Comparative analysis of regulatory information and circuits across distant species
Alan P. Boyle,Carlos L. Araya,Cathleen M. Brdlik,Philip Cayting,Chao Cheng,Yong Cheng,Kathryn E. Gardner,LaDeana W. Hillier,J. Janette,Lixia Jiang,Dionna M. Kasper,Trupti Kawli,Pouya Kheradpour,Anshul Kundaje,Anshul Kundaje,Jingyi Jessica Li,Jingyi Jessica Li,Lijia Ma,Wei Niu,E. Jay Rehm,Joel Rozowsky,Matthew Slattery,Rebecca Spokony,Robert Terrell,D. Vafeados,Daifeng Wang,Peter Weisdepp,Yi-Chieh Wu,Dan Xie,Koon-Kiu Yan,Elise A. Feingold,Peter J. Good,Michael J. Pazin,Haiyan Huang,Peter J. Bickel,Steven E. Brenner,Valerie Reinke,Robert H. Waterston,Mark Gerstein,Kevin P. White,Manolis Kellis,Michael Snyder +41 more
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TLDR
The results suggest that gene-regulatory properties previously observed for individual factors are general principles of metazoan regulation that are remarkably well-preserved despite extensive functional divergence of individual network connections.Abstract:
Despite the large evolutionary distances between metazoan species, they can show remarkable commonalities in their biology, and this has helped to establish fly and worm as model organisms for human biology. Although studies of individual elements and factors have explored similarities in gene regulation, a large-scale comparative analysis of basic principles of transcriptional regulatory features is lacking. Here we map the genome-wide binding locations of 165 human, 93 worm and 52 fly transcription regulatory factors, generating a total of 1,019 data sets from diverse cell types, developmental stages, or conditions in the three species, of which 498 (48.9%) are presented here for the first time. We find that structural properties of regulatory networks are remarkably conserved and that orthologous regulatory factor families recognize similar binding motifs in vivo and show some similar co-associations. Our results suggest that gene-regulatory properties previously observed for individual factors are general principles of metazoan regulation that are remarkably well-preserved despite extensive functional divergence of individual network connections. The comparative maps of regulatory circuitry provided here will drive an improved understanding of the regulatory underpinnings of model organism biology and how these relate to human biology, development and disease.read more
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Novel genetic associations for blood pressure identified via gene-alcohol interaction in up to 570K individuals across multiple ancestries
Mary F. Feitosa,Aldi T. Kraja,Daniel I. Chasman,Yun J. Sung,Thomas W. Winkler,Ioanna Ntalla,Xiuqing Guo,Nora Franceschini,Ching-Yu Cheng,Ching-Yu Cheng,Xueling Sim,Dina Vojinovic,Jonathan Marten,Solomon K. Musani,Changwei Li,Amy R. Bentley,Michael R. Brown,Karen Schwander,Melissa A. Richard,Raymond Noordam,Hugues Aschard,Hugues Aschard,Traci M. Bartz,Lawrence F. Bielak,Rajkumar Dorajoo,Virginia Fisher,Fernando Pires Hartwig,Fernando Pires Hartwig,Andrea R. V. R. Horimoto,Kurt Lohman,Alisa K. Manning,Tuomo Rankinen,Albert V. Smith,Salman M. Tajuddin,Mary K. Wojczynski,Maris Alver,Mathilde Boissel,Qiuyin Cai,Archie Campbell,Jin-Fang Chai,Xu Chen,Jasmin Divers,Chuan Gao,Anuj Goel,Yanick Hagemeijer,Sarah E. Harris,Meian He,Fang-Chi Hsu,Anne U. Jackson,Mika Kähönen,Anuradhani Kasturiratne,Pirjo Komulainen,Brigitte Kühnel,Federica Laguzzi,Jian'an Luan,Nana Matoba,Ilja M. Nolte,Sandosh Padmanabhan,Muhammad Riaz,Muhammad Riaz,Rico Rueedi,Antonietta Robino,M. Abdullah Said,Robert A. Scott,Tamar Sofer,Alena Stančáková,Fumihiko Takeuchi,Bamidele O. Tayo,Peter J. van der Most,Tibor V. Varga,Veronique Vitart,Yajuan Wang,Erin B. Ware,Helen R. Warren,Stefan Weiss,Wanqing Wen,Lisa R. Yanek,Weihua Zhang,Weihua Zhang,Jing Hua Zhao,Saima Afaq,Najaf Amin,Marzyeh Amini,Dan E. Arking,Tin Aung,Tin Aung,Eric Boerwinkle,Eric Boerwinkle,Ingrid B. Borecki,Ulrich Broeckel,Morris J. Brown,Marco Brumat,Gregory L. Burke,Mickaël Canouil,Aravinda Chakravarti,Sabanayagam Charumathi,Sabanayagam Charumathi,Yii-Der Ida Chen,John M. C. Connell,Adolfo Correa,Lisa de las Fuentes,Renée de Mutsert,H. Janaka de Silva,Xuan Deng,Jingzhong Ding,Qing Duan,Charles B. Eaton,Georg Ehret,Ruben N. Eppinga,Evangelos Evangelou,Evangelos Evangelou,Jessica D. Faul,Stephan B. Felix,Nita G. Forouhi,Terrence Forrester,Oscar H. Franco,Yechiel Friedlander,Ilaria Gandin,He Gao,Mohsen Ghanbari,Mohsen Ghanbari,Bruna Gigante,C. Charles Gu,Dongfeng Gu,Saskia P. Hagenaars,Göran Hallmans,Tamara B. Harris,Jiang He,Sami Heikkinen,Chew-Kiat Heng,Makoto Hirata,Barbara V. Howard,M. Arfan Ikram,Ulrich John,Tomohiro Katsuya,Chiea Chuen Khor,Chiea Chuen Khor,Tuomas O. Kilpeläinen,Tuomas O. Kilpeläinen,Woon-Puay Koh,José Eduardo Krieger,Stephen B. Kritchevsky,Michiaki Kubo,Johanna Kuusisto,Timo A. Lakka,Carl D. Langefeld,Claudia Langenberg,Lenore J. Launer,Benjamin Lehne,Cora E. Lewis,Yize Li,Shiow Lin,Jianjun Liu,Jianjun Liu,Jingmin Liu,Marie Loh,Marie Loh,Tin Louie,Reedik Mägi,Colin A. McKenzie,Thomas Meitinger,Andres Metspalu,Yuri Milaneschi,Lili Milani,Karen L. Mohlke,Yukihide Momozawa,Mike A. Nalls,Christopher P. Nelson,Christopher P. Nelson,Nona Sotoodehnia,Jill M. Norris,Jeffrey R. O'Connell,Nicholette D. Palmer,Thomas T. Perls,Nancy L. Pedersen,Annette Peters,Patricia A. Peyser,Neil Poulter,Leslie J. Raffel,Olli T. Raitakari,Kathryn Roll,Lynda M. Rose,Frits R. Rosendaal,Jerome I. Rotter,Carsten Oliver Schmidt,Pamela J. Schreiner,Nicole Schupf,William R. Scott,Peter S. Sever,Yuan Shi,Stephen Sidney,Mario Sims,Colleen M. Sitlani,Jennifer A. Smith,Harold Snieder,John M. Starr,Konstantin Strauch,Heather M. Stringham,Nicholas Y.Q. Tan,Hua Tang,Kent D. Taylor,Yik Ying Teo,Yik Ying Teo,Yih Chung Tham,Stephen Turner,André G. Uitterlinden,Peter Vollenweider,Melanie Waldenberger,Lihua Wang,Ya Xing Wang,Wen Bin Wei,Christine Williams,Jie Yao,Caizheng Yu,Jian-Min Yuan,Wei Zhao,Alan B. Zonderman,Diane M. Becker,Michael Boehnke,Donald W. Bowden,John C. Chambers,John C. Chambers,John C. Chambers,Ian J. Deary,Tõnu Esko,Tõnu Esko,Martin Farrall,Paul W. Franks,Paul W. Franks,Barry I. Freedman,Philippe Froguel,Philippe Froguel,Paolo Gasparini,Christian Gieger,Jost B. Jonas,Jost B. Jonas,Yoichiro Kamatani,Norihiro Kato,Jaspal S. Kooner,Jaspal S. Kooner,Zoltán Kutalik,Markku Laakso,Cathy C. Laurie,Karin Leander,Terho Lehtimäki,Patrik K. E. Magnusson,Albertine J. Oldehinkel,Brenda W.J.H. Penninx,Ozren Polasek,Ozren Polasek,David J. Porteous,Rainer Rauramaa,Nilesh J. Samani,Nilesh J. Samani,James Scott,Xiao-Ou Shu,Pim van der Harst,Lynne E. Wagenknecht,Nicholas J. Wareham,Hugh Watkins,David R. Weir,Ananda R. Wickremasinghe,Tangchun Wu,Wei Zheng,Claude Bouchard,Kaare Christensen,Michele K. Evans,Vilmundur Gudnason,Bernardo L. Horta,Sharon L.R. Kardia,Yongmei Liu,Alexandre C. Pereira,Bruce M. Psaty,Bruce M. Psaty,Paul M. Ridker,Rob M. van Dam,W. James Gauderman,Xiaofeng Zhu,Dennis O. Mook-Kanamori,Myriam Fornage,Charles N. Rotimi,L. Adrienne Cupples,L. Adrienne Cupples,Tanika N. Kelly,Ervin R. Fox,Caroline Hayward,Cornelia M. van Duijn,E. Shyong Tai,Tien Yin Wong,Tien Yin Wong,Charles Kooperberg,Walter Palmas,Kenneth Rice,Alanna C. Morrison,Paul Elliott,Mark J. Caulfield,Patricia B. Munroe,Dabeeru C. Rao,Michael A. Province,Daniel Levy +299 more
TL;DR: In insights into the role of alcohol consumption in the genetic architecture of hypertension, a large two-stage investigation incorporating joint testing of main genetic effects and single nucleotide variant (SNV)-alcohol consumption interactions is conducted.
Journal ArticleDOI
The ENCODE Blacklist: Identification of Problematic Regions of the Genome.
TL;DR: The ENCODE blacklist is defined- a comprehensive set of regions in the human, mouse, worm, and fly genomes that have anomalous, unstructured, or high signal in next-generation sequencing experiments independent of cell line or experiment.
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ENCODE data at the ENCODE portal
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TL;DR: This phase of the ENCODE project includes an expansion of assays that measure diverse RNA populations, identify proteins that interact with RNA and DNA, probe regions of DNA hypersensitivity, and measure levels of DNA methylation in a wide range of cell and tissue types to identify putative regulatory elements.
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Comparative analysis of metazoan chromatin organization
Joshua W. K. Ho,Joshua W. K. Ho,Youngsook L. Jung,Tao Liu,Tao Liu,Burak H. Alver,Soohyun Lee,Kohta Ikegami,Kohta Ikegami,Kyung-Ah Sohn,Kyung-Ah Sohn,Aki Minoda,Aki Minoda,Michael Y. Tolstorukov,Alex Appert,Stephen C. J. Parker,Tingting Gu,Anshul Kundaje,Anshul Kundaje,Anshul Kundaje,Nicole C. Riddle,Nicole C. Riddle,Eric Bishop,Eric Bishop,Thea A. Egelhofer,Sheng'en Shawn Hu,Artyom A. Alekseyenko,Andreas Rechtsteiner,Dalal Asker,Dalal Asker,Jason A. Belsky,Sarah K. Bowman,Q. Brent Chen,Ron A.-J. Chen,Daniel S. Day,Yan Dong,Andréa C. Dosé,Xikun Duan,Charles B. Epstein,Sevinc Ercan,Elise A. Feingold,Francesco Ferrari,Jacob M. Garrigues,Nils Gehlenborg,Nils Gehlenborg,Peter J. Good,Psalm Haseley,Daniel He,Moritz Herrmann,Michael M. Hoffman,Tess E. Jeffers,Tess E. Jeffers,Peter V. Kharchenko,P. Kolasinska-Zwierz,Chitra V. Kotwaliwale,Chitra V. Kotwaliwale,Nischay Kumar,Nischay Kumar,Sasha A. Langley,Sasha A. Langley,Erica Larschan,Isabel J. Latorre,Maxwell W. Libbrecht,Xueqiu Lin,Richard W. Park,Richard W. Park,Michael J. Pazin,Hoang N. Pham,Hoang N. Pham,Hoang N. Pham,Annette Plachetka,Bo Qin,Yuri B. Schwartz,Yuri B. Schwartz,Noam Shoresh,Przemyslaw Stempor,A. Vielle,Chengyang Wang,Christina M. Whittle,Christina M. Whittle,Huiling Xue,Robert E. Kingston,Ju Han Kim,Bradley E. Bernstein,Bradley E. Bernstein,Bradley E. Bernstein,Abby F. Dernburg,Abby F. Dernburg,Abby F. Dernburg,Vincenzo Pirrotta,Mitzi I. Kuroda,William Stafford Noble,Thomas D. Tullius,Manolis Kellis,Manolis Kellis,David M. MacAlpine,Susan Strome,Sarah C. R. Elgin,Xiaole Shirley Liu,Xiaole Shirley Liu,Jason D. Lieb,Julie Ahringer,Gary H. Karpen,Gary H. Karpen,Peter J. Park +104 more
TL;DR: Comparison of combinatorial patterns of histone modifications, nuclear lamina-associated domains, organization of large-scale topological domains, chromatin environment at promoters and enhancers, nucleosome positioning, and DNA replication patterns reveals many conserved features of chromatin organization among the three organisms.
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