 cells ( Jia et al, 2017 ). As no evidence of HELLS/TET interaction in meiotic cells is available, a PRDM9-dependent chromatin modification might be implicated in recruiting the putative TET activity.…”