title: Genome-wide chromatin footprinting reveals changes in replication origin architecture induced by pre-RC assembly.
abstract: Start sites of DNA replication are marked by the origin recognition complex (ORC), which coordinates Mcm2-7 helicase loading to form the prereplicative complex (pre-RC). Although pre-RC assembly is well characterized in vitro, the process is poorly understood within the local chromatin environment surrounding replication origins. To reveal how the chromatin architecture modulates origin selection and activation, we "footprinted" nucleosomes, transcription factors, and replication proteins at multiple points during the Saccharomyces cerevisiae cell cycle. Our nucleotide-resolution protein occupancy profiles resolved a precise ORC-dependent footprint at 269 origins in G2. A separate class of inefficient origins exhibited protein occupancy only in G1, suggesting that stable ORC chromatin association in G2 is a determinant of origin efficiency. G1 nucleosome remodeling concomitant with pre-RC assembly expanded the origin nucleosome-free region and enhanced activation efficiency. Finally, the local chromatin environment restricts the loading of the Mcm2-7 double hexamer either upstream of or downstream from the ARS consensus sequence (ACS).
authors.affiliation: Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA; Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA;
authors.forename: Jason A
authors.identifier: http://orcid.org/0000-0003-2945-6282
authors.initials: JA
authors.lastname: Belsky
authors.affiliation: Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA; david.macalpine@duke.edu.
authors.forename: Heather K
authors.initials: HK
authors.lastname: MacAlpine
authors.affiliation: Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA;
authors.forename: Yoav
authors.initials: Y
authors.lastname: Lubelsky
authors.affiliation: Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA; Department of Computer Science, Duke University, Durham, North Carolina 27708, USA.
authors.forename: Alexander J
authors.initials: AJ
authors.lastname: Hartemink
authors.affiliation: Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA; Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA; david.macalpine@duke.edu.
authors.forename: David M
authors.initials: DM
authors.lastname: MacAlpine
mesh_terms: D002453:Cell Cycle / Q000235:genetics*; D002843:Chromatin / Q000235:genetics*; D016193:G1 Phase / Q000235:genetics; D016195:G2 Phase / Q000235:genetics; D055106:Genome-Wide Association Study; D064110:Minichromosome Maintenance Proteins / Q000378:metabolism; D009707:Nucleosomes / Q000378:metabolism; D051738:Origin Recognition Complex / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism
chemical_list: D002843:Chromatin; D009707:Nucleosomes; D051738:Origin Recognition Complex; D029701:Saccharomyces cerevisiae Proteins; D064110:Minichromosome Maintenance Proteins
keywords: DNA replication; chromatin; nucleosome; origin recognition complex (ORC)