Methylation-directed glycosylation of chromatin factors represses retrotransposon promoters

Proc Natl Acad Sci U S A. 2020 Jun 23;117(25):14292-14298. doi: 10.1073/pnas.1912074117. Epub 2020 Jun 10.

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 with O-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 of N-acetylglucosamine (O-GlcNAc) to serine and threonine hydroxyls. Whole-genome analysis showed that O-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 of O-GlcNAc from multiple transcriptional repressor proteins associated with TRIM28. A newly developed Cas9-based editing method for targeted removal of O-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 that O-linked glycosylation of chromatin factors is essential for the transcriptional repression of methylated retrotransposons.

Keywords: DNA methylation; gene silencing; protein O-glycosylation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetylglucosamine / metabolism
  • Animals
  • Chromatin / metabolism*
  • DNA (Cytosine-5-)-Methyltransferase 1 / genetics
  • DNA (Cytosine-5-)-Methyltransferase 1 / metabolism
  • DNA Methylation
  • Epigenesis, Genetic
  • Gene Silencing
  • Glycosylation
  • Humans
  • Methylation
  • N-Acetylglucosaminyltransferases
  • Nuclear Proteins / metabolism
  • Promoter Regions, Genetic*
  • Protein Processing, Post-Translational
  • Proteomics
  • Repressor Proteins / metabolism
  • Retroelements / physiology*
  • Transcription Factors / metabolism
  • Tripartite Motif-Containing Protein 28 / metabolism*

Substances

  • Chromatin
  • Nuclear Proteins
  • Repressor Proteins
  • Retroelements
  • Transcription Factors
  • DNA (Cytosine-5-)-Methyltransferase 1
  • DNMT1 protein, human
  • Tripartite Motif-Containing Protein 28
  • N-Acetylglucosaminyltransferases
  • UDP-N-acetylglucosamine-peptide beta-N-acetylglucosaminyltransferase
  • Acetylglucosamine