title: lncRNA maturation to initiate heterochromatin formation in the nucleolus is required for exit from pluripotency in ESCs.
abstract: The open chromatin of embryonic stem cells (ESCs) condenses into repressive heterochromatin as cells exit the pluripotent state. How the 3D genome organization is orchestrated and implicated in pluripotency and lineage specification is not understood. Here, we find that maturation of the long noncoding RNA (lncRNA) pRNA is required for establishment of heterochromatin at ribosomal RNA genes, the genetic component of nucleoli, and this process is inactivated in pluripotent ESCs. By using mature pRNA to tether heterochromatin at nucleoli of ESCs, we find that localized heterochromatin condensation of ribosomal RNA genes initiates establishment of highly condensed chromatin structures outside of the nucleolus. Moreover, we reveal that formation of such highly condensed, transcriptionally repressed heterochromatin promotes transcriptional activation of differentiation genes and loss of pluripotency. Our findings unravel the nucleolus as an active regulator of chromatin plasticity and pluripotency and challenge current views on heterochromatin regulation and function in ESCs.
authors.affiliation: Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, 8057 Zurich, Switzerland; Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Nataša
authors.initials: N
authors.lastname: Savić
authors.affiliation: Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Dominik
authors.initials: D
authors.lastname: Bär
authors.affiliation: Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, 8057 Zurich, Switzerland; Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Sergio
authors.initials: S
authors.lastname: Leone
authors.affiliation: Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, 8057 Zurich, Switzerland; Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Sandra C
authors.initials: SC
authors.lastname: Frommel
authors.affiliation: Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland; Institute of Laboratory Animal Science, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Fabienne A
authors.initials: FA
authors.lastname: Weber
authors.affiliation: Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, 8057 Zurich, Switzerland; Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Eva
authors.initials: E
authors.lastname: Vollenweider
authors.affiliation: Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Elena
authors.initials: E
authors.lastname: Ferrari
authors.affiliation: Center for Microscopy and Image Analysis, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Urs
authors.initials: U
authors.lastname: Ziegler
authors.affiliation: Center for Microscopy and Image Analysis, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Andres
authors.initials: A
authors.lastname: Kaech
authors.affiliation: Department of Oncology, University Hospital Zurich, 8952 Schlieren, Switzerland.
authors.forename: Olga
authors.initials: O
authors.lastname: Shakhova
authors.affiliation: Institute of Laboratory Animal Science, University of Zurich, 8057 Zurich, Switzerland; Center for Applied Biotechnology and Molecular Medicine, University of Zurich, 8057 Zurich, Switzerland; Division of Trauma Surgery, Center for Clinical Research, University Hospital Zurich, 8091 Zurich, Switzerland.
authors.forename: Paolo
authors.initials: P
authors.lastname: Cinelli
authors.affiliation: Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, 8057 Zurich, Switzerland; Center for Applied Biotechnology and Molecular Medicine, University of Zurich, 8057 Zurich, Switzerland. Electronic address: raffaella.santoro@vetbio.uzh.ch.
authors.forename: Raffaella
authors.initials: R
authors.lastname: Santoro
mesh_terms: D000818:Animals; D002454:Cell Differentiation; D019070:Cell Lineage; D002466:Cell Nucleolus / Q000378:metabolism*; D042002:Chromatin Assembly and Disassembly; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics / Q000378:metabolism*; D053595:Embryonic Stem Cells / Q000502:physiology*; D044127:Epigenesis, Genetic; D020459:Genes, rRNA / Q000235:genetics; D006570:Heterochromatin / Q000378:metabolism; D006801:Humans; D051379:Mice; D041681:NIH 3T3 Cells; D009474:Neurons / Q000502:physiology*; D039904:Pluripotent Stem Cells / Q000502:physiology*; D021381:Protein Transport; D012323:RNA Processing, Post-Transcriptional; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism*; D000092468:Bromodomain Containing Proteins
chemical_list: D002868:Chromosomal Proteins, Non-Histone; D006570:Heterochromatin; D062085:RNA, Long Noncoding; C499051:Baz2a protein, mouse; D000092468:Bromodomain Containing Proteins