title: High-resolution analysis of DNA synthesis start sites and nucleosome architecture at efficient mammalian replication origins.
abstract: DNA replication origins are poorly characterized genomic regions that are essential to recruit and position the initiation complex to start DNA synthesis. Despite the lack of specific replicator sequences, initiation of replication does not occur at random sites in the mammalian genome. This has lead to the view that DNA accessibility could be a major determinant of mammalian origins. Here, we performed a high-resolution analysis of nucleosome architecture and initiation sites along several origins of different genomic location and firing efficiencies. We found that mammalian origins are highly variable in nucleosome conformation and initiation patterns. Strikingly, initiation sites at efficient CpG island-associated origins always occur at positions of high-nucleosome occupancy. Origin recognition complex (ORC) binding sites, however, occur at adjacent but distinct positions marked by labile nucleosomes. We also found that initiation profiles mirror nucleosome architecture, both at endogenous origins and at a transgene in a heterologous system. Our studies provide a unique insight into the relationship between chromatin structure and initiation sites in the mammalian genome that has direct implications for how the replication programme can be accommodated to diverse epigenetic scenarios.
authors.affiliation: 1Functional Organization of the Genome Group, Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Madrid, Spain.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Lombraña
authors.forename: Ricardo
authors.initials: R
authors.lastname: Almeida
authors.forename: Isabel
authors.initials: I
authors.lastname: Revuelta
authors.forename: Sofia
authors.initials: S
authors.lastname: Madeira
authors.forename: Gonzalo
authors.initials: G
authors.lastname: Herranz
authors.forename: Néstor
authors.initials: N
authors.lastname: Saiz
authors.forename: Ugo
authors.initials: U
authors.lastname: Bastolla
authors.forename: María
authors.initials: M
authors.lastname: Gómez
mesh_terms: D000818:Animals; D002460:Cell Line; D002843:Chromatin; D018899:CpG Islands; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D006367:HeLa Cells; D006801:Humans; D051379:Mice; D041681:NIH 3T3 Cells; D009707:Nucleosomes / Q000378:metabolism*; D051738:Origin Recognition Complex / Q000378:metabolism*; D024363:Transcription Initiation Site
chemical_list: D002843:Chromatin; D009707:Nucleosomes; D051738:Origin Recognition Complex; D004247:DNA