title: Genome-wide identification and characterization of replication origins by deep sequencing.
abstract: BACKGROUND
  DNA replication initiates at distinct origins in eukaryotic genomes, but the genomic features that define these sites are not well understood.
  
  
  RESULTS
  We have taken a combined experimental and bioinformatic approach to identify and characterize origins of replication in three distantly related fission yeasts: Schizosaccharomyces pombe, Schizosaccharomyces octosporus and Schizosaccharomyces japonicus. Using single-molecule deep sequencing to construct amplification-free high-resolution replication profiles, we located origins and identified sequence motifs that predict origin function. We then mapped nucleosome occupancy by deep sequencing of mononucleosomal DNA from the corresponding species, finding that origins tend to occupy nucleosome-depleted regions.
  
  
  CONCLUSIONS
  The sequences that specify origins are evolutionarily plastic, with low complexity nucleosome-excluding sequences functioning in S. pombe and S. octosporus, and binding sites for trans-acting nucleosome-excluding proteins functioning in S. japonicus. Furthermore, chromosome-scale variation in replication timing is conserved independently of origin location and via a mechanism distinct from known heterochromatic effects on origin function. These results are consistent with a model in which origins are simply the nucleosome-depleted regions of the genome with the highest affinity for the origin recognition complex. This approach provides a general strategy for understanding the mechanisms that define DNA replication origins in eukaryotes.
authors.affiliation: Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors.forename: Jia
authors.initials: J
authors.lastname: Xu
authors.forename: Yoshimi
authors.initials: Y
authors.lastname: Yanagisawa
authors.forename: Alexander M
authors.initials: AM
authors.lastname: Tsankov
authors.forename: Christopher
authors.initials: C
authors.lastname: Hart
authors.forename: Keita
authors.initials: K
authors.lastname: Aoki
authors.forename: Naveen
authors.initials: N
authors.lastname: Kommajosyula
authors.forename: Kathleen E
authors.initials: KE
authors.lastname: Steinmann
authors.forename: James
authors.initials: J
authors.lastname: Bochicchio
authors.forename: Carsten
authors.initials: C
authors.lastname: Russ
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
authors.forename: Oliver J
authors.initials: OJ
authors.lastname: Rando
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.forename: Hironori
authors.initials: H
authors.lastname: Niki
authors.forename: Patrice
authors.initials: P
authors.lastname: Milos
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
authors.forename: Nicholas
authors.initials: N
authors.lastname: Rhind
mesh_terms: D001665:Binding Sites; D002874:Chromosome Mapping / Q000379:methods; D015825:Chromosomes, Fungal / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D042522:DNA Replication Timing; D004271:DNA, Fungal / Q000235:genetics; D019143:Evolution, Molecular; D018740:Genetic Heterogeneity; D016681:Genome, Fungal; D006570:Heterochromatin / Q000235:genetics / Q000378:metabolism; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism; D059372:Nucleotide Motifs; D018741:Replication Origin; D012568:Schizosaccharomyces / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity
chemical_list: D004271:DNA, Fungal; D006570:Heterochromatin; D009707:Nucleosomes