dc.contributor.author | Cao, Bo | |
dc.contributor.author | Chen, Chao | |
dc.contributor.author | DeMott, Michael S. | |
dc.contributor.author | Cheng, Qiuxiang | |
dc.contributor.author | Clark, Tyson A. | |
dc.contributor.author | Xiong, Xiaolin | |
dc.contributor.author | Zheng, Xiaoqing | |
dc.contributor.author | Levine, Stuart S. | |
dc.contributor.author | Yuan, George | |
dc.contributor.author | Boitano, Matthew | |
dc.contributor.author | Luong, Khai | |
dc.contributor.author | Song, Yi | |
dc.contributor.author | Zhou, Xiufen | |
dc.contributor.author | Deng, Zixin | |
dc.contributor.author | Turner, Stephen W. | |
dc.contributor.author | Korlach, Jonas | |
dc.contributor.author | You, Delin | |
dc.contributor.author | Wang, Lianrong | |
dc.contributor.author | Chen, Shi | |
dc.contributor.author | Butty, Vincent L G | |
dc.contributor.author | Dedon, Peter C | |
dc.date.accessioned | 2015-10-15T13:19:44Z | |
dc.date.available | 2015-10-15T13:19:44Z | |
dc.date.issued | 2014-06 | |
dc.date.submitted | 2013-12 | |
dc.identifier.issn | 2041-1723 | |
dc.identifier.uri | http://hdl.handle.net/1721.1/99339 | |
dc.description.abstract | Bacterial phosphorothioate (PT) DNA modifications are incorporated by Dnd proteins A-E and often function with DndF-H as a restriction-modification (R-M) system, as in Escherichia coli B7A. However, bacteria such as Vibrio cyclitrophicus FF75 lack dndF-H, which points to other PT functions. Here we report two novel, orthogonal technologies to map PTs across the genomes of B7A and FF75 with >90% agreement: single molecule, real-time sequencing and deep sequencing of iodine-induced cleavage at PT (ICDS). In B7A, we detect PT on both strands of G[subscript ps]AAC/G[subscript ps]TTC motifs, but with only 12% of 40,701 possible sites modified. In contrast, PT in FF75 occurs as a single-strand modification at C[subscript ps]CA, again with only 14% of 160,541 sites modified. Single-molecule analysis indicates that modification could be partial at any particular genomic site even with active restriction by DndF-H, with direct interaction of modification proteins with GAAC/GTTC sites demonstrated with oligonucleotides. These results point to highly unusual target selection by PT-modification proteins and rule out known R-M mechanisms. | en_US |
dc.description.sponsorship | National Natural Science Foundation (China) | en_US |
dc.description.sponsorship | Ministry of Science and Technology of the People's Republic of China (973 and 863 Programs) | en_US |
dc.description.sponsorship | Shanghai Municipal Council of Science and Technology. Shanghai Pujiang Program | en_US |
dc.description.sponsorship | National Science Foundation (U.S.) (CHE-1019990) | en_US |
dc.description.sponsorship | National Institute of Environmental Health Sciences (ES002109) | en_US |
dc.description.sponsorship | Singapore. National Research Foundation (Singapore-MIT Alliance for Research and Technology) | en_US |
dc.language.iso | en_US | |
dc.publisher | Nature Publishing Group | en_US |
dc.relation.isversionof | http://dx.doi.org/10.1038/ncomms4951 | en_US |
dc.rights | Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. | en_US |
dc.source | PMC | en_US |
dc.title | Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences | en_US |
dc.type | Article | en_US |
dc.identifier.citation | Cao, Bo, Chao Chen, Michael S. DeMott, Qiuxiang Cheng, Tyson A. Clark, Xiaolin Xiong, Xiaoqing Zheng, et al. “Genomic Mapping of Phosphorothioates Reveals Partial Modification of Short Consensus Sequences.” Nat Comms 5 (June 5, 2014). | en_US |
dc.contributor.department | Massachusetts Institute of Technology. Center for Environmental Health Sciences | en_US |
dc.contributor.department | Massachusetts Institute of Technology. Department of Biological Engineering | en_US |
dc.contributor.department | Massachusetts Institute of Technology. Department of Biology | en_US |
dc.contributor.mitauthor | Cao, Bo | en_US |
dc.contributor.mitauthor | DeMott, Michael S. | en_US |
dc.contributor.mitauthor | Butty, Vincent | en_US |
dc.contributor.mitauthor | Levine, Stuart S. | en_US |
dc.contributor.mitauthor | Dedon, Peter C. | en_US |
dc.relation.journal | Nature Communications | en_US |
dc.eprint.version | Author's final manuscript | en_US |
dc.type.uri | http://purl.org/eprint/type/JournalArticle | en_US |
eprint.status | http://purl.org/eprint/status/PeerReviewed | en_US |
dspace.orderedauthors | Cao, Bo; Chen, Chao; DeMott, Michael S.; Cheng, Qiuxiang; Clark, Tyson A.; Xiong, Xiaolin; Zheng, Xiaoqing; Butty, Vincent; Levine, Stuart S.; Yuan, George; Boitano, Matthew; Luong, Khai; Song, Yi; Zhou, Xiufen; Deng, Zixin; Turner, Stephen W.; Korlach, Jonas; You, Delin; Wang, Lianrong; Chen, Shi; Dedon, Peter C. | en_US |
dc.identifier.orcid | https://orcid.org/0000-0003-1615-1578 | |
dc.identifier.orcid | https://orcid.org/0000-0003-0011-3067 | |
mit.license | PUBLISHER_POLICY | en_US |
mit.metadata.status | Complete | |