A Comprehensive Map of Insulator Elements for the Drosophila Genome
Insulators are DNA sequences that control the interactions among genomic regulatory elements and act as chromatin boundaries. A thorough understanding of their location and function is necessary to address the complexities of metazoan gene regulation. We studied by ChIP–chip the genome-wide binding...
| Main Authors: | , , , , , , , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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Public Library of Science
2010
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| Online Access: | http://hdl.handle.net/1721.1/55381 |
| _version_ | 1811086616223023104 |
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| author | White, Kevin P. Henikoff, Steven Stein, Lincoln White, Robert A. H. Russell, Steven Ahmad, Kami Feng, Xin Henikoff, Jorja G. Morrison, Carolyn A. Shah, Parantu K. Brown, Christopher D. Negre, Nicolas Kheradpour, Pouya Kellis, Manolis |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory White, Kevin P. Henikoff, Steven Stein, Lincoln White, Robert A. H. Russell, Steven Ahmad, Kami Feng, Xin Henikoff, Jorja G. Morrison, Carolyn A. Shah, Parantu K. Brown, Christopher D. Negre, Nicolas Kheradpour, Pouya Kellis, Manolis |
| author_sort | White, Kevin P. |
| collection | MIT |
| description | Insulators are DNA sequences that control the interactions among genomic regulatory elements and act as chromatin boundaries. A thorough understanding of their location and function is necessary to address the complexities of metazoan gene regulation. We studied by ChIP–chip the genome-wide binding sites of 6 insulator-associated proteins—dCTCF, CP190, BEAF-32, Su(Hw), Mod(mdg4), and GAF—to obtain the first comprehensive map of insulator elements in Drosophila embryos. We identify over 14,000 putative insulators, including all classically defined insulators. We find two major classes of insulators defined by dCTCF/CP190/BEAF-32 and Su(Hw), respectively. Distributional analyses of insulators revealed that particular sub-classes of insulator elements are excluded between cis-regulatory elements and their target promoters; divide differentially expressed, alternative, and divergent promoters; act as chromatin boundaries; are associated with chromosomal breakpoints among species; and are embedded within active chromatin domains. Together, these results provide a map demarcating the boundaries of gene regulatory units and a framework for understanding insulator function during the development and evolution of Drosophila. |
| first_indexed | 2024-09-23T13:29:04Z |
| format | Article |
| id | mit-1721.1/55381 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T13:29:04Z |
| publishDate | 2010 |
| publisher | Public Library of Science |
| record_format | dspace |
| spelling | mit-1721.1/553812022-09-28T14:32:17Z A Comprehensive Map of Insulator Elements for the Drosophila Genome White, Kevin P. Henikoff, Steven Stein, Lincoln White, Robert A. H. Russell, Steven Ahmad, Kami Feng, Xin Henikoff, Jorja G. Morrison, Carolyn A. Shah, Parantu K. Brown, Christopher D. Negre, Nicolas Kheradpour, Pouya Kellis, Manolis Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Kellis, Manolis Kheradpour, Pouya Kellis, Manolis Insulators are DNA sequences that control the interactions among genomic regulatory elements and act as chromatin boundaries. A thorough understanding of their location and function is necessary to address the complexities of metazoan gene regulation. We studied by ChIP–chip the genome-wide binding sites of 6 insulator-associated proteins—dCTCF, CP190, BEAF-32, Su(Hw), Mod(mdg4), and GAF—to obtain the first comprehensive map of insulator elements in Drosophila embryos. We identify over 14,000 putative insulators, including all classically defined insulators. We find two major classes of insulators defined by dCTCF/CP190/BEAF-32 and Su(Hw), respectively. Distributional analyses of insulators revealed that particular sub-classes of insulator elements are excluded between cis-regulatory elements and their target promoters; divide differentially expressed, alternative, and divergent promoters; act as chromatin boundaries; are associated with chromosomal breakpoints among species; and are embedded within active chromatin domains. Together, these results provide a map demarcating the boundaries of gene regulatory units and a framework for understanding insulator function during the development and evolution of Drosophila. 2010-06-03T18:08:14Z 2010-06-03T18:08:14Z 2010-01 2009-07 Article http://purl.org/eprint/type/JournalArticle 1553-7390 1553-7404 http://hdl.handle.net/1721.1/55381 Nègre, Nicolas et al. “A Comprehensive Map of Insulator Elements for the Drosophila Genome.” PLoS Genet 6.1 (2010): e1000814. © 2010 Nègre et al. en_US http://dx.doi.org/10.1371/journal.pgen.1000814 PLoS Genetics 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. application/pdf Public Library of Science PLoS |
| spellingShingle | White, Kevin P. Henikoff, Steven Stein, Lincoln White, Robert A. H. Russell, Steven Ahmad, Kami Feng, Xin Henikoff, Jorja G. Morrison, Carolyn A. Shah, Parantu K. Brown, Christopher D. Negre, Nicolas Kheradpour, Pouya Kellis, Manolis A Comprehensive Map of Insulator Elements for the Drosophila Genome |
| title | A Comprehensive Map of Insulator Elements for the Drosophila Genome |
| title_full | A Comprehensive Map of Insulator Elements for the Drosophila Genome |
| title_fullStr | A Comprehensive Map of Insulator Elements for the Drosophila Genome |
| title_full_unstemmed | A Comprehensive Map of Insulator Elements for the Drosophila Genome |
| title_short | A Comprehensive Map of Insulator Elements for the Drosophila Genome |
| title_sort | comprehensive map of insulator elements for the drosophila genome |
| url | http://hdl.handle.net/1721.1/55381 |
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