Exploring chromatin structural roles of non-coding RNAs at imprinted domains

Abstract

Different classes of non-coding RNA (ncRNA) influence the organization of chromatin. Imprinted gene domains constitute a paradigm for exploring functional long ncRNAs (lncRNAs). Almost all express an lncRNA in a parent-of-origin dependent manner. The mono-allelic expression of these lncRNAs represses close by and distant protein-coding genes, through diverse mechanisms. Some control genes on other chromosomes as well. Interestingly, several imprinted chromosomal domains show a developmentally regulated, chromatin-based mechanism of imprinting with apparent similarities to X-chromosome inactivation. At these domains, the mono-allelic lncRNAs show a relatively stable, focal accumulation in cis. This facilitates the recruitment of Polycomb repressive complexes, lysine methyltranferases and other nuclear proteins - in part through direct RNA-protein interactions. Recent chromosome conformation capture and microscopy studies indicate that the focal aggregation of lncRNA and interacting proteins could play an architectural role as well, and correlates with close positioning of target genes. Higher-order chromatin structure is strongly influenced by CTCF/cohesin complexes, whose allelic association patterns and actions may be influenced by lncRNAs as well. Here, we review the gene-repressive roles of imprinted non-coding RNAs, particularly of lncRNAs, and discuss emerging links with chromatin architecture.

Keywords: CTCF; chromatin; epigenetics; genomic imprinting; non-coding RNA.

Figure 1.. lncRNA-transcription-mediated interference mechanisms.

(A) One model of transcriptional interference involves collision of RNA Poymerase-II complexes (blue circles). High transcription of an imprinted lncRNA prevents elongation at an overlapping protein-coding gene (black rectangle) transcribed in the opposite direction. In this unidirectional repression model, the promoter of the target gene may show recruitment of transcription factors (TFs, green circles) on both the parental chromosomes. (B) Research on several imprinted genes has evoked another unidirectional model, involving promoter occlusion and repression. lncRNA transcription through a protein-coding gene mediates H3K36me3. This involves SETD2, a KMT brought to the chromatin through interaction with RNA-PolII. This induces de novo DNA methylation by DNMT3B, a methyltransferase that recognizes H3K36me3 through its PWWP domain. Chromatin associated with the target promoter/CpG island may acquire other covalent histone modifications as well — particularly H3K9me3 — with the combined modifications preventing TF binding.

Figure 2.. lncRNA-mediated chromatin repression across imprinted gene domains.

(A) Several imprinted lncRNAs mediate chromatin repression across megabases. This involves enhanced allelic recruitment of PRC1 and -2 complexes, EHMT2 and hnRNPK, in part through direct RNA–protein interactions, leading to allelic spreading of H3K27me3, H2AK119u1 and H3K9me2 across the domain. This bidirectional mechanism of chromatin repression, induced by the lncRNA itself is lineage-specific at several domains and shows certain similarities with X-chromosome inactivation [1]. (B) Some imprinted lncRNAs may repress genes on other chromosomes, in trans, possibly involving a chromatin-based mechanism that could be similar to cis repression [65–68,130].

Figure 3.. lncRNA–protein aggregates in chromatin architecture and gene expression.

The figure depicts a model in which the imprinted lncRNA accumulates in proximity to its transcription site and interacts with different chromatin repressive complexes (PRC1/2, EHMT2, others). This leads to the formation of relatively stable RNA–protein aggregates (green shading), possibly in part through LLPS. Chromosomal gene loci that are in close proximity to the aggregate acquire repressive histone modifications and become silenced. This process could be facilitated by positive effects of the lncRNA on CTCF binding, thereby ensuring appropriate long-range chromatin interactions that bring target gene(s) in close vicinity to the lncRNA–protein aggregate. The model could also explain lncRNA effects in trans, on genes located on other chromosomes, in case these are positioned close to the RNA–protein aggregate(s), at least part of the time.