title: Genome-wide mapping of human DNA-replication origins: levels of transcription at ORC1 sites regulate origin selection and replication timing.
abstract: We report the genome-wide mapping of ORC1 binding sites in mammals, by chromatin immunoprecipitation and parallel sequencing (ChIP-seq). ORC1 binding sites in HeLa cells were validated as active DNA replication origins (ORIs) using Repli-seq, a method that allows identification of ORI-containing regions by parallel sequencing of temporally ordered replicating DNA. ORC1 sites were universally associated with transcription start sites (TSSs) of coding or noncoding RNAs (ncRNAs). Transcription levels at the ORC1 sites directly correlated with replication timing, suggesting the existence of two classes of ORIs: those associated with moderate/high transcription levels (≥1 RNA copy/cell), firing in early S and mapping to the TSSs of coding RNAs; and those associated with low transcription levels (<1 RNA copy/cell), firing throughout the entire S and mapping to TSSs of ncRNAs. These findings are compatible with a scenario whereby TSS expression levels influence the efficiency of ORC1 recruitment at G(1) and the probability of firing during S.
authors.affiliation: Department of Experimental Oncology, European Institute of Oncology, 20141 Milan, Italy. gaetano.dellino@ieo.eu
authors.forename: Gaetano Ivan
authors.initials: GI
authors.lastname: Dellino
authors.forename: Davide
authors.initials: D
authors.lastname: Cittaro
authors.forename: Rossana
authors.initials: R
authors.lastname: Piccioni
authors.forename: Lucilla
authors.initials: L
authors.lastname: Luzi
authors.forename: Stefania
authors.initials: S
authors.lastname: Banfi
authors.forename: Simona
authors.initials: S
authors.lastname: Segalla
authors.forename: Matteo
authors.initials: M
authors.lastname: Cesaroni
authors.forename: Ramiro
authors.initials: R
authors.lastname: Mendoza-Maldonado
authors.forename: Mauro
authors.initials: M
authors.lastname: Giacca
authors.forename: Pier Giuseppe
authors.initials: PG
authors.lastname: Pelicci
mesh_terms: D015496:CD4-Positive T-Lymphocytes; D047369:Chromatin Immunoprecipitation; D042522:DNA Replication Timing; D016193:G1 Phase / Q000235:genetics; D005786:Gene Expression Regulation; D015894:Genome, Human; D006367:HeLa Cells; D006801:Humans; D051738:Origin Recognition Complex / Q000235:genetics / Q000378:metabolism*; D020161:Physical Chromosome Mapping; D022661:RNA, Untranslated / Q000378:metabolism; D018741:Replication Origin / Q000235:genetics*; D016196:S Phase / Q000235:genetics; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: C497223:ORC1 protein, human; D051738:Origin Recognition Complex; D022661:RNA, Untranslated