Using DNA–RNA immunoprecipitation followed by cDNA conversion coupled to high-throughput sequencing (DRIPc–seq), researchers have profiled the genome-wide prevalence and distribution of R loops in mouse and human cells. Mapping of R loops at near base-pair resolution and in a strand-specific manner showed that the co-transcriptional hybridization of nascent RNAs to template DNA is a conserved, prevalent and dynamic feature of mammalian chromatin that can impact gene expression. Epigenomic profiling revealed that R loops associate with specific epigenomic signatures: at promoters, R loops associate with an open, histone H3 lysine 4 (H3K4) hypermethylated and hyperacetylated state characteristic of strong CpG island promoters; at terminators, R loops associate with an enhancer- and insulator-like state; and R-loop formation seems to be a conserved hallmark of a broad class of transcription terminators.
References
Sanz, L. A. et al. Prevalent, dynamic, and conserved R-loop structures associate with specific epigenomic signatures in mammals. Mol. Cell http://dx.doi.org/10.1016/j.molcel.2016.05.032 (2016)
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Koch, L. Programmed R-loop formation. Nat Rev Genet 17, 438 (2016). https://doi.org/10.1038/nrg.2016.92
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DOI: https://doi.org/10.1038/nrg.2016.92