RNA-dependent chromatin targeting of TET2 for endogenous retrovirus control in pluripotent stem cells

Nat Genet. 2018 Mar;50(3):443-451. doi: 10.1038/s41588-018-0060-9. Epub 2018 Feb 26.

Abstract

Ten-eleven translocation (TET) proteins play key roles in the regulation of DNA-methylation status by oxidizing 5-methylcytosine (5mC) to generate 5-hydroxymethylcytosine (5hmC), which can both serve as a stable epigenetic mark and participate in active demethylation. Unlike the other members of the TET family, TET2 does not contain a DNA-binding domain, and it remains unclear how it is recruited to chromatin. Here we show that TET2 is recruited by the RNA-binding protein Paraspeckle component 1 (PSPC1) through transcriptionally active loci, including endogenous retroviruses (ERVs) whose long terminal repeats (LTRs) have been co-opted by mammalian genomes as stage- and tissue-specific transcriptional regulatory modules. We found that PSPC1 and TET2 contribute to ERVL and ERVL-associated gene regulation by both transcriptional repression via histone deacetylases and post-transcriptional destabilization of RNAs through 5hmC modification. Our findings provide evidence for a functional role of transcriptionally active ERVs as specific docking sites for RNA epigenetic modulation and gene regulation.

Publication types

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

MeSH terms

  • Animals
  • Cells, Cultured
  • Chromatin / genetics
  • Chromatin / metabolism*
  • DNA Methylation
  • DNA-Binding Proteins / metabolism*
  • Dioxygenases
  • Endogenous Retroviruses / physiology*
  • Epigenesis, Genetic / physiology
  • Female
  • HEK293 Cells
  • Humans
  • Male
  • Mice
  • Nuclear Proteins / metabolism*
  • Pluripotent Stem Cells / metabolism*
  • Protein Binding
  • Proto-Oncogene Proteins / metabolism*
  • RNA / physiology*
  • RNA-Binding Proteins / metabolism*

Substances

  • Chromatin
  • DNA-Binding Proteins
  • Nuclear Proteins
  • PSPC1 protein, human
  • Proto-Oncogene Proteins
  • RNA-Binding Proteins
  • RNA
  • Dioxygenases
  • TET2 protein, human