Perspectives on the mechanism of transcriptional regulation by long non-coding RNAs

Abstract

Long non-coding RNAs (lncRNAs) are increasingly being recognized as epigenetic regulators of gene transcription. The diversity and complexity of lncRNA genes means that they exert their regulatory effects by a variety of mechanisms. Although there is still much to be learned about the mechanism of lncRNA function, general principles are starting to emerge. In particular, the application of high throughput (deep) sequencing methodologies has greatly advanced our understanding of lncRNA gene function. lncRNAs function as adaptors that link specific chromatin loci with chromatin-remodeling complexes and transcription factors. lncRNAs can act in cis or trans to guide epigenetic-modifier complexes to distinct genomic sites, or act as scaffolds which recruit multiple proteins simultaneously, thereby coordinating their activities. In this review we discuss the genomic organization of lncRNAs, the importance of RNA secondary structure to lncRNA functionality, the multitude of ways in which they interact with the genome, and what evolutionary conservation tells us about their function.

Keywords: RNA; RNA scaffolds; RNA structure; RNAi; TGA; TGS; chromatin; epigenetics; lncRNA; ncRNA.

Figure 1. Application of high throughput sequencing in the identification and function of lncRNAs. Cartoon schematic of typical ChIP-seq and (poly A+) RNA-seq data tracks. (A) A hypothetical lncRNA gene is identified by the presence of a ‘K4-K36 domain’ and evidence of transcription from RNA-seq data. (B) The lncRNA transcript adopts a secondary structure that binds a chromatin-modifying protein (e.g., EZH2) and guides it to a protein-coding gene target locus. H3K4me3 and H3K36me3 ChIP-seq signals at the target locus are reduced indicating reduced transcriptional activity. The histone K27 trimethylase EZH2, and the silent state chromatin mark H3K27me3 are enriched at the target promoter indicating transcriptional silencing which corresponds with reduced RNA-seq signals from the target protein-coding gene.

Figure 2. Interactions of lncRNAs with the genome. lncRNAs interact with genomic DNA and chromatin in a variety of ways. (A) lncRNAs can bind to regions of single stranded DNA to form a DNA-RNA heteroduplex by Watson-Crick base pairing. (B) lncRNAs can also form DNA-DNA-RNA triplexes by Hoogsteen or reverse Hoogsteen base pairing. (C) lncRNAs can be tethered to a chromatin through association with RNAP II and thereby act as an allele-specific signatures for specific locus. (D) lncRNAs can be indirectly bound to chromatin through binding to chromatin-associated proteins or transcription factors. (E) lncRNAs can form structures which directly sense chromatin structure.