Genome-wide identification and characterization of replication origins by deep sequencing
Authors
Xu, JiaYanagisawa, Yoshimi
Tsankov, Alexander M.
Hart, Christopher
Aoki, Keita
Kommajosyula, Naveen
Steinmann, Kathleen E.
Bochicchio, James
Russ, Carsten
Regev, Aviv
Rando, Oliver J.
Nusbaum, Chad
Niki, Hironori
Milos, Patrice
Weng, Zhiping
Rhind, Nicholas R.
UMass Chan Affiliations
Program in Bioinformatics and Integrative BiologyDepartment of Biochemistry and Molecular Pharmacology
Document Type
Journal ArticlePublication Date
2012-04-24
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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.Source
Genome Biol. 2012 Apr 24;13(4):R27. Link to article on publisher's site 2012 Xu et al.; licensee BioMed Central Ltd.DOI
10.1186/gb-2012-13-4-r27Permanent Link to this Item
http://hdl.handle.net/20.500.14038/39528PubMed ID
22531001Related Resources
Link to Article in PubMedRights
© 2012 Xu et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.ae974a485f413a2113503eed53cd6c53
10.1186/gb-2012-13-4-r27