title: GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris.
abstract: The well-studied DNA replication origins of the model budding and fission yeasts are A/T-rich elements. However, unlike their yeast counterparts, both plant and metazoan origins are G/C-rich and are associated with transcription start sites. Here we show that an industrially important methylotrophic budding yeast, Pichia pastoris, simultaneously employs at least two types of replication origins--a G/C-rich type associated with transcription start sites and an A/T-rich type more reminiscent of typical budding and fission yeast origins. We used a suite of massively parallel sequencing tools to map and dissect P. pastoris origins comprehensively, to measure their replication dynamics, and to assay the global positioning of nucleosomes across the genome. Our results suggest that some functional overlap exists between promoter sequences and G/C-rich replication origins in P. pastoris and imply an evolutionary bifurcation of the modes of replication initiation.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Ivan
authors.initials: I
authors.lastname: Liachko
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Rachel A
authors.initials: RA
authors.lastname: Youngblood
authors.affiliation: Department of Molecular Genetics, University of Toronto, Toronto, Canada; Department of Pharmaceutical Sciences, University of Toronto, Toronto, Canada.
authors.forename: Kyle
authors.initials: K
authors.lastname: Tsui
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Kerry L
authors.initials: KL
authors.lastname: Bubb
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Christine
authors.initials: C
authors.lastname: Queitsch
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: M K
authors.initials: MK
authors.lastname: Raghuraman
authors.affiliation: Department of Molecular Genetics, University of Toronto, Toronto, Canada; Donnelly Centre, University of Toronto, Toronto, Canada.
authors.forename: Corey
authors.initials: C
authors.lastname: Nislow
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Bonita J
authors.initials: BJ
authors.lastname: Brewer
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Maitreya J
authors.initials: MJ
authors.lastname: Dunham
mesh_terms: D002843:Chromatin / Q000235:genetics; D004247:DNA / Q000235:genetics*; D004261:DNA Replication / Q000235:genetics*; D020862:GC Rich Sequence / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D009707:Nucleosomes / Q000235:genetics; D010843:Pichia / Q000235:genetics*; D018741:Replication Origin / Q000235:genetics*; D024363:Transcription Initiation Site
chemical_list: D002843:Chromatin; D009707:Nucleosomes; D004247:DNA