The Yin and Yang of R-loop biology

Abstract

RNA performs diverse functions in cells, directing translation, modulating transcription and catalyzing enzymatic reactions. Remarkably RNA can also anneal to its genomic template co- or post-transcriptionally to generate an RNA-DNA hybrid and a displaced single-stranded DNA. These unusual nucleic acid structures are called R-loops. Studies in the last decades concentrated on the detrimental effects of R-loop formation, particularly on genome stability. In fact, R-loops are thought to play a role in several human diseases like cancer and neurodegenerative syndromes. But recent data has revealed that R-loops can also have a positive impact on cell processes, like regulating gene expression, chromosome structure and DNA repair. Here we summarize our current understanding of the formation and dissolution of R-loops, and discuss their negative and positive impact on genome structure and function.

Regulated Formation of lncRNA-DNA Hybrids Enables Faster Transcriptional Induction and Environmental Adaptation

“…R-loops have been shown to function as transcriptional regulators at the level of initiation, elongation and termination, as well as etiological agents of DNA damage (Costantino and Koshland, 2015). As transcriptional regulators, R-loops protect CpG-containing promoters from transcriptional silencing by blocking recruitment of the DNA methyltransferase DNMT3B1 (Ginno et al, 2013; Ginno et al, 2012), promote efficient termination by pausing RNA polymerase (Skourti-Stathaki et al, 2011), and repress transcription by promoter occlusion (Sun et al, 2013).…”

“…There are two proposed mechanisms for formation of R loops in vivo (Costantino and Koshland, 2015). The first envisions that nascent RNA emerging from RNA polymerase folds back onto the DNA, forming an R-loop in cis from defects in elongation, termination and mRNA-protein packaging (Costantino and Koshland, 2015; Dominguez-Sanchez et al, 2011; Gomez-Gonzalez et al, 2011; Stirling et al, 2012).…”

Cytosine deamination and base excision repair cause R-loop–induced CAG repeat fragility and instability in Saccharomyces cerevisiae

“…Despite their prevalence and physiological functions, R-loops can be detrimental to cells due to increased R-loop-associated DNA damage and genome instability (13)(14)(15). In human cells, transcription-coupled nucleotide excision repair (TC-NER) nucleases XPG and XPF have been shown to process R-loops into DSBs (16).…”

Enzymatically Generated CRISPR Libraries for Genome Labeling and Screening

“…We note that the 3.4 MB region on X. laevis chromosome 4 (Figure 3) is visible with a mean labeling density of one guide per 2,664 bp, which is unlikely to affect global chromatin state. However, because an R-loop (an RNA-DNA hybrid opposite a region of single-stranded DNA) is produced by guide RNA binding, it is possible that nucleosome assembly and chromatin structure are affected (Costantino and Koshland, 2015), particularly in the case of the RHM2 probe that densely labels abundant pericentric repeats.…”