title: R loops regulate promoter-proximal chromatin architecture and cellular differentiation.
abstract: 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.
authors.affiliation: Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.|Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
authors.forename: Poshen B
authors.initials: PB
authors.lastname: Chen
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
authors.forename: Hsiuyi V
authors.initials: HV
authors.lastname: Chen
authors.affiliation: Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.|Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
authors.forename: Diwash
authors.initials: D
authors.lastname: Acharya
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
authors.forename: Oliver J
authors.initials: OJ
authors.lastname: Rando
authors.affiliation: Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.|Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
authors.forename: Thomas G
authors.initials: TG
authors.lastname: Fazzio
mesh_terms: D000818:Animals; D002454:Cell Differentiation; D002843:Chromatin / Q000737:chemistry* / Q000378:metabolism*; D004247:DNA / Q000378:metabolism*; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism; D051548:Histone Acetyltransferases / Q000032:analysis; D053496:Inositol 1,4,5-Trisphosphate Receptors / Q000032:analysis; D000074443:Lysine Acetyltransferase 5; D051379:Mice; D008969:Molecular Sequence Data; D063151:Polycomb Repressive Complex 2 / Q000032:analysis; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D015534:Trans-Activators / Q000032:analysis
chemical_list: D002843:Chromatin; D053496:Inositol 1,4,5-Trisphosphate Receptors; C025389:Itpr1 protein, mouse; D012333:RNA, Messenger; D015534:Trans-Activators; D004247:DNA; D063151:Polycomb Repressive Complex 2; D051548:Histone Acetyltransferases; C523065:Kat5 protein, mouse; D000074443:Lysine Acetyltransferase 5