title: Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae.
abstract: BACKGROUND
  Eukaryotic replication origins exhibit different initiation efficiencies and activation times within S-phase. Although local chromatin structure and function influences origin activity, the exact mechanisms remain poorly understood. A key to understanding the exact features of chromatin that impinge on replication origin function is to define the precise locations of the DNA sequences that control origin function. In S. cerevisiae, Autonomously Replicating Sequences (ARSs) contain a consensus sequence (ACS) that binds the Origin Recognition Complex (ORC) and is essential for origin function. However, an ACS is not sufficient for origin function and the majority of ACS matches do not function as ORC binding sites, complicating the specific identification of these sites.
  
  
  RESULTS
  To identify essential origin sequences genome-wide, we utilized a tiled oligonucleotide array (NimbleGen) to map the ORC and Mcm2p binding sites at high resolution. These binding sites define a set of potential Autonomously Replicating Sequences (ARSs), which we term nimARSs. The nimARS set comprises 529 ORC and/or Mcm2p binding sites, which includes 95% of known ARSs, and experimental verification demonstrates that 94% are functional. The resolution of the analysis facilitated identification of potential ACSs (nimACSs) within 370 nimARSs. Cross-validation shows that the nimACS predictions include 58% of known ACSs, and experimental verification indicates that 82% are essential for ARS activity.
  
  
  CONCLUSIONS
  These findings provide the most comprehensive, accurate, and detailed mapping of ORC binding sites to date, adding to the emerging picture of the chromatin organization of the budding yeast genome.
authors.affiliation: Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA, USA. weihongx@usc.edu <weihongx@usc.edu>
authors.forename: Weihong
authors.initials: W
authors.lastname: Xu
authors.forename: Jennifer G
authors.initials: JG
authors.lastname: Aparicio
authors.forename: Oscar M
authors.initials: OM
authors.lastname: Aparicio
authors.forename: Simon
authors.initials: S
authors.lastname: Tavaré
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods; D015825:Chromosomes, Fungal / Q000235:genetics; D016384:Consensus Sequence / Q000235:genetics; D004261:DNA Replication / Q000235:genetics*; D004271:DNA, Fungal / Q000235:genetics; D016681:Genome, Fungal / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D051738:Origin Recognition Complex / Q000235:genetics* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*
chemical_list: D004271:DNA, Fungal; D051738:Origin Recognition Complex; D029701:Saccharomyces cerevisiae Proteins