Characterization of Novel Paternal ncRNAs at the Plagl1 Locus, Including Hymai, Predicted to Interact with Regulators of Active Chromatin

Isabel Iglesias-Platas,Cristina Camprubi,Franck Court,Gian Tartaglia,Philippe Arnaud,Kenichiro Hata,Davide Cirillo,Alex Martin-Trujillo,David Monk,Amy Guillaumet-Adkins,Robert Feil,Deborah Bourc’His

doi:10.1371/journal.pone.0038907

Abstract

Genomic imprinting is a complex epigenetic mechanism of transcriptional control that utilizes DNA methylation and histone modifications to bring about parent-of-origin specific monoallelic expression in mammals. Genes subject to imprinting are often organised in clusters associated with large non-coding RNAs (ncRNAs), some of which have cis-regulatory functions. Here we have undertaken a detailed allelic expression analysis of an imprinted domain on mouse proximal chromosome 10 comprising the paternally expressed Plagl1 gene. We identified three novel Plagl1 transcripts, only one of which contains protein-coding exons. In addition, we characterised two unspliced ncRNAs, Hymai, the mouse orthologue of HYMAI, and Plagl1it (Plagl1 intronic transcript), a transcript located in intron 5 of Plagl1. Imprinted expression of these novel ncRNAs requires DNMT3L-mediated maternal DNA methylation, which is also indispensable for establishing the correct chromatin profile at the Plagl1 DMR. Significantly, the two ncRNAs are retained in the nucleus, consistent with a potential regulatory function at the imprinted domain. Analysis with catRAPID, a protein-ncRNA association prediction algorithm, suggests that Hymai and Plagl1it RNAs both have potentially high affinity for Trithorax chromatin regulators. The two ncRNAs could therefore help to protect the paternal allele from DNA methylation by attracting Trithorax proteins that mediate H3 lysine-4 methylation. Submitted GenBank nucleotides sequences: Plagl1it: JN595789Hymai: JN595790

Highlights

Genomic imprinting is an epigenetic form of transcriptional regulation that results in the monoallelic expression of genes from the paternal or maternal allele [1]
In accordance with previous reports, we find that the Plagl1 gene covers,71 kb and contains 12 exons [10]
The majority of transcripts arise from the promoter (P1) within the differentially methylated regions (DMRs), whereas less abundant transcripts originate from an unmethylated CpG island,30 kb upstream (P2)

Summary

Introduction

Genomic imprinting is an epigenetic form of transcriptional regulation that results in the monoallelic expression of genes from the paternal or maternal allele [1]. Imprinted genes have been shown to play important roles in development, and code for proteins with diverse biological activities. The allele-specific expression of imprinted genes is mediated by CpG rich sequence elements that show allelic DNA methylation [2]. These differentially methylated regions (DMRs) result from methylation deposition during oogenesis or spermatogenesis, by the DNMT3A/DNMT3L de novo methyltransferase complex [3,4,5]. Non-coding RNAs (ncRNAs) have been shown to be important in recruiting histone methyltransferases to imprinted gene promoters, revealing the diversity of epigenetic mechanisms involved in the imprinting process [7,8]

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Discussion

Conclusion