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  • 1
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    A cis-regulatory map of the Drosophila genome (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-03-25
    Description: Systematic annotation of gene regulatory elements is a major challenge in genome science. Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide has successfully identified specific subtypes of regulatory elements. In Drosophila several pioneering studies have provided genome-wide identification of Polycomb response elements, chromatin states, transcription factor binding sites, RNA polymerase II regulation and insulator elements; however, comprehensive annotation of the regulatory genome remains a significant challenge. Here we describe results from the modENCODE cis-regulatory annotation project. We produced a map of the Drosophila melanogaster regulatory genome on the basis of more than 300 chromatin immunoprecipitation data sets for eight chromatin features, five histone deacetylases and thirty-eight site-specific transcription factors at different stages of development. Using these data we inferred more than 20,000 candidate regulatory elements and validated a subset of predictions for promoters, enhancers and insulators in vivo. We identified also nearly 2,000 genomic regions of dense transcription factor binding associated with chromatin activity and accessibility. We discovered hundreds of new transcription factor co-binding relationships and defined a transcription factor network with over 800 potential regulatory relationships.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179250/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179250/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Negre, Nicolas -- Brown, Christopher D -- Ma, Lijia -- Bristow, Christopher Aaron -- Miller, Steven W -- Wagner, Ulrich -- Kheradpour, Pouya -- Eaton, Matthew L -- Loriaux, Paul -- Sealfon, Rachel -- Li, Zirong -- Ishii, Haruhiko -- Spokony, Rebecca F -- Chen, Jia -- Hwang, Lindsay -- Cheng, Chao -- Auburn, Richard P -- Davis, Melissa B -- Domanus, Marc -- Shah, Parantu K -- Morrison, Carolyn A -- Zieba, Jennifer -- Suchy, Sarah -- Senderowicz, Lionel -- Victorsen, Alec -- Bild, Nicholas A -- Grundstad, A Jason -- Hanley, David -- MacAlpine, David M -- Mannervik, Mattias -- Venken, Koen -- Bellen, Hugo -- White, Robert -- Gerstein, Mark -- Russell, Steven -- Grossman, Robert L -- Ren, Bing -- Posakony, James W -- Kellis, Manolis -- White, Kevin P -- F32 GM074364/GM/NIGMS NIH HHS/ -- F32 GM074364-01/GM/NIGMS NIH HHS/ -- F32 GM074364-02/GM/NIGMS NIH HHS/ -- P50 GM081892/GM/NIGMS NIH HHS/ -- R01 HG004037/HG/NHGRI NIH HHS/ -- R01 HG004037-04/HG/NHGRI NIH HHS/ -- RC2 HG005639/HG/NHGRI NIH HHS/ -- RC2 HG005639-02/HG/NHGRI NIH HHS/ -- U01 HG004264/HG/NHGRI NIH HHS/ -- U01 HG004279/HG/NHGRI NIH HHS/ -- U01HG004264/HG/NHGRI NIH HHS/ -- England -- Nature. 2011 Mar 24;471(7339):527-31. doi: 10.1038/nature09990.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Genomics and Systems Biology, Department of Human Genetics, The University of Chicago, 900 East 57th Street, Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21430782" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chromatin/metabolism ; Chromatin Assembly and Disassembly ; Chromatin Immunoprecipitation ; Drosophila melanogaster/*genetics ; Enhancer Elements, Genetic/genetics ; Genome, Insect/*genetics ; Histone Deacetylases/metabolism ; Insulator Elements/genetics ; *Molecular Sequence Annotation ; Promoter Regions, Genetic/genetics ; Regulatory Sequences, Nucleic Acid/*genetics ; Reproducibility of Results ; Silencer Elements, Transcriptional/genetics ; Transcription Factors/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Architecture of the human regulatory network derived from ENCODE data (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-09-08
    Description: Transcription factors bind in a combinatorial fashion to specify the on-and-off states of genes; the ensemble of these binding events forms a regulatory network, constituting the wiring diagram for a cell. To examine the principles of the human transcriptional regulatory network, we determined the genomic binding information of 119 transcription-related factors in over 450 distinct experiments. We found the combinatorial, co-association of transcription factors to be highly context specific: distinct combinations of factors bind at specific genomic locations. In particular, there are significant differences in the binding proximal and distal to genes. We organized all the transcription factor binding into a hierarchy and integrated it with other genomic information (for example, microRNA regulation), forming a dense meta-network. Factors at different levels have different properties; for instance, top-level transcription factors more strongly influence expression and middle-level ones co-regulate targets to mitigate information-flow bottlenecks. Moreover, these co-regulations give rise to many enriched network motifs (for example, noise-buffering feed-forward loops). Finally, more connected network components are under stronger selection and exhibit a greater degree of allele-specific activity (that is, differential binding to the two parental alleles). The regulatory information obtained in this study will be crucial for interpreting personal genome sequences and understanding basic principles of human biology and disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4154057/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4154057/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gerstein, Mark B -- Kundaje, Anshul -- Hariharan, Manoj -- Landt, Stephen G -- Yan, Koon-Kiu -- Cheng, Chao -- Mu, Xinmeng Jasmine -- Khurana, Ekta -- Rozowsky, Joel -- Alexander, Roger -- Min, Renqiang -- Alves, Pedro -- Abyzov, Alexej -- Addleman, Nick -- Bhardwaj, Nitin -- Boyle, Alan P -- Cayting, Philip -- Charos, Alexandra -- Chen, David Z -- Cheng, Yong -- Clarke, Declan -- Eastman, Catharine -- Euskirchen, Ghia -- Frietze, Seth -- Fu, Yao -- Gertz, Jason -- Grubert, Fabian -- Harmanci, Arif -- Jain, Preti -- Kasowski, Maya -- Lacroute, Phil -- Leng, Jing -- Lian, Jin -- Monahan, Hannah -- O'Geen, Henriette -- Ouyang, Zhengqing -- Partridge, E Christopher -- Patacsil, Dorrelyn -- Pauli, Florencia -- Raha, Debasish -- Ramirez, Lucia -- Reddy, Timothy E -- Reed, Brian -- Shi, Minyi -- Slifer, Teri -- Wang, Jing -- Wu, Linfeng -- Yang, Xinqiong -- Yip, Kevin Y -- Zilberman-Schapira, Gili -- Batzoglou, Serafim -- Sidow, Arend -- Farnham, Peggy J -- Myers, Richard M -- Weissman, Sherman M -- Snyder, Michael -- T32 GM007205/GM/NIGMS NIH HHS/ -- T32GM008283-24/GM/NIGMS NIH HHS/ -- U01 HG004695/HG/NHGRI NIH HHS/ -- U54 HG004558/HG/NHGRI NIH HHS/ -- England -- Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA. mark.gerstein@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22955619" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Cell Line ; DNA/*genetics ; *Encyclopedias as Topic ; GATA1 Transcription Factor/metabolism ; Gene Expression Profiling ; Gene Regulatory Networks/*genetics ; Genome, Human/*genetics ; Genomics ; Humans ; K562 Cells ; *Molecular Sequence Annotation ; Organ Specificity ; Phosphorylation/genetics ; Polymorphism, Single Nucleotide/genetics ; Protein Interaction Maps ; RNA, Untranslated/genetics/metabolism ; Regulatory Sequences, Nucleic Acid/*genetics ; Selection, Genetic/genetics ; Transcription Factors/*metabolism ; Transcription Initiation Site
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-12-24
    Description: We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor-binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142569/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142569/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gerstein, Mark B -- Lu, Zhi John -- Van Nostrand, Eric L -- Cheng, Chao -- Arshinoff, Bradley I -- Liu, Tao -- Yip, Kevin Y -- Robilotto, Rebecca -- Rechtsteiner, Andreas -- Ikegami, Kohta -- Alves, Pedro -- Chateigner, Aurelien -- Perry, Marc -- Morris, Mitzi -- Auerbach, Raymond K -- Feng, Xin -- Leng, Jing -- Vielle, Anne -- Niu, Wei -- Rhrissorrakrai, Kahn -- Agarwal, Ashish -- Alexander, Roger P -- Barber, Galt -- Brdlik, Cathleen M -- Brennan, Jennifer -- Brouillet, Jeremy Jean -- Carr, Adrian -- Cheung, Ming-Sin -- Clawson, Hiram -- Contrino, Sergio -- Dannenberg, Luke O -- Dernburg, Abby F -- Desai, Arshad -- Dick, Lindsay -- Dose, Andrea C -- Du, Jiang -- Egelhofer, Thea -- Ercan, Sevinc -- Euskirchen, Ghia -- Ewing, Brent -- Feingold, Elise A -- Gassmann, Reto -- Good, Peter J -- Green, Phil -- Gullier, Francois -- Gutwein, Michelle -- Guyer, Mark S -- Habegger, Lukas -- Han, Ting -- Henikoff, Jorja G -- Henz, Stefan R -- Hinrichs, Angie -- Holster, Heather -- Hyman, Tony -- Iniguez, A Leo -- Janette, Judith -- Jensen, Morten -- Kato, Masaomi -- Kent, W James -- Kephart, Ellen -- Khivansara, Vishal -- Khurana, Ekta -- Kim, John K -- Kolasinska-Zwierz, Paulina -- Lai, Eric C -- Latorre, Isabel -- Leahey, Amber -- Lewis, Suzanna -- Lloyd, Paul -- Lochovsky, Lucas -- Lowdon, Rebecca F -- Lubling, Yaniv -- Lyne, Rachel -- MacCoss, Michael -- Mackowiak, Sebastian D -- Mangone, Marco -- McKay, Sheldon -- Mecenas, Desirea -- Merrihew, Gennifer -- Miller, David M 3rd -- Muroyama, Andrew -- Murray, John I -- Ooi, Siew-Loon -- Pham, Hoang -- Phippen, Taryn -- Preston, Elicia A -- Rajewsky, Nikolaus -- Ratsch, Gunnar -- Rosenbaum, Heidi -- Rozowsky, Joel -- Rutherford, Kim -- Ruzanov, Peter -- Sarov, Mihail -- Sasidharan, Rajkumar -- Sboner, Andrea -- Scheid, Paul -- Segal, Eran -- Shin, Hyunjin -- Shou, Chong -- Slack, Frank J -- Slightam, Cindie -- Smith, Richard -- Spencer, William C -- Stinson, E O -- Taing, Scott -- Takasaki, Teruaki -- Vafeados, Dionne -- Voronina, Ksenia -- Wang, Guilin -- Washington, Nicole L -- Whittle, Christina M -- Wu, Beijing -- Yan, Koon-Kiu -- Zeller, Georg -- Zha, Zheng -- Zhong, Mei -- Zhou, Xingliang -- modENCODE Consortium -- Ahringer, Julie -- Strome, Susan -- Gunsalus, Kristin C -- Micklem, Gos -- Liu, X Shirley -- Reinke, Valerie -- Kim, Stuart K -- Hillier, LaDeana W -- Henikoff, Steven -- Piano, Fabio -- Snyder, Michael -- Stein, Lincoln -- Lieb, Jason D -- Waterston, Robert H -- 054523/Wellcome Trust/United Kingdom -- R01 GM088565/GM/NIGMS NIH HHS/ -- R01 GM088565-03/GM/NIGMS NIH HHS/ -- R01GM088565/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2010 Dec 24;330(6012):1775-87. doi: 10.1126/science.1196914. Epub 2010 Dec 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA. modencode.worm.pi@gersteinlab.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21177976" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Caenorhabditis elegans/*genetics/growth & development/metabolism ; Caenorhabditis elegans Proteins/genetics/metabolism ; Chromatin/genetics/metabolism/ultrastructure ; *Chromosomes/genetics/metabolism/ultrastructure ; Computational Biology/methods ; Conserved Sequence ; Evolution, Molecular ; *Gene Expression Profiling ; *Gene Expression Regulation ; Gene Regulatory Networks ; Genes, Helminth ; *Genome, Helminth ; Genomics/methods ; Histones/metabolism ; Models, Genetic ; *Molecular Sequence Annotation ; RNA, Helminth/genetics/metabolism ; RNA, Untranslated/genetics/metabolism ; Regulatory Sequences, Nucleic Acid ; Transcription Factors/genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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