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A Large Multiethnic Genome-Wide Association Study of Adult Body Mass Index Identifies Novel Loci. Genetics 2018; 210:499-515. [PMID: 30108127 DOI: 10.1534/genetics.118.301479] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/08/2018] [Indexed: 12/31/2022] Open
Abstract
Body mass index (BMI), a proxy measure for obesity, is determined by both environmental (including ethnicity, age, and sex) and genetic factors, with > 400 BMI-associated loci identified to date. However, the impact, interplay, and underlying biological mechanisms among BMI, environment, genetics, and ancestry are not completely understood. To further examine these relationships, we utilized 427,509 calendar year-averaged BMI measurements from 100,418 adults from the single large multiethnic Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort. We observed substantial independent ancestry and nationality differences, including ancestry principal component interactions and nonlinear effects. To increase the list of BMI-associated variants before assessing other differences, we conducted a genome-wide association study (GWAS) in GERA, with replication in the Genetic Investigation of Anthropomorphic Traits (GIANT) consortium combined with the UK Biobank (UKB), followed by GWAS in GERA combined with GIANT, with replication in the UKB. We discovered 30 novel independent BMI loci (P < 5.0 × 10-8) that replicated. We then assessed the proportion of BMI variance explained by sex in the UKB using previously identified loci compared to previously and newly identified loci and found slight increases: from 3.0 to 3.3% for males and from 2.7 to 3.0% for females. Further, the variance explained by previously and newly identified variants decreased with increasing age in the GERA and UKB cohorts, echoed in the variance explained by the entire genome, which also showed gene-age interaction effects. Finally, we conducted a tissue expression QTL enrichment analysis, which revealed that GWAS BMI-associated variants were enriched in the cerebellum, consistent with prior work in humans and mice.
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TLR10 and NFKBIA contributed to the risk of hip osteoarthritis: systematic evaluation based on Han Chinese population. Sci Rep 2018; 8:10243. [PMID: 29980729 PMCID: PMC6035240 DOI: 10.1038/s41598-018-28597-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/20/2018] [Indexed: 12/21/2022] Open
Abstract
Multiple lines of evidence have confirmed the importance of genetic factors for hip osteoarthritis (HOA). Our study aimed to investigate the associations of TLR10 and NFKBIA with respect to the HOA risk in Han Chinese individuals. A total of 1,043 HOA patients and 2,664 controls were recruited. Then, 23 tag single-nucleotide polymorphisms (SNPs) in the TLR10 and NFKBIA genes were selected for genotyping. Genetic association analyses were conducted in both single-marker and haplotype-based ways. Gene by gene, two-way interactions were analysed using a case-only method. Multiple bioinformatics tools were utilised to examine the potential functional significance of the SNPs. Two significant SNPs, rs11096957 (OR = 1.26, P = 1.35 × 10−5) and rs2273650 (OR = 1.2, P = 1.57 × 10−3), were significantly associated with HOA risk. Rs11096957 was also associated with the severity of the HOA. Bioinformatics analysis indicated that the allele T of rs2273650 would create new miRNA/SNP target duplexes, which suggests that rs2273650 could alter the NFKBIA expression by affecting the miRNA/SNP target duplexes. Our study identified significant association signals from NFKBIA with HOA for the first time, and it also confirmed the contribution of TLR10 to the HOA risk. These findings would provide clues for identifying individuals at high risk of HOA.
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Zenke K, Muroi M, Tanamoto KI. IRF1 supports DNA binding of STAT1 by promoting its phosphorylation. Immunol Cell Biol 2018; 96:1095-1103. [DOI: 10.1111/imcb.12185] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/07/2018] [Accepted: 06/08/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Kosuke Zenke
- Research Institute of Pharmaceutical Sciences; Musashino University; 1-1-20 Shinmachi Nishitokyo-shi, Tokyo 202-8585 Japan
| | - Masashi Muroi
- Research Institute of Pharmaceutical Sciences; Musashino University; 1-1-20 Shinmachi Nishitokyo-shi, Tokyo 202-8585 Japan
| | - Ken-ichi Tanamoto
- Research Institute of Pharmaceutical Sciences; Musashino University; 1-1-20 Shinmachi Nishitokyo-shi, Tokyo 202-8585 Japan
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Feitosa MF, Kraja AT, Chasman DI, Sung YJ, Winkler TW, Ntalla I, Guo X, Franceschini N, Cheng CY, Sim X, Vojinovic D, Marten J, Musani SK, Li C, Bentley AR, Brown MR, Schwander K, Richard MA, Noordam R, Aschard H, Bartz TM, Bielak LF, Dorajoo R, Fisher V, Hartwig FP, Horimoto ARVR, Lohman KK, Manning AK, Rankinen T, Smith AV, Tajuddin SM, Wojczynski MK, Alver M, Boissel M, Cai Q, Campbell A, Chai JF, Chen X, Divers J, Gao C, Goel A, Hagemeijer Y, Harris SE, He M, Hsu FC, Jackson AU, Kähönen M, Kasturiratne A, Komulainen P, Kühnel B, Laguzzi F, Luan J, Matoba N, Nolte IM, Padmanabhan S, Riaz M, Rueedi R, Robino A, Said MA, Scott RA, Sofer T, Stančáková A, Takeuchi F, Tayo BO, van der Most PJ, Varga TV, Vitart V, Wang Y, Ware EB, Warren HR, Weiss S, Wen W, Yanek LR, Zhang W, Zhao JH, Afaq S, Amin N, Amini M, Arking DE, Aung T, Boerwinkle E, Borecki I, Broeckel U, Brown M, Brumat M, Burke GL, Canouil M, Chakravarti A, Charumathi S, Ida Chen YD, Connell JM, Correa A, de las Fuentes L, de Mutsert R, de Silva HJ, Deng X, Ding J, Duan Q, Eaton CB, Ehret G, Eppinga RN, Evangelou E, Faul JD, Felix SB, Forouhi NG, Forrester T, Franco OH, Friedlander Y, Gandin I, Gao H, Ghanbari M, Gigante B, Gu CC, Gu D, Hagenaars SP, Hallmans G, Harris TB, He J, Heikkinen S, Heng CK, Hirata M, Howard BV, Ikram MA, John U, Katsuya T, Khor CC, Kilpeläinen TO, Koh WP, Krieger JE, Kritchevsky SB, Kubo M, Kuusisto J, Lakka TA, Langefeld CD, Langenberg C, Launer LJ, Lehne B, Lewis CE, Li Y, Lin S, Liu J, Liu J, Loh M, Louie T, Mägi R, McKenzie CA, Meitinger T, Metspalu A, Milaneschi Y, Milani L, Mohlke KL, Momozawa Y, Nalls MA, Nelson CP, Sotoodehnia N, Norris JM, O'Connell JR, Palmer ND, Perls T, Pedersen NL, Peters A, Peyser PA, Poulter N, Raffel LJ, Raitakari OT, Roll K, Rose LM, Rosendaal FR, Rotter JI, Schmidt CO, Schreiner PJ, Schupf N, Scott WR, Sever PS, Shi Y, Sidney S, Sims M, Sitlani CM, Smith JA, Snieder H, Starr JM, Strauch K, Stringham HM, Tan NYQ, Tang H, Taylor KD, Teo YY, Tham YC, Turner ST, Uitterlinden AG, Vollenweider P, Waldenberger M, Wang L, Wang YX, Wei WB, Williams C, Yao J, Yu C, Yuan JM, Zhao W, Zonderman AB, Becker DM, Boehnke M, Bowden DW, Chambers JC, Deary IJ, Esko T, Farrall M, Franks PW, Freedman BI, Froguel P, Gasparini P, Gieger C, Jonas JB, Kamatani Y, Kato N, Kooner JS, Kutalik Z, Laakso M, Laurie CC, Leander K, Lehtimäki T, Study LC, Magnusson PKE, Oldehinkel AJ, Penninx BWJH, Polasek O, Porteous DJ, Rauramaa R, Samani NJ, Scott J, Shu XO, van der Harst P, Wagenknecht LE, Wareham NJ, Watkins H, Weir DR, Wickremasinghe AR, Wu T, Zheng W, Bouchard C, Christensen K, Evans MK, Gudnason V, Horta BL, Kardia SLR, Liu Y, Pereira AC, Psaty BM, Ridker PM, van Dam RM, Gauderman WJ, Zhu X, Mook-Kanamori DO, Fornage M, Rotimi CN, Cupples LA, Kelly TN, Fox ER, Hayward C, van Duijn CM, Tai ES, Wong TY, Kooperberg C, Palmas W, Rice K, Morrison AC, Elliott P, Caulfield MJ, Munroe PB, Rao DC, Province MA, Levy D. Novel genetic associations for blood pressure identified via gene-alcohol interaction in up to 570K individuals across multiple ancestries. PLoS One 2018; 13:e0198166. [PMID: 29912962 PMCID: PMC6005576 DOI: 10.1371/journal.pone.0198166] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/15/2018] [Indexed: 01/01/2023] Open
Abstract
Heavy alcohol consumption is an established risk factor for hypertension; the mechanism by which alcohol consumption impact blood pressure (BP) regulation remains unknown. We hypothesized that a genome-wide association study accounting for gene-alcohol consumption interaction for BP might identify additional BP loci and contribute to the understanding of alcohol-related BP regulation. We conducted a large two-stage investigation incorporating joint testing of main genetic effects and single nucleotide variant (SNV)-alcohol consumption interactions. In Stage 1, genome-wide discovery meta-analyses in ≈131K individuals across several ancestry groups yielded 3,514 SNVs (245 loci) with suggestive evidence of association (P < 1.0 x 10-5). In Stage 2, these SNVs were tested for independent external replication in ≈440K individuals across multiple ancestries. We identified and replicated (at Bonferroni correction threshold) five novel BP loci (380 SNVs in 21 genes) and 49 previously reported BP loci (2,159 SNVs in 109 genes) in European ancestry, and in multi-ancestry meta-analyses (P < 5.0 x 10-8). For African ancestry samples, we detected 18 potentially novel BP loci (P < 5.0 x 10-8) in Stage 1 that warrant further replication. Additionally, correlated meta-analysis identified eight novel BP loci (11 genes). Several genes in these loci (e.g., PINX1, GATA4, BLK, FTO and GABBR2) have been previously reported to be associated with alcohol consumption. These findings provide insights into the role of alcohol consumption in the genetic architecture of hypertension.
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Affiliation(s)
- Mary F. Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Aldi T. Kraja
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Daniel I. Chasman
- Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yun J. Sung
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Thomas W. Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Ioanna Ntalla
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Xiuqing Guo
- Genomic Outcomes, Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Nora Franceschini
- Epidemiology, University of North Carolina Gilling School of Global Public Health, Chapel Hill, North Carolina, United States of America
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University Health System and National University of Singapore, Singapore, Singapore
| | - Dina Vojinovic
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Solomon K. Musani
- Jackson Heart Study, Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Changwei Li
- Epidemiology and Biostatistics, University of Georgia at Athens College of Public Health, Athens, Georgia, United States of America
| | - Amy R. Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael R. Brown
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Karen Schwander
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Melissa A. Richard
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Raymond Noordam
- Internal Medicine, Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hugues Aschard
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, Paris, France
| | - Traci M. Bartz
- Cardiovascular Health Research Unit, Biostatistics and Medicine, University of Washington, Seattle, Washington, United States of America
| | - Lawrence F. Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Virginia Fisher
- Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Fernando P. Hartwig
- Postgraduate Programme in Epidemiology, Federal University of Pelotas, Pelotas, RS, Brazil
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Andrea R. V. R. Horimoto
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, SP, Brazil
| | - Kurt K. Lohman
- Biostatistical Sciences, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Alisa K. Manning
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Tuomo Rankinen
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, Louisiana, United States of America
| | - Albert V. Smith
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Salman M. Tajuddin
- Health Disparities Research Section, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Mary K. Wojczynski
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Maris Alver
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Mathilde Boissel
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Archie Campbell
- Centre for Genomic & Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Jin Fang Chai
- Saw Swee Hock School of Public Health, National University Health System and National University of Singapore, Singapore, Singapore
| | - Xu Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Stockholm, Sweden
| | - Jasmin Divers
- Biostatistical Sciences, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Chuan Gao
- Molecular Genetics and Genomics Program, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Anuj Goel
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, Oxfordshire, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Yanick Hagemeijer
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom
- Medical Genetics Section, Centre for Genomic and Experimental Medicine and MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Meian He
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health for Incubating, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fang-Chi Hsu
- Biostatistical Sciences, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Anne U. Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
- University of Tampere, Tampere, Finland
| | | | - Pirjo Komulainen
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Brigitte Kühnel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Federica Laguzzi
- Unit of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Nana Matoba
- Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Ilja M. Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sandosh Padmanabhan
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Muhammad Riaz
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Rico Rueedi
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Instititute of Bioinformatics, Lausanne, Switzerland
| | - Antonietta Robino
- Institute for Maternal and Child Health—IRCCS "Burlo Garofolo", Trieste, Italy
| | - M. Abdullah Said
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Robert A. Scott
- MRC Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Tamar Sofer
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, United States of America
| | - Alena Stančáková
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Bamidele O. Tayo
- Department of Public Health Sciences, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Peter J. van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tibor V. Varga
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Skåne University Hospital, Malmö, Sweden
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Yajuan Wang
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Erin B. Ware
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Helen R. Warren
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- NIHR Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, London, London, United Kingdom
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional genomics, University Medicine Ernst Moritz Arndt University Greifsald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Lisa R. Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
- Department of Cardiology, Ealing Hospital, Middlesex, United Kingdom
| | - Jing Hua Zhao
- MRC Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Saima Afaq
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
| | - Najaf Amin
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marzyeh Amini
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dan E. Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, The University of Texas School of Public Health, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ingrid Borecki
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Ulrich Broeckel
- Section of Genomic Pediatrics, Department of Pediatrics, Medicine and Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Morris Brown
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- NIHR Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, London, London, United Kingdom
| | - Marco Brumat
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Gregory L. Burke
- Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Mickaël Canouil
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sabanayagam Charumathi
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Yii-Der Ida Chen
- Genomic Outcomes, Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - John M. Connell
- Ninewells Hospital & Medical School, University of Dundee, Dundee, Scotland, United Kingdom
| | - Adolfo Correa
- Jackson Heart Study, Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Lisa de las Fuentes
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Cardiovascular Division, Department of Medicine, Washington University, St. Louis, Missouri, United States of America
| | - Renée de Mutsert
- Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - H. Janaka de Silva
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - Xuan Deng
- Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Jingzhong Ding
- Center on Diabetes, Obesity, and Metabolism, Gerontology and Geriatric Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
| | - Qing Duan
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Charles B. Eaton
- Department of Family Medicine and Epidemiology, Alpert Medical School of Brown University, Providence, Rhode Island, United States of America
| | - Georg Ehret
- Cardiology, Geneva University Hospital, Geneva, Switzerland
| | - Ruben N. Eppinga
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Evangelos Evangelou
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Jessica D. Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Stephan B. Felix
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Nita G. Forouhi
- MRC Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Terrence Forrester
- The Caribbean Institute for Health Research (CAIHR), University of the West Indies, Mona, Jamaica
| | - Oscar H. Franco
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yechiel Friedlander
- Braun School of Public Health, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Ilaria Gandin
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - He Gao
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Bruna Gigante
- Unit of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - C. Charles Gu
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Dongfeng Gu
- Department of Epidemiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center of Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Saskia P. Hagenaars
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom
- Psychology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Göran Hallmans
- Department of Public Health and Clinical Medicine, Nutritional Research, Umeå University, Umeå, Västerbotten, Sweden
| | - Tamara B. Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jiang He
- Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
- Medicine, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Sami Heikkinen
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Finland
| | - Chew-Kiat Heng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Khoo Teck Puat–National University Children's Medical Institute, National University Health System, Singapore
| | - Makoto Hirata
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Minato-ku, Japan
| | - Barbara V. Howard
- MedStar Health Research Institute, Hyattsville, Maryland, United States of America
- Center for Clinical and Translational Sciences and Department of Medicine, Georgetown-Howard Universities, Washington, DC, United States of America
| | - M. Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Ulrich John
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
- Institute of Social Medicine and Prevention, University Medicine Greifswald, Greifswald, Germany
| | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Geriatric Medicine and Nephrology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Tuomas O. Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Environmental Medicine and Public Health, The Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Woon-Puay Koh
- Saw Swee Hock School of Public Health, National University Health System and National University of Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - José E. Krieger
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, SP, Brazil
| | - Stephen B. Kritchevsky
- Sticht Center for Healthy Aging and Alzheimer's Prevention, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Michiaki Kubo
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Timo A. Lakka
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Carl D. Langefeld
- Biostatistical Sciences, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Lenore J. Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
| | - Cora E. Lewis
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Yize Li
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Shiow Lin
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jianjun Liu
- Saw Swee Hock School of Public Health, National University Health System and National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Jingmin Liu
- WHI CCC, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Marie Loh
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
- Translational Laboratory in Genetic Medicine, Agency for Science, Technology and Research, Singapore
| | - Tin Louie
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Colin A. McKenzie
- The Caribbean Institute for Health Research (CAIHR), University of the West Indies, Mona, Jamaica
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | | | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health Research Institute, VU University Medical Center, Amsterdam, The Netherlands
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Mike A. Nalls
- Data Tecnica International, Glen Echo, Maryland, United States of America
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, United States of America
| | - Christopher P. Nelson
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Division of Cardiology, University of Washington, Seattle, Washington, United States of America
| | - Jill M. Norris
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, United States of America
| | - Jeff R. O'Connell
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Nicholette D. Palmer
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Thomas Perls
- Geriatrics Section, Boston University Medical Center, Boston, Massachusetts, United States of America
| | - Nancy L. Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Stockholm, Sweden
| | - Annette Peters
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Neuherberg, Germany
| | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Neil Poulter
- School of Public Health, Imperial College London, London, London, United Kingdom
| | - Leslie J. Raffel
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of California, Irvine, California, United States of America
| | - Olli T. Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Kathryn Roll
- Genomic Outcomes, Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Lynda M. Rose
- Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Frits R. Rosendaal
- Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jerome I. Rotter
- Genomic Outcomes, Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Carsten O. Schmidt
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Pamela J. Schreiner
- Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Nicole Schupf
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, New York, United States of America
| | - William R. Scott
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Peter S. Sever
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Yuan Shi
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Stephen Sidney
- Division of Research, Kaiser Permanente of Northern California, Oakland, California, United States of America
| | - Mario Sims
- Jackson Heart Study, Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Colleen M. Sitlani
- Cardiovascular Health Research Unit, Medicine, University of Washington, Seattle, Washington, United States of America
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - John M. Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom
- Alzheimer Scotland Dementia Research Centre, The University of Edinburgh, Edinburgh, United Kingdom
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU, Munich, Germany
| | - Heather M. Stringham
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Nicholas Y. Q. Tan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Hua Tang
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Kent D. Taylor
- Genomic Outcomes, Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University Health System and National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Yih Chung Tham
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Stephen T. Turner
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, United States of America
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Peter Vollenweider
- Service of Internal Medicine, Department of Internal Medicine, University Hospital, Lausanne, Switzerland
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Lihua Wang
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Ya Xing Wang
- Beijing Institute of Ophthalmology, Beijing Ophthalmology and Visual Science Key Lab, Beijing Tongren Eye Center, Capital Medical University, Beijing, China
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Wen Bin Wei
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Christine Williams
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jie Yao
- Genomic Outcomes, Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Caizheng Yu
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health for Incubating, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jian-Min Yuan
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alan B. Zonderman
- Behavioral Epidemiology Section, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Diane M. Becker
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Donald W. Bowden
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - John C. Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
- Department of Cardiology, Ealing Hospital, Middlesex, United Kingdom
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Imperial College Healthcare NHS Trust, London, United Kingdom
- MRC-PHE Centre for Environment and Health, Department of Epidemiology & Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, United Kingdom
- Psychology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Boston, Massachusetts, United States of America
| | - Martin Farrall
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, Oxfordshire, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Paul W. Franks
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Skåne University Hospital, Malmö, Sweden
- Harvard T. H. Chan School of Public Health, Department of Nutrition, Harvard University, Boston, Massachusetts, United States of America
| | - Barry I. Freedman
- Nephrology, Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Philippe Froguel
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
- Department of Genomics of Common Disease, Imperial College London, London, United Kingdom
| | - Paolo Gasparini
- Institute for Maternal and Child Health—IRCCS "Burlo Garofolo", Trieste, Italy
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Jost Bruno Jonas
- Beijing Institute of Ophthalmology, Beijing Ophthalmology and Visual Science Key Lab, Beijing Tongren Eye Center, Capital Medical University, Beijing, China
- Department of Ophthalmology, Medical Faculty Mannheim, University Heidelberg, Mannheim, Germany, Germany
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Jaspal S. Kooner
- Department of Cardiology, Ealing Hospital, Middlesex, United Kingdom
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
- MRC-PHE Centre for Environment and Health, Department of Epidemiology & Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Zoltán Kutalik
- Swiss Instititute of Bioinformatics, Lausanne, Switzerland
- Institute of Social and Preventive Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Cathy C. Laurie
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Karin Leander
- Unit of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center—Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | | | - Patrik K. E. Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Stockholm, Sweden
| | - Albertine J. Oldehinkel
- Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Brenda W. J. H. Penninx
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health Research Institute, VU University Medical Center, Amsterdam, The Netherlands
| | - Ozren Polasek
- Department of Public Health, Department of Medicine, University of Split, Split, Croatia
- Psychiatric Hospital "Sveti Ivan", Zagreb, Croatia
- Gen-info Ltd, Zagreb, Croatia
| | - David J. Porteous
- Centre for Genomic & Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Rainer Rauramaa
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Nilesh J. Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - James Scott
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lynne E. Wagenknecht
- Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | | | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, Oxfordshire, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - David R. Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, Michigan, United States of America
| | | | - Tangchun Wu
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health for Incubating, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, Louisiana, United States of America
| | - Kaare Christensen
- The Danish Aging Research Center, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Michele K. Evans
- Health Disparities Research Section, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Bernardo L. Horta
- Postgraduate Programme in Epidemiology, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yongmei Liu
- Public Health Sciences, Epidemiology and Prevention, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
| | - Alexandre C. Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, SP, Brazil
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Epidemiology, Medicine and Health Services, University of Washington, Seattle, Washington, United States of America
- Kaiser Permanente Washington, Health Research Institute, Seattle, Washington, United States of America
| | - Paul M. Ridker
- Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rob M. van Dam
- Saw Swee Hock School of Public Health, National University Health System and National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - W. James Gauderman
- Biostatistics, Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Xiaofeng Zhu
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Dennis O. Mook-Kanamori
- Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - L. Adrienne Cupples
- Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
- The Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Tanika N. Kelly
- Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
| | - Ervin R. Fox
- Cardiology, Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Cornelia M. van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National University Health System and National University of Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Charles Kooperberg
- Fred Hutchinson Cancer Research Center, University of Washington School of Public Health, Seattle, Washington, United States of America
| | - Walter Palmas
- Medicine, Columbia University Medical Center, New York, New York, United States of America
| | - Kenneth Rice
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Paul Elliott
- MRC-PHE Centre for Environment and Health, Department of Epidemiology & Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Mark J. Caulfield
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- NIHR Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, London, London, United Kingdom
| | - Patricia B. Munroe
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- NIHR Barts Cardiovascular Biomedical Research Unit, Queen Mary University of London, London, London, United Kingdom
| | - Dabeeru C. Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michael A. Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Daniel Levy
- The Framingham Heart Study, Framingham, Massachusetts, United States of America
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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Michalska A, Blaszczyk K, Wesoly J, Bluyssen HAR. A Positive Feedback Amplifier Circuit That Regulates Interferon (IFN)-Stimulated Gene Expression and Controls Type I and Type II IFN Responses. Front Immunol 2018; 9:1135. [PMID: 29892288 PMCID: PMC5985295 DOI: 10.3389/fimmu.2018.01135] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/07/2018] [Indexed: 12/14/2022] Open
Abstract
Interferon (IFN)-I and IFN-II both induce IFN-stimulated gene (ISG) expression through Janus kinase (JAK)-dependent phosphorylation of signal transducer and activator of transcription (STAT) 1 and STAT2. STAT1 homodimers, known as γ-activated factor (GAF), activate transcription in response to all types of IFNs by direct binding to IFN-II activation site (γ-activated sequence)-containing genes. Association of interferon regulatory factor (IRF) 9 with STAT1–STAT2 heterodimers [known as interferon-stimulated gene factor 3 (ISGF3)] or with STAT2 homodimers (STAT2/IRF9) in response to IFN-I, redirects these complexes to a distinct group of target genes harboring the interferon-stimulated response element (ISRE). Similarly, IRF1 regulates expression of ISGs in response to IFN-I and IFN-II by directly binding the ISRE or IRF-responsive element. In addition, evidence is accumulating for an IFN-independent and -dependent role of unphosphorylated STAT1 and STAT2, with or without IRF9, and IRF1 in basal as well as long-term ISG expression. This review provides insight into the existence of an intracellular amplifier circuit regulating ISG expression and controlling long-term cellular responsiveness to IFN-I and IFN-II. The exact timely steps that take place during IFN-activated feedback regulation and the control of ISG transcription and long-term cellular responsiveness to IFN-I and IFN-II is currently not clear. Based on existing literature and our novel data, we predict the existence of a multifaceted intracellular amplifier circuit that depends on unphosphorylated and phosphorylated ISGF3 and GAF complexes and IRF1. In a combinatorial and timely fashion, these complexes mediate prolonged ISG expression and control cellular responsiveness to IFN-I and IFN-II. This proposed intracellular amplifier circuit also provides a molecular explanation for the existing overlap between IFN-I and IFN-II activated ISG expression.
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Affiliation(s)
- Agata Michalska
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Katarzyna Blaszczyk
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Joanna Wesoly
- Laboratory of High Throughput Technologies, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Hans A R Bluyssen
- Department of Human Molecular Genetics, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
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Schmitz ML, Shaban MS, Albert BV, Gökçen A, Kracht M. The Crosstalk of Endoplasmic Reticulum (ER) Stress Pathways with NF-κB: Complex Mechanisms Relevant for Cancer, Inflammation and Infection. Biomedicines 2018; 6:biomedicines6020058. [PMID: 29772680 PMCID: PMC6027367 DOI: 10.3390/biomedicines6020058] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 05/08/2018] [Accepted: 05/11/2018] [Indexed: 02/07/2023] Open
Abstract
Stressful conditions occuring during cancer, inflammation or infection activate adaptive responses that are controlled by the unfolded protein response (UPR) and the nuclear factor of kappa light polypeptide gene enhancer in B-cells (NF-κB) signaling pathway. These systems can be triggered by chemical compounds but also by cytokines, toll-like receptor ligands, nucleic acids, lipids, bacteria and viruses. Despite representing unique signaling cascades, new data indicate that the UPR and NF-κB pathways converge within the nucleus through ten major transcription factors (TFs), namely activating transcription factor (ATF)4, ATF3, CCAAT/enhancer-binding protein (CEBP) homologous protein (CHOP), X-box-binding protein (XBP)1, ATF6α and the five NF-κB subunits. The combinatorial occupancy of numerous genomic regions (enhancers and promoters) coordinates the transcriptional activation or repression of hundreds of genes that collectively determine the balance between metabolic and inflammatory phenotypes and the extent of apoptosis and autophagy or repair of cell damage and survival. Here, we also discuss results from genetic experiments and chemical activators of endoplasmic reticulum (ER) stress that suggest a link to the cytosolic inhibitor of NF-κB (IκB)α degradation pathway. These data show that the UPR affects this major control point of NF-κB activation through several mechanisms. Taken together, available evidence indicates that the UPR and NF-κB interact at multiple levels. This crosstalk provides ample opportunities to fine-tune cellular stress responses and could also be exploited therapeutically in the future.
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Affiliation(s)
- M Lienhard Schmitz
- Institute of Biochemistry, Justus Liebig University Giessen, D-35392 Giessen, Germany.
| | - M Samer Shaban
- Rudolf-Buchheim-Institute of Pharmacology, Justus Liebig University Giessen, D-35392 Giessen, Germany.
| | - B Vincent Albert
- Rudolf-Buchheim-Institute of Pharmacology, Justus Liebig University Giessen, D-35392 Giessen, Germany.
| | - Anke Gökçen
- Rudolf-Buchheim-Institute of Pharmacology, Justus Liebig University Giessen, D-35392 Giessen, Germany.
| | - Michael Kracht
- Rudolf-Buchheim-Institute of Pharmacology, Justus Liebig University Giessen, D-35392 Giessen, Germany.
- Rudolf-Buchheim-Institute of Pharmacology, Universities of Giessen and Marburg Lung Center (UGMLC), Schubertstrasse 81, D-35392 Giessen, Germany.
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57
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Li T, Liu Q, Garza N, Kornblau S, Jin VX. Integrative analysis reveals functional and regulatory roles of H3K79me2 in mediating alternative splicing. Genome Med 2018; 10:30. [PMID: 29665865 PMCID: PMC5902843 DOI: 10.1186/s13073-018-0538-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/29/2018] [Indexed: 01/26/2023] Open
Abstract
Background Accumulating evidence suggests alternative splicing (AS) is a co-transcriptional splicing process not only controlled by RNA-binding splicing factors, but also mediated by epigenetic regulators, such as chromatin structure, nucleosome density, and histone modification. Aberrant AS plays an important role in regulating various diseases, including cancers. Methods In this study, we integrated AS events derived from RNA-seq with H3K79me2 ChIP-seq data across 34 different normal and cancer cell types and found the higher enrichment of H3K79me2 in two AS types, skipping exon (SE) and alternative 3′ splice site (A3SS). Results Interestingly, by applying self-organizing map (SOM) clustering, we unveiled two clusters mainly comprised of blood cancer cell types with a strong correlation between H3K79me2 and SE. Remarkably, the expression of transcripts associated with SE was not significantly different from that of those not associated with SE, indicating the involvement of H3K79me2 in splicing has little impact on full mRNA transcription. We further showed that the deletion of DOT1L1, the sole H3K79 methyltransferase, impeded leukemia cell proliferation as well as switched exon skipping to the inclusion isoform in two MLL-rearranged acute myeloid leukemia cell lines. Our data demonstrate H3K79me2 was involved in mediating SE processing, which might in turn influence transformation and disease progression in leukemias. Conclusions Collectively, our work for the first time reveals that H3K79me2 plays functional and regulatory roles through a co-transcriptional splicing mechanism. Electronic supplementary material The online version of this article (10.1186/s13073-018-0538-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tianbao Li
- College of Life Science, Jilin University, Changchun, 130012, China.,Department of Molecular Medicine, University of Texas Health, 8403 Floyd Curl, San Antonio, TX, 78229, USA
| | - Qi Liu
- Department of Molecular Medicine, University of Texas Health, 8403 Floyd Curl, San Antonio, TX, 78229, USA
| | - Nick Garza
- Department of Molecular Medicine, University of Texas Health, 8403 Floyd Curl, San Antonio, TX, 78229, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Steven Kornblau
- Department of Leukemia, UT MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health, 8403 Floyd Curl, San Antonio, TX, 78229, USA.
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58
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Kawalia SB, Raschka T, Naz M, de Matos Simoes R, Senger P, Hofmann-Apitius M. Analytical Strategy to Prioritize Alzheimer's Disease Candidate Genes in Gene Regulatory Networks Using Public Expression Data. J Alzheimers Dis 2018; 59:1237-1254. [PMID: 28800327 PMCID: PMC5611835 DOI: 10.3233/jad-170011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Alzheimer’s disease (AD) progressively destroys cognitive abilities in the aging population with tremendous effects on memory. Despite recent progress in understanding the underlying mechanisms, high drug attrition rates have put a question mark behind our knowledge about its etiology. Re-evaluation of past studies could help us to elucidate molecular-level details of this disease. Several methods to infer such networks exist, but most of them do not elaborate on context specificity and completeness of the generated networks, missing out on lesser-known candidates. In this study, we present a novel strategy that corroborates common mechanistic patterns across large scale AD gene expression studies and further prioritizes potential biomarker candidates. To infer gene regulatory networks (GRNs), we applied an optimized version of the BC3Net algorithm, named BC3Net10, capable of deriving robust and coherent patterns. In principle, this approach initially leverages the power of literature knowledge to extract AD specific genes for generating viable networks. Our findings suggest that AD GRNs show significant enrichment for key signaling mechanisms involved in neurotransmission. Among the prioritized genes, well-known AD genes were prominent in synaptic transmission, implicated in cognitive deficits. Moreover, less intensive studied AD candidates (STX2, HLA-F, HLA-C, RAB11FIP4, ARAP3, AP2A2, ATP2B4, ITPR2, and ATP2A3) are also involved in neurotransmission, providing new insights into the underlying mechanism. To our knowledge, this is the first study to generate knowledge-instructed GRNs that demonstrates an effective way of combining literature-based knowledge and data-driven analysis to identify lesser known candidates embedded in stable and robust functional patterns across disparate datasets.
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Affiliation(s)
- Shweta Bagewadi Kawalia
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin, Germany.,Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn-Aachen International Center for Information Technology, Bonn, Germany
| | - Tamara Raschka
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin, Germany.,University of Applied Sciences Koblenz, RheinAhrCampus, Remagen, Germany
| | - Mufassra Naz
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin, Germany.,Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn-Aachen International Center for Information Technology, Bonn, Germany
| | | | - Philipp Senger
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin, Germany
| | - Martin Hofmann-Apitius
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, Sankt Augustin, Germany.,Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn-Aachen International Center for Information Technology, Bonn, Germany
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59
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Amaral PP, Leonardi T, Han N, Viré E, Gascoigne DK, Arias-Carrasco R, Büscher M, Pandolfini L, Zhang A, Pluchino S, Maracaja-Coutinho V, Nakaya HI, Hemberg M, Shiekhattar R, Enright AJ, Kouzarides T. Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci. Genome Biol 2018; 19:32. [PMID: 29540241 PMCID: PMC5853149 DOI: 10.1186/s13059-018-1405-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/07/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The mammalian genome is transcribed into large numbers of long noncoding RNAs (lncRNAs), but the definition of functional lncRNA groups has proven difficult, partly due to their low sequence conservation and lack of identified shared properties. Here we consider promoter conservation and positional conservation as indicators of functional commonality. RESULTS We identify 665 conserved lncRNA promoters in mouse and human that are preserved in genomic position relative to orthologous coding genes. These positionally conserved lncRNA genes are primarily associated with developmental transcription factor loci with which they are coexpressed in a tissue-specific manner. Over half of positionally conserved RNAs in this set are linked to chromatin organization structures, overlapping binding sites for the CTCF chromatin organiser and located at chromatin loop anchor points and borders of topologically associating domains (TADs). We define these RNAs as topological anchor point RNAs (tapRNAs). Characterization of these noncoding RNAs and their associated coding genes shows that they are functionally connected: they regulate each other's expression and influence the metastatic phenotype of cancer cells in vitro in a similar fashion. Furthermore, we find that tapRNAs contain conserved sequence domains that are enriched in motifs for zinc finger domain-containing RNA-binding proteins and transcription factors, whose binding sites are found mutated in cancers. CONCLUSIONS This work leverages positional conservation to identify lncRNAs with potential importance in genome organization, development and disease. The evidence that many developmental transcription factors are physically and functionally connected to lncRNAs represents an exciting stepping-stone to further our understanding of genome regulation.
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Affiliation(s)
- Paulo P. Amaral
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
| | - Tommaso Leonardi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Namshik Han
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
- Present address: The Milner Therapeutics Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
| | - Emmanuelle Viré
- Present address: MRC Prion Unit, UCL Institute of Neurology, Queen Square House, Queen Square, London, WC1N 3BG UK
| | - Dennis K. Gascoigne
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
| | - Raúl Arias-Carrasco
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Magdalena Büscher
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
| | - Luca Pandolfini
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
| | - Anda Zhang
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Department of Human Genetics, Biomedical Research Building, Miami, FL 33136 USA
| | - Stefano Pluchino
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Vinicius Maracaja-Coutinho
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Helder I. Nakaya
- School of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 580, São Paulo, 05508 Brazil
| | - Martin Hemberg
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Ramin Shiekhattar
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Department of Human Genetics, Biomedical Research Building, Miami, FL 33136 USA
| | - Anton J. Enright
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP UK
| | - Tony Kouzarides
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
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60
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Huang W, Zhang K, Zhu Y, Wang Z, Li Z, Zhang J. Genetic polymorphisms of NOS2 and predisposition to fracture non-union: A case control study based on Han Chinese population. PLoS One 2018. [PMID: 29518099 PMCID: PMC5843262 DOI: 10.1371/journal.pone.0193673] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
A non-union, especially atrophic non-unions, is a permanent failure of healing following a fracture and can be difficult to treat. Approximately 5–10% of fractures will result in a non-union during the healing process. non-unions can be classified into two types: atrophic non-union which is often due to impaired bone healing with a potential biological mechanism, and hypertrophic non-union which is due to inadequate fixation after fracture. Genetic variations also play an important role in the fracture healing response. Previous studies based on animal models have indicated that NOS2 might be greatly involved in the bone fracture healing process. In this case-control study, 346 nonunion patients were compared to 883 patients with normal fracture healing to investigate the potential genetic association between NOS2 and the fracture healing process using study subjects of Chinese Han ancestry. Twenty-seven single nucleotide polymorphisms (SNPs) covering NOS2 were genotyped in our study subjects and analyzed. In addition to the single marker-based analysis, we performed a gene-by-environment analysis to examine the potential interactions between genetic polymorphisms and some environmental factors. SNP rs2297514 showed significant association with the fracture healing process after adjusting for age and gender (OR = 1.38, P = 0.0005). Our results indicated that the T allele of rs2297514 significantly increased the risk of a non-union during the fracture healing process by 38% compared to the C allele. Further stratification analyses conducted for this SNP using data from subgroups classified by different sites of fracture indicated that significance could only be observed in the tibial diaphysis subgroup (N = 428, OR = 1.77, P = 0.0007) but not other groups including femur diaphysis, humeral shaft, ulnar shaft, and femur neck. Gene-by-environment interaction analyses of the three environmental factors showed no significant results. In this study, rs2297514 was significantly associated with the non-union status of fracture healing using a large Chinese population-based study sample. Our findings replicated those of a previous preliminary study and offered strong evidence linking NOS2 and fracture healing.
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Affiliation(s)
- Wei Huang
- Department of Trauma Surgery, Honghui Hospital, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Kun Zhang
- Department of Trauma Surgery, Honghui Hospital, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Yangjun Zhu
- Department of Trauma Surgery, Honghui Hospital, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Zhan Wang
- Department of Trauma Surgery, Honghui Hospital, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Zijun Li
- Department of Trauma Surgery, Honghui Hospital, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
| | - Jun Zhang
- Department of Trauma Surgery, Honghui Hospital, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi, China
- * E-mail:
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61
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Abstract
Transcription is regulated by transcription factor (TF) binding at promoters and distal regulatory elements and histone modifications that control the accessibility of these elements. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become the standard assay for identifying genome-wide protein-DNA interactions in vitro and in vivo. As large-scale ChIP-seq data sets have been collected for different TFs and histone modifications, their potential to predict gene expression can be used to test hypotheses about the mechanisms of gene regulation. In addition, complementary functional genomics assays provide a global view of chromatin accessibility and long-range cis-regulatory interactions that are being combined with TF binding and histone remodeling to study the regulation of gene expression. Thus, ChIP-seq analysis is now widely integrated with other functional genomics assays to better understand gene regulatory mechanisms. In this review, we discuss advances and challenges in integrating ChIP-seq data to identify context-specific chromatin states associated with gene activity. We describe the overall computational design of integrating ChIP-seq data with other functional genomics assays. We also discuss the challenges of extending these methods to low-input ChIP-seq assays and related single-cell assays.
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Affiliation(s)
| | - Ali Mortazavi
- Corresponding author: Ali Mortazavi, Department of Developmental and Cell Biology, 2300 Biological Sciences 3, University of California, Irvine, CA 92697, USA. Tel: (949)824-6762; E-mail:
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62
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Diehl AG, Boyle AP. Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse. Nucleic Acids Res 2018; 46:1878-1894. [PMID: 29361190 PMCID: PMC5829737 DOI: 10.1093/nar/gky018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/15/2017] [Accepted: 01/08/2018] [Indexed: 12/24/2022] Open
Abstract
The mouse is widely used as system to study human genetic mechanisms. However, extensive rewiring of transcriptional regulatory networks often confounds translation of findings between human and mouse. Site-specific gain and loss of individual transcription factor binding sites (TFBS) has caused functional divergence of orthologous regulatory loci, and so we must look beyond this positional conservation to understand common themes of regulatory control. Fortunately, transcription factor co-binding patterns shared across species often perform conserved regulatory functions. These can be compared to 'regulatory sentences' that retain the same meanings regardless of sequence and species context. By analyzing TFBS co-occupancy patterns observed in four human and mouse cell types, we learned a regulatory grammar: the rules by which TFBS are combined into meaningful regulatory sentences. Different parts of this grammar associate with specific sets of functional annotations regardless of sequence conservation and predict functional signatures more accurately than positional conservation. We further show that both species-specific and conserved portions of this grammar are involved in gene expression divergence and human disease risk. These findings expand our understanding of transcriptional regulatory mechanisms, suggesting that phenotypic divergence and disease risk are driven by a complex interplay between deeply conserved and species-specific transcriptional regulatory pathways.
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Affiliation(s)
- Adam G Diehl
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alan P Boyle
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
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63
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Spadafore M, Najarian K, Boyle AP. A proximity-based graph clustering method for the identification and application of transcription factor clusters. BMC Bioinformatics 2017; 18:530. [PMID: 29187152 PMCID: PMC5706350 DOI: 10.1186/s12859-017-1935-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/14/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Transcription factors (TFs) form a complex regulatory network within the cell that is crucial to cell functioning and human health. While methods to establish where a TF binds to DNA are well established, these methods provide no information describing how TFs interact with one another when they do bind. TFs tend to bind the genome in clusters, and current methods to identify these clusters are either limited in scope, unable to detect relationships beyond motif similarity, or not applied to TF-TF interactions. METHODS Here, we present a proximity-based graph clustering approach to identify TF clusters using either ChIP-seq or motif search data. We use TF co-occurrence to construct a filtered, normalized adjacency matrix and use the Markov Clustering Algorithm to partition the graph while maintaining TF-cluster and cluster-cluster interactions. We then apply our graph structure beyond clustering, using it to increase the accuracy of motif-based TFBS searching for an example TF. RESULTS We show that our method produces small, manageable clusters that encapsulate many known, experimentally validated transcription factor interactions and that our method is capable of capturing interactions that motif similarity methods might miss. Our graph structure is able to significantly increase the accuracy of motif TFBS searching, demonstrating that the TF-TF connections within the graph correlate with biological TF-TF interactions. CONCLUSION The interactions identified by our method correspond to biological reality and allow for fast exploration of TF clustering and regulatory dynamics.
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Affiliation(s)
- Maxwell Spadafore
- University of Michigan Medical School, 1301 Catherine, Ann Arbor, 48109-5624 USA
| | - Kayvan Najarian
- University of Michigan Department of Computational Medicine and Bioinformatics, 100 Washtenaw Avenue, Ann Arbor, 48109 USA
- University of Michigan Medical School Department of Emergency Medicine, 1500 E Medical Center Drive, Ann Arbor, 48109 USA
| | - Alan P. Boyle
- University of Michigan Department of Computational Medicine and Bioinformatics, 100 Washtenaw Avenue, Ann Arbor, 48109 USA
- University of Michigan Department of Genetics, 1241 E Catherine, Ann Arbor, 48109 USA
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64
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Ramaker RC, Savic D, Hardigan AA, Newberry K, Cooper GM, Myers RM, Cooper SJ. A genome-wide interactome of DNA-associated proteins in the human liver. Genome Res 2017; 27:1950-1960. [PMID: 29021291 PMCID: PMC5668951 DOI: 10.1101/gr.222083.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022]
Abstract
Large-scale efforts like the ENCODE Project have made tremendous progress in cataloging the genomic binding patterns of DNA-associated proteins (DAPs), such as transcription factors (TFs). However, most chromatin immunoprecipitation-sequencing (ChIP-seq) analyses have focused on a few immortalized cell lines whose activities and physiology differ in important ways from endogenous cells and tissues. Consequently, binding data from primary human tissue are essential to improving our understanding of in vivo gene regulation. Here, we identify and analyze more than 440,000 binding sites using ChIP-seq data for 20 DAPs in two human liver tissue samples. We integrated binding data with transcriptome and phased WGS data to investigate allelic DAP interactions and the impact of heterozygous sequence variation on the expression of neighboring genes. Our tissue-based data set exhibits binding patterns more consistent with liver biology than cell lines, and we describe uses of these data to better prioritize impactful noncoding variation. Collectively, our rich data set offers novel insights into genome function in human liver tissue and provides a valuable resource for assessing disease-related disruptions.
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Affiliation(s)
- Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Daniel Savic
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Kimberly Newberry
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Sara J Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
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65
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Sharafeldin N, Slattery ML, Liu Q, Franco-Villalobos C, Caan BJ, Potter JD, Yasui Y. Multiple Gene-Environment Interactions on the Angiogenesis Gene-Pathway Impact Rectal Cancer Risk and Survival. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 14:ijerph14101146. [PMID: 28956832 PMCID: PMC5664647 DOI: 10.3390/ijerph14101146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/06/2017] [Accepted: 09/23/2017] [Indexed: 12/25/2022]
Abstract
Characterization of gene-environment interactions (GEIs) in cancer is limited. We aimed at identifying GEIs in rectal cancer focusing on a relevant biologic process involving the angiogenesis pathway and relevant environmental exposures: cigarette smoking, alcohol consumption, and animal protein intake. We analyzed data from 747 rectal cancer cases and 956 controls from the Diet, Activity and Lifestyle as a Risk Factor for Rectal Cancer study. We applied a 3-step analysis approach: first, we searched for interactions among single nucleotide polymorphisms on the pathway genes; second, we searched for interactions among the genes, both steps using Logic regression; third, we examined the GEIs significant at the 5% level using logistic regression for cancer risk and Cox proportional hazards models for survival. Permutation-based test was used for multiple testing adjustment. We identified 8 significant GEIs associated with risk among 6 genes adjusting for multiple testing: TNF (OR = 1.85, 95% CI: 1.10, 3.11), TLR4 (OR = 2.34, 95% CI: 1.38, 3.98), and EGR2 (OR = 2.23, 95% CI: 1.04, 4.78) with smoking; IGF1R (OR = 1.69, 95% CI: 1.04, 2.72), TLR4 (OR = 2.10, 95% CI: 1.22, 3.60) and EGR2 (OR = 2.12, 95% CI: 1.01, 4.46) with alcohol; and PDGFB (OR = 1.75, 95% CI: 1.04, 2.92) and MMP1 (OR = 2.44, 95% CI: 1.24, 4.81) with protein. Five GEIs were associated with survival at the 5% significance level but not after multiple testing adjustment: CXCR1 (HR = 2.06, 95% CI: 1.13, 3.75) with smoking; and KDR (HR = 4.36, 95% CI: 1.62, 11.73), TLR2 (HR = 9.06, 95% CI: 1.14, 72.11), EGR2 (HR = 2.45, 95% CI: 1.42, 4.22), and EGFR (HR = 6.33, 95% CI: 1.95, 20.54) with protein. GEIs between angiogenesis genes and smoking, alcohol, and animal protein impact rectal cancer risk. Our results support the importance of considering the biologic hypothesis to characterize GEIs associated with cancer outcomes.
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Affiliation(s)
- Noha Sharafeldin
- School of Public Health, University of Alberta, Edmonton, AB T6G 2R3, Canada.
- Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah Health Sciences Center, Salt Lake City, UT 84132, USA.
| | - Qi Liu
- School of Public Health, University of Alberta, Edmonton, AB T6G 2R3, Canada.
| | | | - Bette J Caan
- Division of Research, Kaiser Permanente Medical Care Program, Oakland, CA 94612, USA.
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA 98195, USA.
- Centre for Public Health Research, Massey University, P.O. Box 756, Wellington 6140, New Zealand.
| | - Yutaka Yasui
- School of Public Health, University of Alberta, Edmonton, AB T6G 2R3, Canada.
- Department of Epidemiology & Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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66
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Jiang Y, Loh YHE, Rajarajan P, Hirayama T, Liao W, Kassim BS, Javidfar B, Hartley BJ, Kleofas L, Park RB, Labonte B, Ho SM, Chandrasekaran S, Do C, Ramirez BR, Peter CJ, C W JT, Safaie BM, Morishita H, Roussos P, Nestler EJ, Schaefer A, Tycko B, Brennand KJ, Yagi T, Shen L, Akbarian S. The methyltransferase SETDB1 regulates a large neuron-specific topological chromatin domain. Nat Genet 2017; 49:1239-1250. [PMID: 28671686 PMCID: PMC5560095 DOI: 10.1038/ng.3906] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/05/2017] [Indexed: 12/14/2022]
Abstract
We report locus-specific disintegration of megabase-scale chromosomal conformations in brain after neuronal ablation of Kmt1e/Setdb1 histone H3-lysine 9 methyltransferase, including a large topologically associated 1.2Mb domain conserved in human and mouse and encompassing >70 genes at the clustered Protocadherin (cPcdh) locus. TADcPcdh in mutant neurons showed abnormal accumulations of CTCF transcriptional regulator and 3D genome organizer at cryptic binding sites, converted into permissive state with DNA cytosine hypomethylation and histone hyperacetylation. Broadly upregulated expression across cPcdh included defective S-type Protocadherin single-cell stochastic constraint. Setdb1-dependent loop formations, bypassing 0.2–1Mb of linear genome, radiated from TADPcdh fringes towards cPcdh cis-regulatory sequences, counterbalanced shorter-range facilitative promoter-enhancer contacts and carried loop-bound polymorphisms associated with genetic risk for schizophrenia. We show that KRAB-zinc finger Setdb1 repressor complex, shielding neuronal 3D genomes from excess CTCF binding, is critically required for structural maintenance of TADcPcdh.
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Affiliation(s)
- Yan Jiang
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yong-Hwee Eddie Loh
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Prashanth Rajarajan
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Teruyoshi Hirayama
- Kokoro-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Will Liao
- New York Genome Center, New York, New York, USA
| | - Bibi S Kassim
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Behnam Javidfar
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Brigham J Hartley
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lisa Kleofas
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Royce B Park
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Benoit Labonte
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Seok-Man Ho
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sandhya Chandrasekaran
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Catherine Do
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, Columbia University, New York, New York, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Brianna R Ramirez
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Cyril J Peter
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Julia T C W
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Brian M Safaie
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hirofumi Morishita
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Panos Roussos
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Mental Illness Research, Education and Clinical Center, James J. Peters Virginia Medical Center, New York, New York, USA
| | - Eric J Nestler
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anne Schaefer
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Benjamin Tycko
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, Columbia University, New York, New York, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA
| | - Kristen J Brennand
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Takeshi Yagi
- Kokoro-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Li Shen
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Schahram Akbarian
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Dubois-Chevalier J, Dubois V, Dehondt H, Mazrooei P, Mazuy C, Sérandour AA, Gheeraert C, Guillaume P, Baugé E, Derudas B, Hennuyer N, Paumelle R, Marot G, Carroll JS, Lupien M, Staels B, Lefebvre P, Eeckhoute J. The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions. Genome Res 2017; 27:985-996. [PMID: 28400425 PMCID: PMC5453331 DOI: 10.1101/gr.217075.116] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 04/05/2017] [Indexed: 02/06/2023]
Abstract
Control of gene transcription relies on concomitant regulation by multiple transcriptional regulators (TRs). However, how recruitment of a myriad of TRs is orchestrated at cis-regulatory modules (CRMs) to account for coregulation of specific biological pathways is only partially understood. Here, we have used mouse liver CRMs involved in regulatory activities of the hepatic TR, NR1H4 (FXR; farnesoid X receptor), as our model system to tackle this question. Using integrative cistromic, epigenomic, transcriptomic, and interactomic analyses, we reveal a logical organization where trans-regulatory modules (TRMs), which consist of subsets of preferentially and coordinately corecruited TRs, assemble into hierarchical combinations at hepatic CRMs. Different combinations of TRMs add to a core TRM, broadly found across the whole landscape of CRMs, to discriminate promoters from enhancers. These combinations also specify distinct sets of CRM differentially organized along the genome and involved in regulation of either housekeeping/cellular maintenance genes or liver-specific functions. In addition to these TRMs which we define as obligatory, we show that facultative TRMs, such as one comprising core circadian TRs, are further recruited to selective subsets of CRMs to modulate their activities. TRMs transcend TR classification into ubiquitous versus liver-identity factors, as well as TR grouping into functional families. Hence, hierarchical superimpositions of obligatory and facultative TRMs bring about independent transcriptional regulatory inputs defining different sets of CRMs with logical connection to regulation of specific gene sets and biological pathways. Altogether, our study reveals novel principles of concerted transcriptional regulation by multiple TRs at CRMs.
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Affiliation(s)
- Julie Dubois-Chevalier
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Vanessa Dubois
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Hélène Dehondt
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Parisa Mazrooei
- The Princess Margaret Cancer Centre, University Health Network, Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Claire Mazuy
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Aurélien A Sérandour
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Céline Gheeraert
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Penderia Guillaume
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Eric Baugé
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Bruno Derudas
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Nathalie Hennuyer
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Réjane Paumelle
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Guillemette Marot
- Université Lille, MODAL Team, Inria Lille-Nord Europe, 59650 Villeneuve-d'Ascq, France
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Mathieu Lupien
- The Princess Margaret Cancer Centre, University Health Network, Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Bart Staels
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Philippe Lefebvre
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Jérôme Eeckhoute
- Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
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Xie Y, Li HF, Sun L, Kusner LL, Wang S, Meng Y, Zhang X, Hong Y, Gao X, Li Y, Kaminski HJ. The Role of Osteopontin and Its Gene on Glucocorticoid Response in Myasthenia Gravis. Front Neurol 2017; 8:230. [PMID: 28620344 PMCID: PMC5450020 DOI: 10.3389/fneur.2017.00230] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 05/11/2017] [Indexed: 12/12/2022] Open
Abstract
Biomarkers that assess treatment response for patients with the autoimmune disorder, myasthenia gravis (MG), have not been evaluated to a significant extent. We hypothesized the pro-inflammatory cytokine, osteopontin (OPN), may be associated with variability of response to glucocorticoids (GCs) in patients with MG. A cohort of 250 MG patients treated with standardized protocol of GCs was recruited, and plasma OPN and polymorphisms of its gene, secreted phosphoprotein 1 (SPP1), were evaluated. Mean OPN levels were higher in patients compared to healthy controls. Carriers of rs11728697*T allele (allele definition: one of two or more alternative forms of a gene) were more frequent in the poorly GC responsive group compared to the GC responsive group indicating an association of rs11728697*T allele with GC non-responsiveness. One risk haplotype (AGTACT) was identified associated with GC non-responsiveness compared with GC responsive MG group. Genetic variations of SPP1 were found associated with the response to GC among MG patients.
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Affiliation(s)
- Yanchen Xie
- Department of Neurology, The George Washington University, Washington, DC, United States.,Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Hai-Feng Li
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, China
| | - Liang Sun
- The Key Laboratory of Geriatrics, Beijing Hospital, Beijing Institute of Geriatrics, Ministry of Health, Beijing, China
| | - Linda L Kusner
- Department of Pharmacology, The George Washington University, Washington, DC, United States.,Department of Physiology, The George Washington University, Washington, DC, United States
| | - Shuhui Wang
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Yunxiao Meng
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Beijing, China
| | - Xu Zhang
- Department of Neurology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yu Hong
- Department of Neurology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiang Gao
- Department of Neurology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yao Li
- Department of Neurology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Henry J Kaminski
- Department of Neurology, The George Washington University, Washington, DC, United States.,Department of Pharmacology, The George Washington University, Washington, DC, United States.,Department of Physiology, The George Washington University, Washington, DC, United States
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69
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Suske G. NF-Y and SP transcription factors — New insights in a long-standing liaison. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:590-597. [DOI: 10.1016/j.bbagrm.2016.08.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/18/2016] [Accepted: 08/24/2016] [Indexed: 12/31/2022]
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70
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Doan TB, Graham JD, Clarke CL. Emerging functional roles of nuclear receptors in breast cancer. J Mol Endocrinol 2017; 58:R169-R190. [PMID: 28087820 DOI: 10.1530/jme-16-0082] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 01/12/2017] [Indexed: 12/13/2022]
Abstract
Nuclear receptors (NRs) have been targets of intensive drug development for decades due to their roles as key regulators of multiple developmental, physiological and disease processes. In breast cancer, expression of the estrogen and progesterone receptor remains clinically important in predicting prognosis and determining therapeutic strategies. More recently, there is growing evidence supporting the involvement of multiple nuclear receptors other than the estrogen and progesterone receptors, in the regulation of various processes important to the initiation and progression of breast cancer. We review new insights into the mechanisms of action of NRs made possible by recent advances in genomic technologies and focus on the emerging functional roles of NRs in breast cancer biology, including their involvement in circadian regulation, metabolic reprogramming and breast cancer migration and metastasis.
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Affiliation(s)
- Tram B Doan
- Westmead Institute for Medical ResearchSydney Medical School - Westmead, University of Sydney, Sydney, New South Wales, Australia
| | - J Dinny Graham
- Westmead Institute for Medical ResearchSydney Medical School - Westmead, University of Sydney, Sydney, New South Wales, Australia
| | - Christine L Clarke
- Westmead Institute for Medical ResearchSydney Medical School - Westmead, University of Sydney, Sydney, New South Wales, Australia
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71
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Zhang TX, Saccone NL, Bierut LJ, Rice JP. Targeted sequencing identifies genetic polymorphisms of flavin-containing monooxygenase genes contributing to susceptibility of nicotine dependence in European American and African American. Brain Behav 2017; 7:e00651. [PMID: 28413702 PMCID: PMC5390834 DOI: 10.1002/brb3.651] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 11/27/2016] [Accepted: 12/22/2016] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Smoking is a leading cause of preventable death. Early studies based on samples of twins have linked the lifetime smoking practices to genetic predisposition. The flavin-containing monooxygenase (FMO) protein family consists of a group of enzymes that metabolize drugs and xenobiotics. Both FMO1 and FMO3 were potentially susceptible genes for nicotine metabolism process. METHODS In this study, we investigated the potential of FMO genes to confer risk of nicotine dependence via deep targeted sequencing in 2,820 study subjects comprising 1,583 nicotine dependents and 1,237 controls from European American and African American. Specifically, we focused on the two genomic segments including FMO1,FMO3, and pseudo gene FMO6P, and aimed to investigate the potential association between FMO genes and nicotine dependence. Both common and low-frequency/rare variants were analyzed using different algorithms. The potential functional significance of SNPs with association signal was investigated with relevant bioinformatics tools. RESULTS We identified different clusters of significant common variants in European (with most significant SNP rs6674596, p = .0004, OR = 0.67, MAF_EA = 0.14, FMO1) and African Americans (with the most significant SNP rs6608453, p = .001, OR = 0.64, MAF_AA = 0.1, FMO6P). No significant signals were identified through haplotype-based analyses. Gene network investigation indicated that both FMO1 and FMO3 have a strong relation with a variety of genes belonging to CYP gene families (with combined score greater than 0.9). Most of the significant variants identified were SNPs located within intron regions or with unknown functional significance, indicating a need for future work to understand the underlying functional significance of these signals. CONCLUSIONS Our findings indicated significant association between FMO genes and nicotine dependence. Replications of our findings in other ethnic groups were needed in the future. Most of the significant variants identified were SNPs located within intronic regions or with unknown functional significance, indicating a need for future work to understand the underlying functional significance of these signals.
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Affiliation(s)
- Tian-Xiao Zhang
- Department of Psychiatry Washington University School of Medicine St. Louis MO USA
| | - Nancy L Saccone
- Department of Genetics Washington University School of Medicine St. Louis MO USA
| | - Laura J Bierut
- Department of Psychiatry Washington University School of Medicine St. Louis MO USA
| | - John P Rice
- Department of Psychiatry Washington University School of Medicine St. Louis MO USA
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72
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Abou El Hassan M, Huang K, Eswara MBK, Xu Z, Yu T, Aubry A, Ni Z, Livne-Bar I, Sangwan M, Ahmad M, Bremner R. Properties of STAT1 and IRF1 enhancers and the influence of SNPs. BMC Mol Biol 2017; 18:6. [PMID: 28274199 PMCID: PMC5343312 DOI: 10.1186/s12867-017-0084-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/02/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND STAT1 and IRF1 collaborate to induce interferon-γ (IFNγ) stimulated genes (ISGs), but the extent to which they act alone or together is unclear. The effect of single nucleotide polymorphisms (SNPs) on in vivo binding is also largely unknown. RESULTS We show that IRF1 binds at proximal or distant ISG sites twice as often as STAT1, increasing to sixfold at the MHC class I locus. STAT1 almost always bound with IRF1, while most IRF1 binding events were isolated. Dual binding sites at remote or proximal enhancers distinguished ISGs that were responsive to IFNγ versus cell-specific resistant ISGs, which showed fewer and mainly single binding events. Surprisingly, inducibility in one cell type predicted ISG-responsiveness in other cells. Several dbSNPs overlapped with STAT1 and IRF1 binding motifs, and we developed methodology to rapidly assess their effects. We show that in silico prediction of SNP effects accurately reflects altered binding both in vitro and in vivo. CONCLUSIONS These data reveal broad cooperation between STAT1 and IRF1, explain cell type specific differences in ISG-responsiveness, and identify genetic variants that may participate in the pathogenesis of immune disorders.
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Affiliation(s)
- Mohamed Abou El Hassan
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, ON, Canada.,Clinical Chemistry Division, Provincial Laboratory Services, Queen Elizabeth Hospital, Charlottetown, PE, Canada.,Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Katherine Huang
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, ON, Canada
| | - Manoja B K Eswara
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, ON, Canada
| | - Zhaodong Xu
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, ON, Canada
| | - Tao Yu
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, ON, Canada
| | - Arthur Aubry
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, ON, Canada
| | - Zuyao Ni
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, ON, Canada.,Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Izzy Livne-Bar
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, ON, Canada
| | - Monika Sangwan
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, ON, Canada
| | - Mohamad Ahmad
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, ON, Canada
| | - Rod Bremner
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Toronto, ON, Canada. .,Department of Lab Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada. .,Department of Ophthalmology and Vision Science, University of Toronto, Toronto, ON, Canada.
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73
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Abstract
Schizophrenia (SZ) is a debilitating brain disorder with a complex genetic architecture. Genetic studies, especially recent genome-wide association studies (GWAS), have identified multiple variants (loci) conferring risk to SZ. However, how to efficiently extract meaningful biological information from bulk genetic findings of SZ remains a major challenge. There is a pressing need to integrate multiple layers of data from various sources, eg, genetic findings from GWAS, copy number variations (CNVs), association and linkage studies, gene expression, protein-protein interaction (PPI), co-expression, expression quantitative trait loci (eQTL), and Encyclopedia of DNA Elements (ENCODE) data, to provide a comprehensive resource to facilitate the translation of genetic findings into SZ molecular diagnosis and mechanism study. Here we developed the SZDB database (http://www.szdb.org/), a comprehensive resource for SZ research. SZ genetic data, gene expression data, network-based data, brain eQTL data, and SNP function annotation information were systematically extracted, curated and deposited in SZDB. In-depth analyses and systematic integration were performed to identify top prioritized SZ genes and enriched pathways. Multiple types of data from various layers of SZ research were systematically integrated and deposited in SZDB. In-depth data analyses and integration identified top prioritized SZ genes and enriched pathways. We further showed that genes implicated in SZ are highly co-expressed in human brain and proteins encoded by the prioritized SZ risk genes are significantly interacted. The user-friendly SZDB provides high-confidence candidate variants and genes for further functional characterization. More important, SZDB provides convenient online tools for data search and browse, data integration, and customized data analyses.
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Affiliation(s)
- Yong Wu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China;,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China;,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China;,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China,YGY and XJL are co-corresponding authors who jointly directed this work
| | - Xiong-Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China;,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China;,YGY and XJL are co-corresponding authors who jointly directed this work
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74
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Qin Q, Feng J. Imputation for transcription factor binding predictions based on deep learning. PLoS Comput Biol 2017; 13:e1005403. [PMID: 28234893 PMCID: PMC5345877 DOI: 10.1371/journal.pcbi.1005403] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 03/10/2017] [Accepted: 02/09/2017] [Indexed: 01/11/2023] Open
Abstract
Understanding the cell-specific binding patterns of transcription factors (TFs) is fundamental to studying gene regulatory networks in biological systems, for which ChIP-seq not only provides valuable data but is also considered as the gold standard. Despite tremendous efforts from the scientific community to conduct TF ChIP-seq experiments, the available data represent only a limited percentage of ChIP-seq experiments, considering all possible combinations of TFs and cell lines. In this study, we demonstrate a method for accurately predicting cell-specific TF binding for TF-cell line combinations based on only a small fraction (4%) of the combinations using available ChIP-seq data. The proposed model, termed TFImpute, is based on a deep neural network with a multi-task learning setting to borrow information across transcription factors and cell lines. Compared with existing methods, TFImpute achieves comparable accuracy on TF-cell line combinations with ChIP-seq data; moreover, TFImpute achieves better accuracy on TF-cell line combinations without ChIP-seq data. This approach can predict cell line specific enhancer activities in K562 and HepG2 cell lines, as measured by massively parallel reporter assays, and predicts the impact of SNPs on TF binding. Transcription factors play a central role in regulating various cellular processes. They bind to DNA in a cell-specific way. To study where a TF would bind to DNA, ChIP-seq experiment has been developed and widely adopted by the science community to study genome-wide in vivo protein-DNA interactions. However, for each TF, only a limited number of cell types have been explored by ChIP-seq experiments. To study the binding of a TF to a DNA sequence in a cell line without corresponding ChIP-seq data, researchers would check whether there is a motif for the TF in the sequence. However, motif alone contains only sequence information and therefore cannot reflect the cell specificity of TF binding. In this work, we demonstrate how to model the TF binding problem using deep learning and achieve cell specific binding prediction for TF-cell line combinations without ChIP-seq data.
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Affiliation(s)
- Qian Qin
- Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jianxing Feng
- Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, China
- * E-mail:
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75
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Rodríguez-Martínez JA, Reinke AW, Bhimsaria D, Keating AE, Ansari AZ. Combinatorial bZIP dimers display complex DNA-binding specificity landscapes. eLife 2017; 6:e19272. [PMID: 28186491 PMCID: PMC5349851 DOI: 10.7554/elife.19272] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 02/06/2017] [Indexed: 01/06/2023] Open
Abstract
How transcription factor dimerization impacts DNA-binding specificity is poorly understood. Guided by protein dimerization properties, we examined DNA binding specificities of 270 human bZIP pairs. DNA interactomes of 80 heterodimers and 22 homodimers revealed that 72% of heterodimer motifs correspond to conjoined half-sites preferred by partnering monomers. Remarkably, the remaining motifs are composed of variably-spaced half-sites (12%) or 'emergent' sites (16%) that cannot be readily inferred from half-site preferences of partnering monomers. These binding sites were biochemically validated by EMSA-FRET analysis and validated in vivo by ChIP-seq data from human cell lines. Focusing on ATF3, we observed distinct cognate site preferences conferred by different bZIP partners, and demonstrated that genome-wide binding of ATF3 is best explained by considering many dimers in which it participates. Importantly, our compendium of bZIP-DNA interactomes predicted bZIP binding to 156 disease associated SNPs, of which only 20 were previously annotated with known bZIP motifs.
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Affiliation(s)
| | - Aaron W Reinke
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Devesh Bhimsaria
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
- Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, Unites States
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Aseem Z Ansari
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
- The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, United States
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Garaeva AF, Babushkina NP, Rudko AA, Goncharova IA, Bragina EY, Freidin MB. Differential genetic background of primary and secondary tuberculosis in Russians. Meta Gene 2017. [DOI: 10.1016/j.mgene.2016.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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77
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Guo Y, Gifford DK. Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding. BMC Genomics 2017; 18:45. [PMID: 28061806 PMCID: PMC5219757 DOI: 10.1186/s12864-016-3434-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 12/19/2016] [Indexed: 11/25/2022] Open
Abstract
Background The combinatorial binding of trans-acting factors (TFs) to the DNA is critical to the spatial and temporal specificity of gene regulation. For certain regulatory regions, more than one regulatory module (set of TFs that bind together) are combined to achieve context-specific gene regulation. However, previous approaches are limited to either pairwise TF co-association analysis or assuming that only one module is used in each regulatory region. Results We present a new computational approach that models the modular organization of TF combinatorial binding. Our method learns compact and coherent regulatory modules from in vivo binding data using a topic model. We found that the binding of 115 TFs in K562 cells can be organized into 49 interpretable modules. Furthermore, we found that tens of thousands of regulatory regions use multiple modules, a structure that cannot be observed with previous hard clustering based methods. The modules discovered recapitulate many published protein-protein physical interactions, have consistent functional annotations of chromatin states, and uncover context specific co-binding such as gene proximal binding of NFY + FOS + SP and distal binding of NFY + FOS + USF. For certain TFs, the co-binding partners of direct binding (motif present) differs from those of indirect binding (motif absent); the distinct set of co-binding partners can predict whether the TF binds directly or indirectly with up to 95% accuracy. Joint analysis across two cell types reveals both cell-type-specific and shared regulatory modules. Conclusions Our results provide comprehensive cell-type-specific combinatorial binding maps and suggest a modular organization of combinatorial binding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3434-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuchun Guo
- MIT, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, 02139, USA
| | - David K Gifford
- MIT, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, 02139, USA.
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78
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Wong KC, Peng C, Yan S, Liang C. Probabilistic Inference on Multiple Normalized Genome-Wide Signal Profiles With Model Regularization. IEEE Trans Nanobioscience 2016; 16:43-50. [PMID: 27893398 DOI: 10.1109/tnb.2016.2631406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Understanding genome-wide protein-DNA interaction signals forms the basis for further focused studies in gene regulation. In particular, the chromatin immunoprecipitation with massively parallel DNA sequencing technology (ChIP-Seq) can enable us to measure the in vivo genome-wide occupancy of the DNA-binding protein of interest in a single run. Multiple ChIP-Seq runs thus inherent the potential for us to decipher the combinatorial occupancies of multiple DNA-binding proteins. To handle the genome-wide signal profiles from those multiple runs, we propose to integrate regularized regression functions (i.e., LASSO, Elastic Net, and Ridge Regression) into the well-established SignalRanker and FullSignalRanker frameworks, resulting in six additional probabilistic models for inference on multiple normalized genome-wide signal profiles. The corresponding model training algorithms are devised with computational complexity analysis. Comprehensive benchmarking is conducted to demonstrate and compare the performance of nine related probabilistic models on the ENCODE ChIP-Seq datasets. The results indicate that the regularized SignalRanker models, in contrast to the original SignalRanker models, can demonstrate excellent inference performance comparable to the FullSignalRanker models with low model complexities and time complexities. Such a feature is especially valuable in the context of the rapidly growing genome-wide signal profile data in the recent years.
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79
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Abstract
Chromatin immunoprecipitation followed by sequencing is an invaluable assay for identifying the genomic binding sites of transcription factors. However, transcription factors rarely bind chromatin alone but often bind together with other cofactors, forming protein complexes. Here, we describe a computational method that integrates multiple ChIP-seq and RNA-seq datasets to discover protein complexes and determine their role as activators or repressors. This chapter outlines a detailed computational pipeline for discovering and predicting binding partners from ChIP-seq data and inferring their role in regulating gene expression. This work aims at developing hypotheses about gene regulation via binding partners and deciphering the combinatorial nature of DNA-binding proteins.
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80
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Hanson C, Cairns J, Wang L, Sinha S. Computational discovery of transcription factors associated with drug response. THE PHARMACOGENOMICS JOURNAL 2016; 16:573-582. [PMID: 26503816 PMCID: PMC4848185 DOI: 10.1038/tpj.2015.74] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 08/04/2015] [Accepted: 08/07/2015] [Indexed: 02/01/2023]
Abstract
This study integrates gene expression, genotype and drug response data in lymphoblastoid cell lines with transcription factor (TF)-binding sites from ENCODE (Encyclopedia of Genomic Elements) in a novel methodology that elucidates regulatory contexts associated with cytotoxicity. The method, GENMi (Gene Expression iN the Middle), postulates that single-nucleotide polymorphisms within TF-binding sites putatively modulate its regulatory activity, and the resulting variation in gene expression leads to variation in drug response. Analysis of 161 TFs and 24 treatments revealed 334 significantly associated TF-treatment pairs. Investigation of 20 selected pairs yielded literature support for 13 of these associations, often from studies where perturbation of the TF expression changes drug response. Experimental validation of significant GENMi associations in taxanes and anthracyclines across two triple-negative breast cancer cell lines corroborates our findings. The method is shown to be more sensitive than an alternative, genome-wide association study-based approach that does not use gene expression. These results demonstrate the utility of GENMi in identifying TFs that influence drug response and provide a number of candidates for further testing.
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Affiliation(s)
- C Hanson
- Department of Computer Science, University of Illinois at Urbana–Champaign, Urbana, IL, USA
| | - J Cairns
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - L Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - S Sinha
- Department of Computer Science and Institute of Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL, USA
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81
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Haubrock M, Hartmann F, Wingender E. NF-Y Binding Site Architecture Defines a C-Fos Targeted Promoter Class. PLoS One 2016; 11:e0160803. [PMID: 27517874 PMCID: PMC4982600 DOI: 10.1371/journal.pone.0160803] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/25/2016] [Indexed: 12/27/2022] Open
Abstract
ChIP-seq experiments detect the chromatin occupancy of known transcription factors in a genome-wide fashion. The comparisons of several species-specific ChIP-seq libraries done for different transcription factors have revealed a complex combinatorial and context-specific co-localization behavior for the identified binding regions. In this study we have investigated human derived ChIP-seq data to identify common cis-regulatory principles for the human transcription factor c-Fos. We found that in four different cell lines, c-Fos targeted proximal and distal genomic intervals show prevalences for either AP-1 motifs or CCAAT boxes as known binding motifs for the transcription factor NF-Y, and thereby act in a mutually exclusive manner. For proximal regions of co-localized c-Fos and NF-YB binding, we gathered evidence that a characteristic configuration of repeating CCAAT motifs may be responsible for attracting c-Fos, probably provided by a nearby AP-1 bound enhancer. Our results suggest a novel regulatory function of NF-Y in gene-proximal regions. Specific CCAAT dimer repeats bound by the transcription factor NF-Y define this novel cis-regulatory module. Based on this behavior we propose a new enhancer promoter interaction model based on AP-1 motif defined enhancers which interact with CCAAT-box characterized promoter regions.
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Affiliation(s)
- Martin Haubrock
- Institute of Bioinformatics, University Medical Center Göttingen (UMG), Georg-August-University Göttingen, Goldschmidtstrasse 1, 37077 Göttingen, Germany
- * E-mail:
| | - Fabian Hartmann
- Institute of Bioinformatics, University Medical Center Göttingen (UMG), Georg-August-University Göttingen, Goldschmidtstrasse 1, 37077 Göttingen, Germany
| | - Edgar Wingender
- Institute of Bioinformatics, University Medical Center Göttingen (UMG), Georg-August-University Göttingen, Goldschmidtstrasse 1, 37077 Göttingen, Germany
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82
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Beagrie RA, Pombo A. Gene activation by metazoan enhancers: Diverse mechanisms stimulate distinct steps of transcription. Bioessays 2016; 38:881-93. [PMID: 27452946 DOI: 10.1002/bies.201600032] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Enhancers can stimulate transcription by a number of different mechanisms which control different stages of the transcription cycle of their target genes, from recruitment of the transcription machinery to elongation by RNA polymerase. These mechanisms may not be mutually exclusive, as a single enhancer may act through different pathways by binding multiple transcription factors. Multiple enhancers may also work together to regulate transcription of a shared target gene. Most of the evidence supporting different enhancer mechanisms comes from the study of single genes, but new high-throughput experimental frameworks offer the opportunity to integrate and generalize disparate mechanisms identified at single genes. This effort is especially important if we are to fully understand how sequence variation within enhancers contributes to human disease.
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Affiliation(s)
- Robert A Beagrie
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin-Buch, Germany
| | - Ana Pombo
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin-Buch, Germany
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83
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A high-resolution transcriptome map of cell cycle reveals novel connections between periodic genes and cancer. Cell Res 2016; 26:946-62. [PMID: 27364684 DOI: 10.1038/cr.2016.84] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 12/16/2015] [Accepted: 03/22/2016] [Indexed: 12/16/2022] Open
Abstract
Progression through the cell cycle is largely dependent on waves of periodic gene expression, and the regulatory networks for these transcriptome dynamics have emerged as critical points of vulnerability in various aspects of tumor biology. Through RNA-sequencing of human cells during two continuous cell cycles (>2.3 billion paired reads), we identified over 1 000 mRNAs, non-coding RNAs and pseudogenes with periodic expression. Periodic transcripts are enriched in functions related to DNA metabolism, mitosis, and DNA damage response, indicating these genes likely represent putative cell cycle regulators. Using our set of periodic genes, we developed a new approach termed "mitotic trait" that can classify primary tumors and normal tissues by their transcriptome similarity to different cell cycle stages. By analyzing >4 000 tumor samples in The Cancer Genome Atlas (TCGA) and other expression data sets, we found that mitotic trait significantly correlates with genetic alterations, tumor subtype and, notably, patient survival. We further defined a core set of 67 genes with robust periodic expression in multiple cell types. Proteins encoded by these genes function as major hubs of protein-protein interaction and are mostly required for cell cycle progression. The core genes also have unique chromatin features including increased levels of CTCF/RAD21 binding and H3K36me3. Loss of these features in uterine and kidney cancers is associated with altered expression of the core 67 genes. Our study suggests new chromatin-associated mechanisms for periodic gene regulation and offers a predictor of cancer patient outcomes.
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84
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Ye BY, Shen WL, Wang D, Li P, Zhang Z, Shi ML, Zhang Y, Zhang FX, Zhao ZH. ZNF143 is involved in CTCF-mediated chromatin interactions by cooperation with cohesin and other partners. Mol Biol 2016. [DOI: 10.1134/s0026893316030031] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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85
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Di Narzo AF, Peters LA, Argmann C, Stojmirovic A, Perrigoue J, Li K, Telesco S, Kidd B, Walker J, Dudley J, Cho J, Schadt EE, Kasarskis A, Curran M, Dobrin R, Hao K. Blood and Intestine eQTLs from an Anti-TNF-Resistant Crohn's Disease Cohort Inform IBD Genetic Association Loci. Clin Transl Gastroenterol 2016; 7:e177. [PMID: 27336838 PMCID: PMC4931595 DOI: 10.1038/ctg.2016.34] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 04/15/2016] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES: Genome-wide association studies (GWAS) have identified loci reproducibly associated with inflammatory bowel disease (IBD) and other immune-mediated diseases; however, the molecular mechanisms underlying most of genetic susceptibility remain undefined. Expressional quantitative trait loci (eQTL) of disease-relevant tissue can be employed in order to elucidate the genes and pathways affected by disease-specific genetic variance. METHODS: In this study, we derived eQTLs for human whole blood and intestine tissues of anti-tumor necrosis factor-resistant Crohn's disease (CD) patients. We interpreted these eQTLs in the context of published IBD GWAS hits to inform on the disease process. RESULTS: At 10% false discovery rate, we discovered that 5,174 genes in blood and 2,063 genes in the intestine were controlled by a nearby single-nucleotide polymorphism (SNP) (i.e., cis-eQTL), among which 1,360 were shared between the two tissues. A large fraction of the identified eQTLs were supported by the regulomeDB database, showing that the eQTLs reside in regulatory elements (odds ratio; OR=3.44 and 3.24 for blood and intestine eQTLs, respectively) as opposed to protein-coding regions. Published IBD GWAS hits as a whole were enriched for blood and intestine eQTLs (OR=2.88 and 2.05; and P value=2.51E-9 and 0.013, respectively), thereby linking genetic susceptibility to control of gene expression in these tissues. Through a systematic search, we used eQTL data to inform 109 out of 372 IBD GWAS SNPs documented in National Human Genome Research Institute catalog, and we categorized the genes influenced by eQTLs according to their functions. Many of these genes have experimentally validated roles in specific cell types contributing to intestinal inflammation. CONCLUSIONS: The blood and intestine eQTLs described in this study represent a powerful tool to link GWAS loci to a regulatory function and thus elucidate the mechanisms underlying the genetic loci associated with IBD and related conditions. Overall, our eQTL discovery approach empirically identifies the disease-associated variants including their impact on the direction and extent of expression changes in the context of disease-relevant cellular pathways in order to infer the functional outcome of this aspect of genetic susceptibility.
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Affiliation(s)
- Antonio F Di Narzo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lauren A Peters
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | - Katherine Li
- Janssen R&D, LLC, 1400 McKean Road, Spring House, PA, USA
| | | | - Brian Kidd
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jennifer Walker
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Joel Dudley
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Judy Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mark Curran
- Janssen R&D, LLC, 1400 McKean Road, Spring House, PA, USA
| | - Radu Dobrin
- Janssen R&D, LLC, 1400 McKean Road, Spring House, PA, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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86
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Wang Y, Jiang R, Wong WH. Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data. Natl Sci Rev 2016; 3:240-251. [PMID: 28690910 DOI: 10.1093/nsr/nww025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cell packs a lot of genetic and regulatory information through a structure known as chromatin, i.e. DNA is wrapped around histone proteins and is tightly packed in a remarkable way. To express a gene in a specific coding region, the chromatin would open up and DNA loop may be formed by interacting enhancers and promoters. Furthermore, the mediator and cohesion complexes, sequence-specific transcription factors, and RNA polymerase II are recruited and work together to elaborately regulate the expression level. It is in pressing need to understand how the information, about when, where, and to what degree genes should be expressed, is embedded into chromatin structure and gene regulatory elements. Thanks to large consortia such as Encyclopedia of DNA Elements (ENCODE) and Roadmap Epigenomic projects, extensive data on chromatin accessibility and transcript abundance are available across many tissues and cell types. This rich data offer an exciting opportunity to model the causal regulatory relationship. Here, we will review the current experimental approaches, foundational data, computational problems, interpretive frameworks, and integrative models that will enable the accurate interpretation of regulatory landscape. Particularly, we will discuss the efforts to organize, analyze, model, and integrate the DNA accessibility data, transcriptional data, and functional genomic regions together. We believe that these efforts will eventually help us understand the information flow within the cell and will influence research directions across many fields.
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Affiliation(s)
- Yong Wang
- Department of Statistics, Department of Biomedical Data Science, Bio-X Program, Stanford University, Stanford, CA 94305, USA.,Academy of Mathematics and Systems Science, National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing 100080, China
| | - Rui Jiang
- Department of Statistics, Department of Biomedical Data Science, Bio-X Program, Stanford University, Stanford, CA 94305, USA.,MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Wing Hung Wong
- Department of Statistics, Department of Biomedical Data Science, Bio-X Program, Stanford University, Stanford, CA 94305, USA
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87
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Dolfini D, Zambelli F, Pedrazzoli M, Mantovani R, Pavesi G. A high definition look at the NF-Y regulome reveals genome-wide associations with selected transcription factors. Nucleic Acids Res 2016; 44:4684-702. [PMID: 26896797 PMCID: PMC4889920 DOI: 10.1093/nar/gkw096] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 02/09/2016] [Indexed: 12/11/2022] Open
Abstract
NF-Y is a trimeric transcription factor (TF), binding the CCAAT box element, for which several results suggest a pioneering role in activation of transcription. In this work, we integrated 380 ENCODE ChIP-Seq experiments for 154 TFs and cofactors with sequence analysis, protein–protein interactions and RNA profiling data, in order to identify genome-wide regulatory modules resulting from the co-association of NF-Y with other TFs. We identified three main degrees of co-association with NF-Y for sequence-specific TFs. In the most relevant one, we found TFs having a significant overlap with NF-Y in their DNA binding loci, some with a precise spacing of binding sites with respect to the CCAAT box, others (FOS, Sp1/2, RFX5, IRF3, PBX3) mostly lacking their canonical binding site and bound to arrays of well spaced CCAAT boxes. As expected, NF-Y binding also correlates with RNA Pol II General TFs and with subunits of complexes involved in the control of H3K4 methylations. Co-association patterns are confirmed by protein–protein interactions, and correspond to specific functional categorizations and expression level changes of target genes following NF-Y inactivation. These data define genome-wide rules for the organization of NF-Y-centered regulatory modules, supporting a model of distinct categorization and synergy with well defined sets of TFs.
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Affiliation(s)
- Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Via Celoria 26, 20133, Italy
| | - Federico Zambelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Via Celoria 26, 20133, Italy Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Bari, Via Amendola 165/A, 70126, Italy
| | - Maurizio Pedrazzoli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Via Celoria 26, 20133, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Via Celoria 26, 20133, Italy
| | - Giulio Pavesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Via Celoria 26, 20133, Italy
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88
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Xu C, Corces VG. Towards a predictive model of chromatin 3D organization. Semin Cell Dev Biol 2015; 57:24-30. [PMID: 26658098 DOI: 10.1016/j.semcdb.2015.11.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 11/24/2015] [Accepted: 11/26/2015] [Indexed: 01/19/2023]
Abstract
Architectural proteins mediate interactions between distant regions in the genome to bring together different regulatory elements while establishing a specific three-dimensional organization of the genetic material. Depletion of specific architectural proteins leads to miss regulation of gene expression and alterations in nuclear organization. The specificity of interactions mediated by architectural proteins depends on the nature, number, and orientation of their binding site at individual genomic locations. Knowledge of the mechanisms and rules governing interactions among architectural proteins may provide a code to predict the 3D organization of the genome.
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Affiliation(s)
- Chenhuan Xu
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA
| | - Victor G Corces
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA.
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89
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Liu L, Zhao W, Zhou X. Modeling co-occupancy of transcription factors using chromatin features. Nucleic Acids Res 2015; 44:e49. [PMID: 26590261 PMCID: PMC4797273 DOI: 10.1093/nar/gkv1281] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 11/04/2015] [Indexed: 12/11/2022] Open
Abstract
Regulation of gene expression requires both transcription factor (TFs) and epigenetic modifications, and interplays between the two types of factors have been discovered. However study of relationships between chromatin features and TF–TF co-occupancy remains limited. Here, we revealed the relationship by first illustrating distinct profile patterns of chromatin features related to different binding events, including single TF binding and TF–TF co-occupancy of 71 TFs from five human cell lines. We further implemented statistical analyses to demonstrate the relationship by accurately predicting co-occupancy genome-widely using chromatin features including DNase I hypersensitivity, 11 histone modifications (HMs) and GC content. Remarkably, our results showed that the combination of chromatin features enables accurate predictions across the five cells. For individual chromatin features, DNase I enables high and consistent predictions. H3K27ac, H3K4me 2, H3K4me3 and H3K9ac are more reliable predictors than other HMs. Although the combination of 11 HMs achieves accurate predictions, their predictive ability varies considerably when a model obtained from one cell is applied to others, indicating relationship between HMs and TF–TF co-occupancy is cell type dependent. GC content is not a reliable predictor, but the addition of GC content to any other features enhances their predictive ability. Together, our results elucidate a strong relationship between TF–TF co-occupancy and chromatin features.
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Affiliation(s)
- Liang Liu
- Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Weiling Zhao
- Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Xiaobo Zhou
- Center for Bioinformatics and Systems Biology, Department of Radiology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
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90
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Wong KC, Peng C, Li Y. Probabilistic Inference on Multiple Normalized Signal Profiles from Next Generation Sequencing: Transcription Factor Binding Sites. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:1416-1428. [PMID: 26671811 DOI: 10.1109/tcbb.2015.2424421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
With the prevalence of chromatin immunoprecipitation (ChIP) with sequencing (ChIP-Seq) technology, massive ChIP-Seq data has been accumulated. The ChIP-Seq technology measures the genome-wide occupancy of DNA-binding proteins in vivo. It is well-known that different DNA-binding protein occupancies may result in a gene being regulated in different conditions (e.g. different cell types). To fully understand a gene's function, it is essential to develop probabilistic models on multiple ChIP-Seq profiles for deciphering the gene transcription causalities. In this work, we propose and describe two probabilistic models. Assuming the conditional independence of different DNA-binding proteins' occupancies, the first method (SignalRanker) is developed as an intuitive method for ChIP-Seq genome-wide signal profile inference. Unfortunately, such an assumption may not always hold in some gene regulation cases. Thus, we propose and describe another method (FullSignalRanker) which does not make the conditional independence assumption. The proposed methods are compared with other existing methods on ENCODE ChIP-Seq datasets, demonstrating its regression and classification ability. The results suggest that FullSignalRanker is the best-performing method for recovering the signal ranks on the promoter and enhancer regions. In addition, FullSignalRanker is also the best-performing method for peak sequence classification. We envision that SignalRanker and FullSignalRanker will become important in the era of next generation sequencing. FullSignalRanker program is available on the following website: http://www.cs.toronto.edu/~wkc/FullSignalRanker/.
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91
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Cenik C, Cenik ES, Byeon GW, Grubert F, Candille SI, Spacek D, Alsallakh B, Tilgner H, Araya CL, Tang H, Ricci E, Snyder MP. Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans. Genome Res 2015; 25:1610-21. [PMID: 26297486 PMCID: PMC4617958 DOI: 10.1101/gr.193342.115] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 08/20/2015] [Indexed: 11/24/2022]
Abstract
Elucidating the consequences of genetic differences between humans is essential for understanding phenotypic diversity and personalized medicine. Although variation in RNA levels, transcription factor binding, and chromatin have been explored, little is known about global variation in translation and its genetic determinants. We used ribosome profiling, RNA sequencing, and mass spectrometry to perform an integrated analysis in lymphoblastoid cell lines from a diverse group of individuals. We find significant differences in RNA, translation, and protein levels suggesting diverse mechanisms of personalized gene expression control. Combined analysis of RNA expression and ribosome occupancy improves the identification of individual protein level differences. Finally, we identify genetic differences that specifically modulate ribosome occupancy—many of these differences lie close to start codons and upstream ORFs. Our results reveal a new level of gene expression variation among humans and indicate that genetic variants can cause changes in protein levels through effects on translation.
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Affiliation(s)
- Can Cenik
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Elif Sarinay Cenik
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Gun W Byeon
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Fabian Grubert
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Sophie I Candille
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Damek Spacek
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Bilal Alsallakh
- Institute of Software Technology and Interactive Systems, Vienna University of Technology, A-140 Vienna, Austria
| | - Hagen Tilgner
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Carlos L Araya
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Emiliano Ricci
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; CIRI, International Center for Infectiology Research, Eukaryotic and Viral Translation Team, Université de Lyon, INSERM U1111, Lyon, 69634, France
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
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92
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Niskanen EA, Malinen M, Sutinen P, Toropainen S, Paakinaho V, Vihervaara A, Joutsen J, Kaikkonen MU, Sistonen L, Palvimo JJ. Global SUMOylation on active chromatin is an acute heat stress response restricting transcription. Genome Biol 2015; 16:153. [PMID: 26259101 PMCID: PMC4531811 DOI: 10.1186/s13059-015-0717-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 07/06/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Cells have developed many ways to cope with external stress. One distinctive feature in acute proteotoxic stresses, such as heat shock (HS), is rapid post-translational modification of proteins by SUMOs (small ubiquitin-like modifier proteins; SUMOylation). While many of the SUMO targets are chromatin proteins, there is scarce information on chromatin binding of SUMOylated proteins in HS and the role of chromatin SUMOylation in the regulation of transcription. RESULTS We mapped HS-induced genome-wide changes in chromatin occupancy of SUMO-2/3-modified proteins in K562 and VCaP cells using ChIP-seq. Chromatin SUMOylation was further correlated with HS-induced global changes in transcription using GRO-seq and RNA polymerase II (Pol2) ChIP-seq along with ENCODE data for K562 cells. HS induced a rapid and massive rearrangement of chromatin SUMOylation pattern: SUMOylation was gained at active promoters and enhancers associated with multiple transcription factors, including heat shock factor 1. Concomitant loss of SUMOylation occurred at inactive intergenic chromatin regions that were associated with CTCF-cohesin complex and SETDB1 methyltransferase complex. In addition, HS triggered a dynamic chromatin binding of SUMO ligase PIAS1, especially onto promoters. The HS-induced SUMOylation on chromatin was most notable at promoters of transcribed genes where it positively correlated with active transcription and Pol2 promoter-proximal pausing. Furthermore, silencing of SUMOylation machinery either by depletion of UBC9 or PIAS1 enhanced expression of HS-induced genes. CONCLUSIONS HS-triggered SUMOylation targets promoters and enhancers of actively transcribed genes where it restricts the transcriptional activity of the HS-induced genes. PIAS1-mediated promoter SUMOylation is likely to regulate Pol2-associated factors in HS.
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Affiliation(s)
- Einari A Niskanen
- Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland.
| | - Marjo Malinen
- Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland.
| | - Päivi Sutinen
- Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland.
| | - Sari Toropainen
- Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland.
| | - Ville Paakinaho
- Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland. .,Present Address: Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Building 41, 41 Library Drive, Bethesda, MD, 20892, USA.
| | - Anniina Vihervaara
- Department of Biosciences, Åbo Akademi University, Turku, Finland. .,Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, P.O. Box 123, FI-20521, Turku, Finland.
| | - Jenny Joutsen
- Department of Biosciences, Åbo Akademi University, Turku, Finland. .,Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, P.O. Box 123, FI-20521, Turku, Finland.
| | - Minna U Kaikkonen
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland.
| | - Lea Sistonen
- Department of Biosciences, Åbo Akademi University, Turku, Finland. .,Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, P.O. Box 123, FI-20521, Turku, Finland.
| | - Jorma J Palvimo
- Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland.
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93
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Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 2015; 523:486-90. [PMID: 26083756 PMCID: PMC4685948 DOI: 10.1038/nature14590] [Citation(s) in RCA: 1322] [Impact Index Per Article: 146.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/26/2015] [Indexed: 12/15/2022]
Abstract
Cell-to-cell variation is a universal feature of life that impacts a wide range of biological phenomena, from developmental plasticity1,2 to tumor heterogeneity3. While recent advances have improved our ability to document cellular phenotypic variation4–8 the fundamental mechanisms that generate variability from identical DNA sequences remain elusive. Here we reveal the landscape and principles of cellular DNA regulatory variation by developing a robust method for mapping the accessible genome of individual cells via assay for transposase-accessible chromatin using sequencing (ATAC-seq). Single-cell ATAC-seq (scATAC-seq) maps from hundreds of single-cells in aggregate closely resemble accessibility profiles from tens of millions of cells and provides insights into cell-to-cell variation. Accessibility variance is systematically associated with specific trans-factors and cis-elements, and we discover combinations of trans-factors associated with either induction or suppression of cell-to-cell variability. We further identify sets of trans-factors associated with cell-type specific accessibility variance across 8 cell types. Targeted perturbations of cell cycle or transcription factor signaling evoke stimulus-specific changes in this observed variability. The pattern of accessibility variation in cis across the genome recapitulates chromosome topological domains9de novo, linking single-cell accessibility variation to three-dimensional genome organization. All together, single-cell analysis of DNA accessibility provides new insight into cellular variation of the “regulome.”
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94
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van Luijn MM, Kreft KL, Jongsma ML, Mes SW, Wierenga-Wolf AF, van Meurs M, Melief MJ, der Kant RV, Janssen L, Janssen H, Tan R, Priatel JJ, Neefjes J, Laman JD, Hintzen RQ. Multiple sclerosis-associated CLEC16A controls HLA class II expression via late endosome biogenesis. Brain 2015; 138:1531-47. [PMID: 25823473 DOI: 10.1093/brain/awv080] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 01/26/2015] [Indexed: 01/20/2023] Open
Abstract
C-type lectins are key players in immune regulation by driving distinct functions of antigen-presenting cells. The C-type lectin CLEC16A gene is located at 16p13, a susceptibility locus for several autoimmune diseases, including multiple sclerosis. However, the function of this gene and its potential contribution to these diseases in humans are poorly understood. In this study, we found a strong upregulation of CLEC16A expression in the white matter of multiple sclerosis patients (n = 14) compared to non-demented controls (n = 11), mainly in perivascular leukocyte infiltrates. Moreover, CLEC16A levels were significantly enhanced in peripheral blood mononuclear cells of multiple sclerosis patients (n = 69) versus healthy controls (n = 46). In peripheral blood mononuclear cells, CLEC16A was most abundant in monocyte-derived dendritic cells, in which it strongly co-localized with human leukocyte antigen class II. Treatment of these professional antigen-presenting cells with vitamin D, a key protective environmental factor in multiple sclerosis, downmodulated CLEC16A in parallel with human leukocyte antigen class II. Knockdown of CLEC16A in distinct types of model and primary antigen-presenting cells resulted in severely impaired cytoplasmic distribution and formation of human leucocyte antigen class II-positive late endosomes, as determined by immunofluorescence and electron microscopy. Mechanistically, CLEC16A participated in the molecular machinery of human leukocyte antigen class II-positive late endosome formation and trafficking to perinuclear regions, involving the dynein motor complex. By performing co-immunoprecipitations, we found that CLEC16A directly binds to two critical members of this complex, RILP and the HOPS complex. CLEC16A silencing in antigen-presenting cells disturbed RILP-mediated recruitment of human leukocyte antigen class II-positive late endosomes to perinuclear regions. Together, we identify CLEC16A as a pivotal gene in multiple sclerosis that serves as a direct regulator of the human leukocyte antigen class II pathway in antigen-presenting cells. These findings are a first step in coupling multiple sclerosis-associated genes to the regulation of the strongest genetic factor in multiple sclerosis, human leukocyte antigen class II.
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Affiliation(s)
- Marvin M van Luijn
- 1 Department of Immunology and MS Center ErasMS, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Karim L Kreft
- 2 Department of Neurology and MS Center ErasMS, Erasmus MC, University Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - Marlieke L Jongsma
- 3 Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Steven W Mes
- 1 Department of Immunology and MS Center ErasMS, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Annet F Wierenga-Wolf
- 1 Department of Immunology and MS Center ErasMS, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Marjan van Meurs
- 1 Department of Immunology and MS Center ErasMS, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Marie-José Melief
- 1 Department of Immunology and MS Center ErasMS, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Rik van der Kant
- 3 Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Lennert Janssen
- 3 Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Hans Janssen
- 3 Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Rusung Tan
- 4 Department of Pathology, Sidra Medical and Research Center, Doha, Qatar 5 BC Children's Hospital and Department of Pathology and Laboratory Medicine, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - John J Priatel
- 5 BC Children's Hospital and Department of Pathology and Laboratory Medicine, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Jacques Neefjes
- 3 Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Jon D Laman
- 1 Department of Immunology and MS Center ErasMS, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Rogier Q Hintzen
- 2 Department of Neurology and MS Center ErasMS, Erasmus MC, University Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
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95
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Bailey SD, Zhang X, Desai K, Aid M, Corradin O, Cowper-Sal Lari R, Akhtar-Zaidi B, Scacheri PC, Haibe-Kains B, Lupien M. ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters. Nat Commun 2015; 2:6186. [PMID: 25645053 PMCID: PMC4431651 DOI: 10.1038/ncomms7186] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 12/30/2014] [Indexed: 12/21/2022] Open
Abstract
Chromatin interactions connect distal regulatory elements to target gene promoters
guiding stimulus- and lineage-specific transcription. Few factors securing chromatin
interactions have so far been identified. Here, by integrating chromatin interaction
maps with the large collection of transcription factor-binding profiles provided by
the ENCODE project, we demonstrate that the zinc-finger protein ZNF143 preferentially occupies anchors of
chromatin interactions connecting promoters with distal regulatory elements. It
binds directly to promoters and associates with lineage-specific chromatin
interactions and gene expression. Silencing ZNF143 or modulating its DNA-binding affinity using
single-nucleotide polymorphisms (SNPs) as a surrogate of site-directed mutagenesis
reveals the sequence dependency of chromatin interactions at gene promoters. We also
find that chromatin interactions alone do not regulate gene expression. Together,
our results identify ZNF143 as a
novel chromatin-looping factor that contributes to the architectural foundation of
the genome by providing sequence specificity at promoters connected with distal
regulatory elements. Chromatin interactions can connect distal regulatory elements to
promoters via protein factors, but few such factors have been identified. Here, the
authors show that zinc-finger protein ZNF143 is a sequence-specific chromatin-looping
factor that connects promoters with distal regulatory elements.
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Affiliation(s)
- Swneke D Bailey
- The Princess Margaret Cancer Centre-University Health Network, Toronto, M5G 1L7, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Ontario, Canada
| | - Xiaoyang Zhang
- Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, 03755, New Hampshire, USA.,Present address: Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Kinjal Desai
- Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, 03755, New Hampshire, USA
| | - Malika Aid
- Bioinformatics and Computational Genomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, H2W 1R7, Quebec, Canada
| | - Olivia Corradin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, 44106, Ohio, USA
| | - Richard Cowper-Sal Lari
- The Princess Margaret Cancer Centre-University Health Network, Toronto, M5G 1L7, Ontario, Canada.,Present address: The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
| | - Batool Akhtar-Zaidi
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, 44106, Ohio, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, 44106, Ohio, USA.,Present address: Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02142, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, 44106, Ohio, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, 44106, Ohio, USA
| | - Benjamin Haibe-Kains
- The Princess Margaret Cancer Centre-University Health Network, Toronto, M5G 1L7, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Ontario, Canada.,Bioinformatics and Computational Genomics Laboratory, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, H2W 1R7, Quebec, Canada
| | - Mathieu Lupien
- The Princess Margaret Cancer Centre-University Health Network, Toronto, M5G 1L7, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Ontario, Canada. .,Ontario Institute for Cancer Research, Toronto, M5G 1L7, Ontario, Canada.
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96
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Narasimhan K, Pillay S, Huang YH, Jayabal S, Udayasuryan B, Veerapandian V, Kolatkar P, Cojocaru V, Pervushin K, Jauch R. DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors. Nucleic Acids Res 2015; 43:1513-28. [PMID: 25578969 PMCID: PMC4330359 DOI: 10.1093/nar/gku1390] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Sox2 and Pax6 are transcription factors that direct cell fate decision during neurogenesis, yet the mechanism behind how they cooperate on enhancer DNA elements and regulate gene expression is unclear. By systematically interrogating Sox2 and Pax6 interaction on minimal enhancer elements, we found that cooperative DNA recognition relies on combinatorial nucleotide switches and precisely spaced, but cryptic composite DNA motifs. Surprisingly, all tested Sox and Pax paralogs have the capacity to cooperate on such enhancer elements. NMR and molecular modeling reveal very few direct protein-protein interactions between Sox2 and Pax6, suggesting that cooperative binding is mediated by allosteric interactions propagating through DNA structure. Furthermore, we detected and validated several novel sites in the human genome targeted cooperatively by Sox2 and Pax6. Collectively, we demonstrate that Sox-Pax partnerships have the potential to substantially alter DNA target specificities and likely enable the pleiotropic and context-specific action of these cell-lineage specifiers.
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Affiliation(s)
- Kamesh Narasimhan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Shubhadra Pillay
- Genome Regulation Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences,190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Yong-Heng Huang
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Sriram Jayabal
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada Integrated Program in Neuroscience, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Barath Udayasuryan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Veeramohan Veerapandian
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, Singapore 138672, Singapore University of Chinese Academy of Sciences, No. 19A Yuquanlu, Beijing 100049, China
| | - Prasanna Kolatkar
- Qatar Biomedical Research Institute, Qatar Foundation, PO Box 5825, Doha, Qatar
| | - Vlad Cojocaru
- Computational Structural Biology Laboratory, Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - Konstantin Pervushin
- Genome Regulation Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences,190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Ralf Jauch
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, Singapore 138672, Singapore
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97
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Griffon A, Barbier Q, Dalino J, van Helden J, Spicuglia S, Ballester B. Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape. Nucleic Acids Res 2014; 43:e27. [PMID: 25477382 PMCID: PMC4344487 DOI: 10.1093/nar/gku1280] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The large collections of ChIP-seq data rapidly accumulating in public data warehouses provide genome-wide binding site maps for hundreds of transcription factors (TFs). However, the extent of the regulatory occupancy space in the human genome has not yet been fully apprehended by integrating public ChIP-seq data sets and combining it with ENCODE TFs map. To enable genome-wide identification of regulatory elements we have collected, analysed and retained 395 available ChIP-seq data sets merged with ENCODE peaks covering a total of 237 TFs. This enhanced repertoire complements and refines current genome-wide occupancy maps by increasing the human genome regulatory search space by 14% compared to ENCODE alone, and also increases the complexity of the regulatory dictionary. As a direct application we used this unified binding repertoire to annotate variant enhancer loci (VELs) from H3K4me1 mark in two cancer cell lines (MCF-7, CRC) and observed enrichments of specific TFs involved in biological key functions to cancer development and proliferation. Those enrichments of TFs within VELs provide a direct annotation of non-coding regions detected in cancer genomes. Finally, full access to this catalogue is available online together with the TFs enrichment analysis tool (http://tagc.univ-mrs.fr/remap/).
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Affiliation(s)
- Aurélien Griffon
- INSERM, UMR1090 TAGC, Marseille, F-13288, France Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288, France
| | - Quentin Barbier
- INSERM, UMR1090 TAGC, Marseille, F-13288, France Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288, France
| | - Jordi Dalino
- INSERM, UMR1090 TAGC, Marseille, F-13288, France Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288, France
| | - Jacques van Helden
- INSERM, UMR1090 TAGC, Marseille, F-13288, France Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288, France
| | - Salvatore Spicuglia
- INSERM, UMR1090 TAGC, Marseille, F-13288, France Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288, France
| | - Benoit Ballester
- INSERM, UMR1090 TAGC, Marseille, F-13288, France Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288, France
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98
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Heidari N, Phanstiel DH, He C, Grubert F, Jahanbani F, Kasowski M, Zhang MQ, Snyder MP. Genome-wide map of regulatory interactions in the human genome. Genome Res 2014; 24:1905-17. [PMID: 25228660 PMCID: PMC4248309 DOI: 10.1101/gr.176586.114] [Citation(s) in RCA: 205] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 09/11/2014] [Indexed: 01/09/2023]
Abstract
Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. Bound regions covered 80% of DNase I hypersensitive sites including 99.7% of TSS and 98% of enhancers. Correlating this map with ChIP-seq and RNA-seq data sets revealed cohesin, CTCF, and ZNF143 as key components of three-dimensional chromatin structure and revealed how the distal chromatin state affects gene transcription. Comparison of interactions between cell types revealed that enhancer-promoter interactions were highly cell-type-specific. Construction and comparison of distal and proximal regulatory networks revealed stark differences in structure and biological function. Proximal binding events are enriched at genes with housekeeping functions, while distal binding events interact with genes involved in dynamic biological processes including response to stimulus. This study reveals new mechanistic and functional insights into regulatory region organization in the nucleus.
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Affiliation(s)
- Nastaran Heidari
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Douglas H Phanstiel
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Chao He
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Fabian Grubert
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Fereshteh Jahanbani
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Maya Kasowski
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Michael Q Zhang
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China; Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Richardson, Texas 75080-3021, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA;
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99
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Regulatory analysis of the C. elegans genome with spatiotemporal resolution. Nature 2014; 512:400-5. [PMID: 25164749 PMCID: PMC4530805 DOI: 10.1038/nature13497] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 05/22/2014] [Indexed: 12/17/2022]
Abstract
Discovering the structure and dynamics of transcriptional regulatory events in the genome with cellular and temporal resolution is crucial to understanding the regulatory underpinnings of development and disease. We determined the genomic distribution of binding sites for 92 transcription factors (TFs) and regulatory proteins across multiple stages of C. elegans development by performing 241 ChIP-seq experiments. Integrating regulatory binding and cellular-resolution expression data yielded a spatiotemporally-resolved metazoan TF binding map. Using this map, we explore developmental regulatory circuits that encode combinatorial logic at the levels of co-binding and co-expression of TFs, characterizing (1) the genomic coverage and clustering of regulatory binding, (2) the binding preferences of and biological processes regulated by TFs, (3) the global TF co-associations and genomic subdomains that suggest shared patterns of regulation, and (4) key TFs and TF co-associations for fate specification of individual lineages and cell-types.
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100
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Comparative analysis of regulatory information and circuits across distant species. Nature 2014; 512:453-6. [PMID: 25164757 PMCID: PMC4336544 DOI: 10.1038/nature13668] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 07/10/2014] [Indexed: 12/20/2022]
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.
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