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

• Published in: PLoS genetics 2011-03, Vol.7 (3), p.e1001347-e1001347
• Main Authors: Williamson, Christine M, Ball, Simon T, Dawson, Claire, Mehta, Stuti, Beechey, Colin V, Fray, Martin, Teboul, Lydia, Dear, T Neil, Kelsey, Gavin, Peters, Jo
• Format: Article
• Language: English
• Subjects: Alleles; Animals; Animals, Genetically Modified; Chromogranins; Deoxyribonucleic acid; DNA; DNA methylation; DNA Methylation - genetics; Female; Gene Expression Regulation - genetics; Gene Order; Gene Silencing; Gene Targeting; Genes; Genetics; Genetics and Genomics/Epigenetics; Genetics and Genomics/Gene Expression; Genetics and Genomics/Gene Function; Genomic Imprinting - genetics; GTP-Binding Protein alpha Subunits, Gs - genetics; GTP-Binding Protein alpha Subunits, Gs - metabolism; Histones - metabolism; Male; Methylation; Mice; Mutation - genetics; Physiological aspects; RNA; RNA, Antisense - genetics
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1001347

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.