Uncoupling antisense-mediated silencing and DNA methylation in the imprinted Gnas cluster

PLoS Genet. 2011 Mar;7(3):e1001347. doi: 10.1371/journal.pgen.1001347. Epub 2011 Mar 24.

Abstract

There is increasing evidence that non-coding macroRNAs are major elements for silencing imprinted genes, but their mechanism of action is poorly understood. Within the imprinted Gnas cluster on mouse chromosome 2, Nespas is a paternally expressed macroRNA that arises from an imprinting control region and runs antisense to Nesp, a paternally repressed protein coding transcript. Here we report a knock-in mouse allele that behaves as a Nespas hypomorph. The hypomorph mediates down-regulation of Nesp in cis through chromatin modification at the Nesp promoter but in the absence of somatic DNA methylation. Notably there is reduced demethylation of H3K4me3, sufficient for down-regulation of Nesp, but insufficient for DNA methylation; in addition, there is depletion of the H3K36me3 mark permissive for DNA methylation. We propose an order of events for the regulation of a somatic imprint on the wild-type allele whereby Nespas modulates demethylation of H3K4me3 resulting in repression of Nesp followed by DNA methylation. This study demonstrates that a non-coding antisense transcript or its transcription is associated with silencing an overlapping protein-coding gene by a mechanism independent of DNA methylation. These results have broad implications for understanding the hierarchy of events in epigenetic silencing by macroRNAs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Animals
  • Animals, Genetically Modified
  • Chromogranins
  • DNA Methylation / genetics*
  • Female
  • GTP-Binding Protein alpha Subunits, Gs / genetics*
  • GTP-Binding Protein alpha Subunits, Gs / metabolism*
  • Gene Expression Regulation / genetics
  • Gene Order
  • Gene Silencing*
  • Gene Targeting
  • Genomic Imprinting / genetics*
  • Histones / metabolism
  • Male
  • Mice
  • Mutation / genetics
  • RNA, Antisense / genetics*

Substances

  • Chromogranins
  • Histones
  • RNA, Antisense
  • Gnas protein, mouse
  • GTP-Binding Protein alpha Subunits, Gs