title: DNA sequence templates adjacent nucleosome and ORC sites at gene amplification origins in Drosophila.
abstract: Eukaryotic origins of DNA replication are bound by the origin recognition complex (ORC), which scaffolds assembly of a pre-replicative complex (pre-RC) that is then activated to initiate replication. Both pre-RC assembly and activation are strongly influenced by developmental changes to the epigenome, but molecular mechanisms remain incompletely defined. We have been examining the activation of origins responsible for developmental gene amplification in Drosophila. At a specific time in oogenesis, somatic follicle cells transition from genomic replication to a locus-specific replication from six amplicon origins. Previous evidence indicated that these amplicon origins are activated by nucleosome acetylation, but how this affects origin chromatin is unknown. Here, we examine nucleosome position in follicle cells using micrococcal nuclease digestion with Ilumina sequencing. The results indicate that ORC binding sites and other essential origin sequences are nucleosome-depleted regions (NDRs). Nucleosome position at the amplicons was highly similar among developmental stages during which ORC is or is not bound, indicating that being an NDR is not sufficient to specify ORC binding. Importantly, the data suggest that nucleosomes and ORC have opposite preferences for DNA sequence and structure. We propose that nucleosome hyperacetylation promotes pre-RC assembly onto adjacent DNA sequences that are disfavored by nucleosomes but favored by ORC.
authors.affiliation: Department of Biology, Indiana University, Bloomington, IN 47405, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Liu
authors.affiliation: School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA.
authors.forename: Kurt
authors.initials: K
authors.lastname: Zimmer
authors.affiliation: Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA.
authors.forename: Douglas B
authors.initials: DB
authors.lastname: Rusch
authors.affiliation: Department of Biology, Indiana University, Bloomington, IN 47405, USA.
authors.forename: Neha
authors.initials: N
authors.lastname: Paranjape
authors.affiliation: School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA.
authors.forename: Ram
authors.initials: R
authors.lastname: Podicheti
authors.affiliation: School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA.
authors.forename: Haixu
authors.initials: H
authors.lastname: Tang
authors.affiliation: Department of Biology, Indiana University, Bloomington, IN 47405, USA bcalvi@indiana.edu.
authors.forename: Brian R
authors.initials: BR
authors.lastname: Calvi
mesh_terms: D000818:Animals; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D004330:Drosophila / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D005260:Female; D005784:Gene Amplification; D009707:Nucleosomes; D051738:Origin Recognition Complex / Q000378:metabolism*; D006080:Ovarian Follicle / Q000378:metabolism; D018741:Replication Origin
chemical_list: D009707:Nucleosomes; D051738:Origin Recognition Complex; D004247:DNA