Meg3 Non-coding RNA Expression Controls Imprinting by Preventing Transcriptional Upregulation in cis

Abstract

Although many long non-coding RNAs (lncRNAs) are imprinted, their roles often remain unknown. The Dlk1-Dio3 domain expresses the lncRNA Meg3 and multiple microRNAs and small nucleolar RNAs (snoRNAs) on the maternal chromosome and constitutes an epigenetic model for development. The domain's Dlk1 (Delta-like-1) gene encodes a ligand that inhibits Notch1 signaling and regulates diverse developmental processes. Using a hybrid embryonic stem cell (ESC) system, we find that Dlk1 becomes imprinted during neural differentiation and that this involves transcriptional upregulation on the paternal chromosome. The maternal Dlk1 gene remains poised. Its protection against activation is controlled in cis by Meg3 expression and also requires the H3-Lys-27 methyltransferase Ezh2. Maternal Meg3 expression additionally protects against de novo DNA methylation at its promoter. We find that Meg3 lncRNA is partially retained in cis and overlaps the maternal Dlk1 in embryonic cells. Combined, our data evoke an imprinting model in which allelic lncRNA expression prevents gene activation in cis.

CTCF controls imprinted gene activity at the mouseDlk1-Dio3andIgf2-H19domains by modulating allele-specific sub-TAD structure

“…To explore if the perturbation of the Dlk1-Meg3 sub-TAD structure leads to incorrect imprinted activation of the Dlk1 gene, we performed in vitro differentiation of our WT and Δsite2 hybrid (BJ1 and JB1) ESCs into neural progenitor cells (NPCs) with cortical identity. In this system, imprinted Dlk1 activation can be readily recapitulated (25,27). In vitro differentiated NPCs from our JB1 and BJ1 deletion ESC lines were developmentally comparable to WT NPCs ( fig.…”

“…Rather, at both imprinted domains, maternal allele-specific CTCF binding hijacks an existing TAD organisation that is formed between bi-allelic CTCF bound clusters. The resulting maternal chromosome-specific sub-TADs are already established in ESCs, before imprinted activation of protein-coding genes on the paternal alleles (25). These allele-specific sub-TADs may thus provide the 'instructive' or 'permissive' context for correct developmentally regulated imprinted gene expression during development (29).…”

“…Next, we determined how the presence of the Dlk1-Meg3 sub-TAD on the maternal chromosome influenced contacts between other regions of the imprinted domain. We assayed Interestingly, significantly longer distances were measured on the maternal chromosome between all pairs of probes that covered the Dlk1, Dio3 and Begain genes; the three protein-coding genes in the TAD that may acquire mono-allelic expression upon differentiation (24,25), yet that are inactive in ESCs (table S2). To gain further insight into these differential configurations, we performed Finally, we determined if the maternal Dlk1-Meg3 sub-TAD itself engaged in differential contacts with other regions in the TAD.…”

“…Using viewpoints at the IG-DMR and the CTCF peak upstream of the Dlk1 gene, we noted that absence of maternal CTCF binding at site 2 strongly reduced interactions within the Dlk1-Meg3 sub-TAD on the maternal chromosome ( Fig. 4 The domain's imprinted protein-coding genes, particularly Dlk1, are activated upon neural differentiation, but only from the paternal allele (24,25). To explore if the perturbation of the Dlk1-Meg3 sub-TAD structure leads to incorrect imprinted activation of the Dlk1 gene, we performed in vitro differentiation of our WT and Δsite2 hybrid (BJ1 and JB1) ESCs into neural progenitor cells (NPCs) with cortical identity.…”

The implication of lncRNA expression pattern and potential function of lncRNA RP4‐576H24.2 in acute myeloid leukemia

“…3,4 Long noncoding RNA (lncRNA) is a class of RNAs with more than 200 nucleotides which have less protein-coding capacities, those molecules function as key regulators in cellular activities (such as the process of cell cycle, differentiation, and imprinting). [5][6][7][8][9] Recent studies have revealed that lncRNAs may hold crucial triggers of the development and progression of hematological malignancies. 10 In AML, the studies aiming at investigating the role of lncRNA are limited, while the findings are minimal yet intriguing.…”