The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes.

Daniel Andergassen,Quanah J Hudson,Takahiko Shimizu,Markus Muckenhuber,Tomasz M Kulinski,Florian M Pauler,Josef M Penninger,Hans-Christian Theussl,Philipp C Bammer,Marisa S Bartolomei

doi:10.1371/journal.pgen.1008268

Abstract

Long non-coding (lnc) RNAs are numerous and found throughout the mammalian genome, and many are thought to be involved in the regulation of gene expression. However, the majority remain relatively uncharacterised and of uncertain function making the use of model systems to uncover their mode of action valuable. Imprinted lncRNAs target and recruit epigenetic silencing factors to a cluster of imprinted genes on the same chromosome, making them one of the best characterized lncRNAs for silencing distant genes in cis. In this study we examined silencing of the distant imprinted gene Slc22a3 by the lncRNA Airn in the Igf2r imprinted cluster in mouse. Previously we proposed that imprinted lncRNAs may silence distant imprinted genes by disrupting promoter-enhancer interactions by being transcribed through the enhancer, which we called the enhancer interference hypothesis. Here we tested this hypothesis by first using allele-specific chromosome conformation capture (3C) to detect interactions between the Slc22a3 promoter and the locus of the Airn lncRNA that silences it on the paternal chromosome. In agreement with the model, we found interactions enriched on the maternal allele across the entire Airn gene consistent with multiple enhancer-promoter interactions. Therefore, to test the enhancer interference hypothesis we devised an approach to delete the entire Airn gene. However, the deletion showed that there are no essential enhancers for Slc22a2, Pde10a and Slc22a3 within the Airn gene, strongly indicating that the Airn RNA rather than its transcription is responsible for silencing distant imprinted genes. Furthermore, we found that silent imprinted genes were covered with large blocks of H3K27me3 on the repressed paternal allele. Therefore we propose an alternative hypothesis whereby the chromosome interactions may initially guide the lncRNA to target imprinted promoters and recruit repressive chromatin, and that these interactions are lost once silencing is established.

Highlights

Long non-coding RNAs are a diverse and numerous group of non-protein-coding RNA species longer than 200 nucleotides, some of which have been shown to be involved in gene regulation [1,2]
Long non-coding RNAs are numerous in the mammalian genome and many have been implicated in gene regulation
In this study we examined how the imprinted lncRNA Airn silences genes in the Igf2r imprinted cluster, focusing primarily on silencing of the distant imprinted gene Slc22a3

Summary

Introduction

Long non-coding (lnc) RNAs are a diverse and numerous group of non-protein-coding RNA species longer than 200 nucleotides, some of which have been shown to be involved in gene regulation [1,2]. The majority of lncRNAs remain relatively uncharacterized and of uncertain function, highlighting the value of model systems to identify modes of lncRNA action. Mechanisms of lncRNA action identified in imprinted lncRNAs, such as the targeting of histone modifying complexes to genomic loci and the role of lncRNA transcription in gene regulation [5,6,7,8], have later been shown for other non-imprinted lncRNAs [2,9], emphasizing their value as model systems. The number of imprinted genes in mammals appears to be limited to approximately one hundred [11], a number of which have been shown to be key regulators of development and disease [12,13]

Objectives

Methods

Results

Discussion

Conclusion