Methylation-directed glycosylation of chromatin factors represses retrotransposon promoters

Abstract

The mechanisms by which methylated mammalian promoters are transcriptionally silenced even in the presence of all of the factors required for their expression have long been a major unresolved issue in the field of epigenetics. Repression requires the assembly of a methylation-dependent silencing complex that contains the TRIM28 protein (also known as KAP1 and TIF1β), a scaffolding protein without intrinsic repressive or DNA-binding properties. The identity of the key effector within this complex that represses transcription is unknown. We developed a methylation-sensitized interaction screen which revealed that TRIM28 was complexed withO-linked β-N-acetylglucosamine transferase (OGT) only in cells that had normal genomic methylation patterns. OGT is the only glycosyltransferase that modifies cytoplasmic and nuclear protein by transfer ofN-acetylglucosamine (O-GlcNAc) to serine and threonine hydroxyls. Whole-genome analysis showed thatO-glycosylated proteins and TRIM28 were specifically bound to promoters of active retrotransposons and to imprinting control regions, the two major regulatory sequences controlled by DNA methylation. Furthermore, genome-wide loss of DNA methylation caused a loss ofO-GlcNAc from multiple transcriptional repressor proteins associated with TRIM28. A newly developed Cas9-based editing method for targeted removal ofO-GlcNAc was directed against retrotransposon promoters. Local chromatin de-GlcNAcylation specifically reactivated the expression of the targeted retrotransposon family without loss of DNA methylation. These data revealed thatO-linked glycosylation of chromatin factors is essential for the transcriptional repression of methylated retrotransposons.

Silencing and Transcriptional Regulation of Endogenous Retroviruses: An Overview

“…Recently, a study identified another novel interaction partner of Trim28. The O-linked beta-N-acetylglucosamine transferase (OGT) and Trim28 have been shown to co-localize at methylated promoter regions of ERVs [73]. O-linked glycosylation is a newly described chromatin mark, which is suggested to play a crucial role in transcriptional silencing of ERVs [73].…”

Epigenetic editing: Dissecting chromatin function in context

“…[34][35][36] However, many other chromatin modifications, such as O-GlcNAc, 5hmC or H3K4me3, are also enriched on subsets of TE, suggesting that the epigenetic regulation of mobile elements may be more complex than previously anticipated and warrants further investigation. [37][38][39][40] Notably, a significant proportion of mammalian noncoding sites enriched for chromatin modifications do not coincide with either enhancers or TE. Epigenetic aberrations at these unannotated regions have already been linked to human syndromes, [41] implying that the functional interrogation of chromatin marks at non-genic regions will be instrumental to understand the mechanisms that govern genome regulation in both physiological and pathological circumstances.…”

O-GlcNAc: Regulator of Signaling and Epigenetics Linked to X-linked Intellectual Disability

“…In addition to its effects on the process of DNA demethylation, OGT has been found to be involved in gene silencing mediated by DNA methylation. OGT selectively associates with the scaffolding protein TRIM28 only in the presence of methylated DNA (Boulard et al, 2020). It has been proposed that O-GlcNAcylation of chromatin modifiers that interact with TRIM28 is required at the sites of retrotransposon promoters to repress their transcription (Boulard et al, 2020).…”

“…OGT selectively associates with the scaffolding protein TRIM28 only in the presence of methylated DNA (Boulard et al, 2020). It has been proposed that O-GlcNAcylation of chromatin modifiers that interact with TRIM28 is required at the sites of retrotransposon promoters to repress their transcription (Boulard et al, 2020). This suggests disruption of O-GlcNAc cycling may lead to increased genome instability in addition to the contribution of impaired DNA damage response described above.…”

“…Transposable elements are another major source of genome instability which have been linked to neurological disorders (Doyle et al, 2017). Mutations in OGT may derepress transposable elements considering the recent findings of OGT working with TRIM28 to silence retrotransposons in a DNA methylation-dependant manner (Boulard et al, 2020). TRIM28 silencing is active in neural progenitor cells, and heterozygous mice present behavioral phenotypes which suggest an important role in brain development (Whitelaw et al, 2010;Grassi et al, 2019).…”