title: A dynamic switch in the replication timing of key regulator genes in embryonic stem cells upon neural induction.
abstract: Mammalian embryonic stem (ES) cells can either self-renew or generate progenitor cells that have a more restricted developmental potential. This provides an important model system to ask how pluripotency, cell commitment and differentiation are regulated at the level of chromatin-based changes that distinguish stem cells from their differentiated progeny. Here we show that the differentiation of ES cells to neural progenitors results in dynamic changes in the epigenetic status of multiple genes that encode transcription factors critical for early embryonic development or lineage specification. In particular, we demonstrate that DNA replication at a subset of neural-associated genes including Pax3, Pax6, Irx3, Nkx2.9 and Mash1 is advanced upon neural induction, consistent with increased locus accessibility. Conversely, many ES-associated genes including Oct4, Nanog, Utf1, Foxd3, Cripto and Rex1 that replicate early in ES cells switch their replication timing to later in S-phase in response to differentiation. Detailed analysis of the Rex1 locus reveals that delayed replication extends to a 2.8 Mb region surrounding the gene and is associated with substantial reductions in the level of histone H3K9 and H4 acetylation at the promoter. These results show that loss of pluripotency (and lineage choice) is associated with extensive and predictable changes in the replication timing of key regulator genes.
authors.affiliation: Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, London, UK.
authors.forename: Pascale
authors.initials: P
authors.lastname: Perry
authors.forename: Stephan
authors.initials: S
authors.lastname: Sauer
authors.forename: Nathalie
authors.initials: N
authors.lastname: Billon
authors.forename: William D
authors.initials: WD
authors.lastname: Richardson
authors.forename: Mikhail
authors.initials: M
authors.lastname: Spivakov
authors.forename: Gary
authors.initials: G
authors.lastname: Warnes
authors.forename: Frederick J
authors.initials: FJ
authors.lastname: Livesey
authors.forename: Matthias
authors.initials: M
authors.lastname: Merkenschlager
authors.forename: Amanda G
authors.initials: AG
authors.lastname: Fisher
authors.forename: Véronique
authors.initials: V
authors.lastname: Azuara
mesh_terms: D000818:Animals; D001482:Base Composition; D002454:Cell Differentiation / Q000187:drug effects; D002460:Cell Line; D002478:Cells, Cultured; D042522:DNA Replication Timing; D005434:Flow Cytometry; D018507:Gene Expression Regulation, Developmental; D005809:Genes, Regulator / Q000235:genetics*; D016678:Genome; D006657:Histones / Q000378:metabolism; D051379:Mice; D008810:Mice, Inbred C57BL; D009420:Nervous System / Q000196:embryology*; D009474:Neurons / Q000166:cytology* / Q000187:drug effects / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D013234:Stem Cells / Q000166:cytology* / Q000187:drug effects / Q000378:metabolism*; D014212:Tretinoin / Q000494:pharmacology
chemical_list: D006657:Histones; D012333:RNA, Messenger; D014212:Tretinoin