RNA matchmaking in chromatin regulation

Abstract

Beyond being the product of gene expression, RNA can also influence the regulation of chromatin. The majority of the human genome has the capacity to be transcribed and the majority of the non-protein-coding transcripts made by RNA Polymerase II are enriched in the nucleus. Many chromatin regulators can bind to these ncRNAs in the nucleus; in some cases, there are clear examples of direct RNA-mediated chromatin regulation mechanisms stemming from these interactions, while others have yet to be determined. Recent studies have highlighted examples of chromatin regulation via RNA matchmaking, a term we use broadly here to describe intermolecular base-pairing interactions between one RNA molecule and an RNA or DNA match. This review provides examples of RNA matchmaking that regulates chromatin processes and summarizes the technical approaches used to capture these events.

Keywords: RNA matchmaking; chromatin; lncRNA; piRNA.

Figure 1.. Mechanisms of RNA Matchmaking.

A) Noncoding RNAs such as small RNAs (piRNAs, siRNAs) and long noncoding RNAs (lncRNAs) can form base-pairing interactions, often mediated by proteins, to target the RNP to chromatin via nascent RNA. B) RNAs can interact with DNA through additional mechanisms such as mediated by protein-protein interaction (does not fall under the definition of “RNA Matchmaking”), triple helix formation, or R-loop pairing with unwound DNA.

Figure 2.. Strategies for capturing RNA-DNA interactions.

Fragmented chromatin is crosslinked directory or indirectly to RNA. Specific RNAs can be enriched by oligo capture prior to sequencing of associated DNA. Specific RNA-DNA structures can be enriched by antibodies recognizing the structure (R-loop, triplex), irrespective of the sequence. All RNA-DNA interactions can be profiled by ligation of the RNA to the DNA and subsequent hybrid sequencing.

Figure 3.. Strategies for capturing RNA-RNA interactions.

Base-paired RNAs can be crosslinked directly with psoralen derivatives such as AMT or indirectly via bridging proteins. Associated RNAs can be identified for a specific RNA bait using oligo capture and subsequent RNA sequencing. All base-pairing RNA interactions can be profiled by ligating AMT-crosslinked RNAs and hybrid sequencing. Droplet barcoding of crosslinked RNAs is an alternative strategy to identify associated pairs. Specific bridging proteins can be isolated to identify which RNAs are being bridged via ligation and hybrid RNA sequencing. Note: protein bridging in the absence of base-pairing does not fall under this review’s definition of “RNA Matchmaking”.