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.

This work was supported by Ayuda Merck Serono- Fundación Salud 2000 de Investigación en Endocrinología 2009 (to DM and IIP); Spanish Ministerio de Educación y Ciencia (grant number SAF2008-1578 to DM); Centre National de la Recherche Scientifique ‘‘Projects for International Scientific Cooperation’’ 34622 (to PA and DM); Agence National de la Recherche (to RF); ‘Ligue Contre le Cancer’ (to RF); Ligue contre le Cancer comité Hérault and Association pour la Recherche sur la cancer- ARC nu 4980- (for PA). DM is a Ramon y Cajal research fellow and AGA is funded by a FPU studentship. Research in the Neonatal Unit in Hospital Sant Joan de Déu is partially funded by an unrestricted grant from BebéDue Spain