R loops regulate promoter-proximal chromatin architecture and cellular differentiation

New data show that R loops differentially modulate binding of chromatin remodelers Tip60–p400 and PRC2 at coding and noncoding gene promoters of mouse ESCs and thereby control transcription and cellular differentiation. Numerous chromatin-remodeling factors are regulated by interactions with RNA, although the contexts and functions of RNA binding are poorly understood. Here we show that R loops, RNA-DNA hybrids consisting of nascent transcripts hybridized to template DNA, modulate the binding of two key chromatin-regulatory complexes, Tip60–p400 and polycomb repressive complex 2 (PRC2) in mouse embryonic stem cells (ESCs). Like PRC2, the Tip60–p400 histone acetyltransferase complex binds to nascent transcripts; however, transcription promotes chromatin binding of Tip60–p400 but not PRC2. Interestingly, we observed higher Tip60–p400 and lower PRC2 levels at genes marked by promoter-proximal R loops. Furthermore, disruption of R loops broadly decreased Tip60–p400 occupancy and increased PRC2 occupancy genome wide. In agreement with these alterations, ESCs partially depleted of R loops exhibited impaired differentiation. These results show that R loops act both positively and negatively in modulating the recruitment of key pluripotency regulators.