The R-loop Grammar predicts R-loop formation under different topological constraints

Abstract

R-loops are transient three-stranded nucleic acids that form during transcription when the nascent RNA hybridizes with the template DNA, freeing the DNA non-template strand. There is growing evidence that R-loops play important roles in physiological processes such as control of gene expression, and that they contribute to chromosomal instability and disease. It is known that R-loop formation is influenced by both the sequence and the topology of the DNA substrate, but many questions remain about how R-loops form and the 3-dimensional structures that they adopt. Here we represent an R-loop as a word in a formal grammar called the R-loop grammar and predict R-loop formation. We train the R-loop grammar on experimental data obtained by single-molecule R-loop footprinting and sequencing (SMRF-seq). Despite not containing explicit topological information, the R-loop grammar accurately predicts R-loop formation on plasmids with varying starting topologies and outperforms previous methods in R-loop prediction. Author summaryR-loops are prevalent triple helices that play regulatory roles in gene expression and are involved in various diseases. Our work improves the understanding of the relationship between the nucleotide sequence and DNA topology in R-loop formation. We use a mathematical approach from formal language theory to define an R-loop language and a set of rules to model R-loops as words in that language. We train the resulting R-loop grammar on experimental data of co-transcriptional R-loops formed on different DNA plasmids of varying topology. The model accurately predicts R-loop formation and outperforms prior methods. The R-loop grammar distills the effect of topology versus sequence, thus advancing our understanding of R-loop structure and formation.