OriDB, the DNA replication origin database updated and extended

Article English OPEN
Siow, Cheuk C. ; Nieduszynska, Sian R. ; Müller, Carolin A. ; Nieduszynski, Conrad A. (2012)
  • Publisher: Oxford Journals
  • Journal: Nucleic Acids Research, volume 40, issue Database issue, pages D682-D686 (issn: 0305-1048, eissn: 1362-4962)
  • Related identifiers: pmc: PMC3245157, doi: 10.1093/nar/gkr1091
  • Subject: Articles
    mesheuropmc: natural sciences

OriDB (http://www.oridb.org/) is a database containing collated genome-wide mapping studies of confirmed and predicted replication origin sites. The original database collated and curated Saccharomyces cerevisiae origin mapping studies. Here, we report that the OriDB database and web site have been revamped to improve user accessibility to curated data sets, to greatly increase the number of curated origin mapping studies, and to include the collation of replication origin sites in the fission yeast Schizosaccharomyces pombe. The revised database structure underlies these improvements and will facilitate further expansion in the future. The updated OriDB for S. cerevisiae is available at http://cerevisiae.oridb.org/ and for S. pombe at http://pombe.oridb.org/.
  • References (36)
    36 references, page 1 of 4

    1. Maundrell,K., Hutchison,A. and Shall,S. (1988) Sequence analysis of ARS elements in fission yeast. EMBO J., 7, 2203-2209.

    2. Stinchcomb,D.T., Struhl,K. and Davis,R.W. (1979) Isolation and characterisation of a yeast chromosomal replicator. Nature, 282, 39-43.

    3. Zhu,J., Brun,C., Kurooka,H., Yanagida,M. and Huberman,J.A. (1992) Identification and characterization of a complex chromosomal replication origin in Schizosaccharomyces pombe. Chromosoma, 102, S7-S16.

    4. Huberman,J.A., Zhu,J.G., Davis,L.R. and Newlon,C.S. (1988) Close association of a DNA replication origin and an ARS element on chromosome III of the yeast, Saccharomyces cerevisiae. Nucleic Acids Res., 16, 6373-6384.

    5. Nieduszynski,C.A., Knox,Y. and Donaldson,A.D. (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev., 20, 1874-1879.

    6. Clyne,R.K. and Kelly,T.J. (1995) Genetic analysis of an ARS element from the fission yeast Schizosaccharomyces pombe. EMBO J., 14, 6348-6357.

    7. Snyder,M., Sapolsky,R.J. and Davis,R.W. (1988) Transcription interferes with elements important for chromosome maintenance in Saccharomyces cerevisiae. Mol. Cell Biol., 8, 2184-2194.

    8. Nieduszynski,C.A., Blow,J.J. and Donaldson,A.D. (2005) The requirement of yeast replication origins for pre-replication complex proteins is modulated by transcription. Nucleic Acids Res., 33, 2410-2420.

    9. Eaton,M.L., Galani,K., Kang,S., Bell,S.P. and MacAlpine,D.M. (2010) Conserved nucleosome positioning defines replication origins. Genes Dev., 24, 748-753.

    10. Muller,P., Park,S., Shor,E., Huebert,D.J., Warren,C.L., Ansari,A.Z., Weinreich,M., Eaton,M.L., MacAlpine,D.M. and Fox,C.A. (2010) The conserved bromo-adjacent homology domain of yeast Orc1 functions in the selection of DNA replication origins within chromatin. Genes Dev., 24, 1418-1433.

  • Related Research Results (1)
  • Metrics
    No metrics available
Share - Bookmark