Often located in the CpG islands of the promoters or transcription stop sites, R-loops have important biological functions in epigenetic and transcriptional regulation. Let’s look at the impact on epigenetic regulation first.

DNA methylation regulation by R- loops
R-loops are enriched at loci with decreased DNA methylation, increased DNase hypersensitivity, and higher chromatin accessibility[1]. R-loops can inhibit DNA methylation by repelling the binding of 5mC DNA methyltransferases (DNMTs)[2,3] or attracting DNA demethylases (TET)(Fig.1)[4].

Figure 1. R-loop with antisense lncRNA TARID binds GADD45A, recruits TET1 to the CpG island of TCF21 gene promoter, demethylates the DNA, and activates the TCF21 transcription [4].

This R-loop mechanism via gene methylation can be studied by DRIP-seq, along with LncRNA Array and MeDIP-seq.

Chromatin remodeling by R-loop
R- loops can cause chromatin remodeling and changes by directly recruiting chromatin modifying complexes, or by serving as an anchor to tether the lncRNA to the specific DNA site.

This mechanism via chromatin remodeling can be studied by DRIP-seq along with LncRNA Array and ChIP-seq.