Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication...
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| Published in | Science (American Association for the Advancement of Science) Vol. 330; no. 6012; pp. 1787 - 1797 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article Web Resource |
| Language | English |
| Published |
Washington, DC
American Association for the Advancement of Science
24.12.2010
The American Association for the Advancement of Science |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0036-8075 1095-9203 1095-9203 |
| DOI | 10.1126/science.1198374 |
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| Abstract | To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation. |
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| AbstractList | For biologists, having a genome in hand is only the beginning--much more investigation is still needed to characterize how the genome is used to help to produce a functional organism (see the Perspective by Blaxter ). In this vein, Gerstein et al. (p. 1775) summarize for the Caenorhabditis elegans genome, and The modENCODE Consortium (p. 1787) summarize for the Drosophila melanogaster genome, full transcriptome analyses over developmental stages, genome-wide identification of transcription factor binding sites, and high-resolution maps of chromatin organization. Both studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized. Overall, the studies provide insights into the organization, structure, and function of the two genomes and provide basic information needed to guide and correlate both focused and genome-wide studies. To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation. [PUBLICATION ABSTRACT] To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation. To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophilo genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage-and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation. To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation. For biologists, having a genome in hand is only the beginning—much more investigation is still needed to characterize how the genome is used to help to produce a functional organism (see the Perspective by Blaxter ). In this vein, Gerstein et al. (p. 1775 ) summarize for the Caenorhabditis elegans genome, and The modENCODE Consortium (p. 1787 ) summarize for the Drosophila melanogaster genome, full transcriptome analyses over developmental stages, genome-wide identification of transcription factor binding sites, and high-resolution maps of chromatin organization. Both studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized. Overall, the studies provide insights into the organization, structure, and function of the two genomes and provide basic information needed to guide and correlate both focused and genome-wide studies. The Drosophila modENCODE project demonstrates the functional regulatory network of flies. To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation. To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation. |
| Author | Washington, Nicole L MacAlpine, David M Okamura, Katsutomo White, Kevin P Samsonova, Anastasia Grossman, Robert Feng, Xin Yang, Li Gingeras, Thomas R Sher, Noa Henikoff, Steven Lai, Eric C Brown, Christopher D Micklem, Gos Riddle, Nicole C Eaton, Matthew L Henikoff, Jorja G Schwartz, Yuri B Robine, Nicolas Dai, Qi Bristow, Christopher A Kent, William Sandler, Jeremy E Minoda, Aki Gorchakov, Andrey A Marbach, Daniel Powell, Sara K Spokony, Rebecca Stein, Lincoln D Sturgill, David Di Stefano, Luisa Malone, John Berger, Bonnie Sealfon, Rachel Li, Renhua Lowdon, Rebecca Karpen, Gary H Gu, Tingting Artieri, Carlo Perry, Marc Ay, Ferhat Duff, Michael O Washietl, Stefan Ahmad, Kami Ren, Bing Oliver, Brian Arshinoff, Bradley I Meyer, Patrick E Booth, Benjamin W Carlson, Joseph W Lin, Michael F Brenner, Steven E Roy, Sushmita Candeias, Rogerio Davis, Carrie A Brent, Michael R Ernst, Jason Kharchenko, Peter V Lewis, Suzanna Russell, Steven Tolstorukov, Michael Y MacAlpine, Heather K Kuroda, Mitzi I Guyer, Mark Park, Peter J Perrimon, Norbert Hoskins, Roger A Go |
| AuthorAffiliation | Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA |
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| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=23703293$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/21177974$$D View this record in MEDLINE/PubMed https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-46221$$DView record from Swedish Publication Index |
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| Contributor | Wang, Huaien White, Kevin P Booth, Benjamin Lin, Wei Bristow, Christopher A Sandler, Jeremy E Minoda, Aki Jung, Youngsook L Marbach, Daniel Spokony, Rebecca Ghosh, Srinka Di Stefano, Luisa Sealfon, Rachel Samsonova, Anastasia A Gu, Tingting Dobin, Alex Carlson, Joseph W Lin, Michael F Brenner, Steven E Linder-Basso, Daniela Candeias, Rogerio Davis, Carrie A Brent, Michael R Ernst, Jason Kharchenko, Peter V Fagegaltier, Delphine Zhang, Dayu Meyer, Folker Russell, Steven Elgin, Sarah C R Kuroda, Mitzi I Perrimon, Norbert Miller, David Kaufman, Thomas C Posakony, James W Dudoit, Sandrine Heinz, Elizabeth Kheradpour, Pouya Domanus, Marc H Suchy, Sarah Ma, Lijia Auburn, Richard Jha, Sonali Bishop, Eric P Yu, Charles Dumais, Jacqueline Graveley, Brenton R Hansen, Kasper D Li, Zirong Andrews, Justen Miller, Steven W Langton, Laura Comstock, Charles L G Hanley, David Yang, Li Gingeras, Thomas R Brown, Christopher D Riddle, Nicole C Schwartz, Yuri B Acevedo, David Gorchakov, Andrey A Bellen, Hugo J Morrison, Carolyn A Shah, Parantu K Zaleski, Chris Scheftner |
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fullname: Kuroda, Mitzi I – sequence: 66 givenname: Vincenzo surname: Pirrotta fullname: Pirrotta, Vincenzo – sequence: 67 givenname: Peter J surname: Park fullname: Park, Peter J – sequence: 68 givenname: Gary H surname: Karpen fullname: Karpen, Gary H – sequence: 69 givenname: David surname: Acevedo fullname: Acevedo, David – sequence: 70 givenname: Eric P surname: Bishop fullname: Bishop, Eric P – sequence: 71 givenname: Sarah E surname: Gadel fullname: Gadel, Sarah E – sequence: 72 givenname: Youngsook L surname: Jung fullname: Jung, Youngsook L – sequence: 73 givenname: Cameron D surname: Kennedy fullname: Kennedy, Cameron D – sequence: 74 givenname: Ok-Kyung surname: Lee fullname: Lee, Ok-Kyung – sequence: 75 givenname: Daniela surname: Linder-Basso fullname: Linder-Basso, Daniela – sequence: 76 givenname: Sarah E surname: Marchetti fullname: Marchetti, Sarah E – sequence: 77 givenname: Gregory surname: Shanower fullname: Shanower, Gregory – sequence: 78 givenname: Nicolas surname: Nègre fullname: Nègre, Nicolas – sequence: 79 givenname: Lijia surname: Ma fullname: Ma, Lijia – sequence: 80 givenname: Christopher D surname: Brown fullname: Brown, Christopher D – sequence: 81 givenname: Rebecca surname: Spokony fullname: Spokony, Rebecca – sequence: 82 givenname: Robert L surname: Grossman fullname: Grossman, Robert L – sequence: 83 givenname: James W surname: Posakony fullname: Posakony, James W – sequence: 84 givenname: Bing surname: Ren fullname: Ren, Bing – sequence: 85 givenname: Steven surname: Russell fullname: Russell, Steven – sequence: 86 givenname: Kevin P surname: White fullname: White, Kevin P – sequence: 87 givenname: Richard surname: Auburn fullname: Auburn, Richard – sequence: 88 givenname: Hugo J surname: Bellen fullname: Bellen, Hugo J – sequence: 89 givenname: Jia surname: Chen fullname: Chen, Jia – sequence: 90 givenname: Marc H surname: Domanus fullname: Domanus, Marc H – sequence: 91 givenname: David surname: Hanley fullname: Hanley, David – sequence: 92 givenname: Elizabeth surname: Heinz fullname: Heinz, Elizabeth – sequence: 93 givenname: Zirong surname: Li fullname: Li, Zirong – sequence: 94 givenname: Folker surname: Meyer fullname: Meyer, Folker – sequence: 95 givenname: Steven W surname: Miller fullname: Miller, Steven W – sequence: 96 givenname: Carolyn A surname: Morrison fullname: Morrison, Carolyn A – sequence: 97 givenname: Douglas A surname: Scheftner fullname: Scheftner, Douglas A – sequence: 98 givenname: Lionel surname: Senderowicz fullname: Senderowicz, Lionel – sequence: 99 givenname: Parantu K surname: Shah fullname: Shah, Parantu K – sequence: 100 givenname: Sarah surname: Suchy fullname: Suchy, Sarah |
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| Keywords | Chromatin Insecta Drosophila Genomics Information Drosophilidae Coding Arthropoda Genetics Replication Regulatory sequence Invertebrata Diptera |
| Language | English |
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| Snippet | To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements... For biologists, having a genome in hand is only the beginning—much more investigation is still needed to characterize how the genome is used to help to produce... For biologists, having a genome in hand is only the beginning--much more investigation is still needed to characterize how the genome is used to help to... To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements... |
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| SubjectTerms | Animals Binding Sites Biochemistry, biophysics & molecular biology Biochimie, biophysique & biologie moléculaire Biological and medical sciences Cellular Chromatin Chromatin - genetics Chromatin - metabolism Chromatin/genetics/metabolism Classical genetics, quantitative genetics, hybrids Coding Computational Biology - methods data collection Datasets Deoxyribonucleic acid Developmental Programs Developmental stages DNA Drosophila Drosophila melanogaster - genetics Drosophila melanogaster - growth & development Drosophila melanogaster - metabolism Drosophila melanogaster/genetics/growth & development/metabolism Drosophila Proteins - genetics Drosophila Proteins - metabolism Drosophila Proteins/genetics/metabolism Epigenesis, Genetic Fundamental and applied biological sciences. Psychology gene expression Gene Expression Regulation Gene Regulatory Networks Genes Genes, Insect Genetics of eukaryotes. Biological and molecular evolution Genome, Insect Genomes Genomics Genomics - methods Histones Histones - metabolism Invertebrata Life sciences Mathematical models MicroRNA Molecular Sequence Annotation Networks Nucleosomes Nucleosomes - genetics Nucleosomes - metabolism Nucleosomes/genetics/metabolism prediction Promoter Regions, Genetic Proteins Replication Ribonucleic acids RNA RNA, Small Untranslated - genetics RNA, Small Untranslated - metabolism RNA, Small Untranslated/genetics/metabolism Sciences du vivant transcription (genetics) transcription factors Transcription Factors - metabolism Transcription, Genetic translation (genetics) |
| Title | Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE |
| URI | https://www.jstor.org/stable/40986582 https://www.ncbi.nlm.nih.gov/pubmed/21177974 https://www.proquest.com/docview/872031235 https://www.proquest.com/docview/2000380179 https://www.proquest.com/docview/837455887 https://www.proquest.com/docview/855716855 http://orbi.ulg.ac.be/handle/2268/163897 https://pubmed.ncbi.nlm.nih.gov/PMC3192495 https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-46221 |
| Volume | 330 |
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