1
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Lippert C, Sabatini R, Maher MC, Kang EY, Lee S, Arikan O, Harley A, Bernal A, Garst P, Lavrenko V, Yocum K, Wong T, Zhu M, Yang WY, Chang C, Lu T, Lee CWH, Hicks B, Ramakrishnan S, Tang H, Xie C, Piper J, Brewerton S, Turpaz Y, Telenti A, Roby RK, Och FJ, Venter JC. Identification of individuals by trait prediction using whole-genome sequencing data. Proc Natl Acad Sci U S A 2017; 114:10166-10171. [PMID: 28874526 PMCID: PMC5617305 DOI: 10.1073/pnas.1711125114] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Prediction of human physical traits and demographic information from genomic data challenges privacy and data deidentification in personalized medicine. To explore the current capabilities of phenotype-based genomic identification, we applied whole-genome sequencing, detailed phenotyping, and statistical modeling to predict biometric traits in a cohort of 1,061 participants of diverse ancestry. Individually, for a large fraction of the traits, their predictive accuracy beyond ancestry and demographic information is limited. However, we have developed a maximum entropy algorithm that integrates multiple predictions to determine which genomic samples and phenotype measurements originate from the same person. Using this algorithm, we have reidentified an average of >8 of 10 held-out individuals in an ethnically mixed cohort and an average of 5 of either 10 African Americans or 10 Europeans. This work challenges current conceptions of personal privacy and may have far-reaching ethical and legal implications.
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Affiliation(s)
| | | | | | | | | | - Okan Arikan
- Human Longevity, Inc., Mountain View, CA 94303
| | | | - Axel Bernal
- Human Longevity, Inc., Mountain View, CA 94303
| | - Peter Garst
- Human Longevity, Inc., Mountain View, CA 94303
| | | | - Ken Yocum
- Human Longevity, Inc., Mountain View, CA 94303
| | | | - Mingfu Zhu
- Human Longevity, Inc., Mountain View, CA 94303
| | | | - Chris Chang
- Human Longevity, Inc., Mountain View, CA 94303
| | - Tim Lu
- Human Longevity, Inc., San Diego, CA 92121
| | | | - Barry Hicks
- Human Longevity, Inc., Mountain View, CA 94303
| | | | - Haibao Tang
- Human Longevity, Inc., Mountain View, CA 94303
| | - Chao Xie
- Human Longevity Singapore, Pte. Ltd., Singapore 138542
| | - Jason Piper
- Human Longevity Singapore, Pte. Ltd., Singapore 138542
| | | | - Yaron Turpaz
- Human Longevity, Inc., San Diego, CA 92121
- Human Longevity Singapore, Pte. Ltd., Singapore 138542
| | | | - Rhonda K Roby
- Human Longevity, Inc., San Diego, CA 92121
- J. Craig Venter Institute, La Jolla, CA 92037
| | - Franz J Och
- Human Longevity, Inc., Mountain View, CA 94303
| | - J Craig Venter
- Human Longevity, Inc., San Diego, CA 92121;
- J. Craig Venter Institute, La Jolla, CA 92037
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2
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Maurer-Stroh S, Lee CWH, Patel C, Lucero M, Nohynek H, Sung WK, Murad C, Ma J, Hibberd ML, Wong CW, Simões EAF. Comparison of microarray-predicted closest genomes to sequencing for poliovirus vaccine strain similarity and influenza A phylogeny. Diagn Microbiol Infect Dis 2015; 84:203-6. [PMID: 26658310 DOI: 10.1016/j.diagmicrobio.2015.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/30/2015] [Accepted: 11/04/2015] [Indexed: 11/26/2022]
Abstract
We evaluate sequence data from the PathChip high-density hybridization array for epidemiological interpretation of detected pathogens. For influenza A, we derive similar relative outbreak clustering in phylogenetic trees from PathChip-derived compared to classical Sanger-derived sequences. For a positive polio detection, recent infection could be excluded based on vaccine strain similarity.
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Affiliation(s)
- Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), A*STAR, 30 Biopolis St, #07-01 Matrix, 138671, Singapore; School of Biological Sciences, Nanyang Technological University (NTU), 60 Nanyang Drive, 637551, Singapore.
| | - Charlie W H Lee
- Genome Institute Singapore (GIS), A*STAR, 60 Biopolis St, #02-01 Genome, 138672, Singapore
| | - Champa Patel
- University of Colorado School of Medicine, 13001 E 17th Place, Aurora, CO 80045, USA
| | - Marilla Lucero
- Medical Department, Research Institute for Tropical Medicine, Alabang, Muntinlupa City, Philippines
| | - Hanna Nohynek
- KTL National Public Health Institute, Helsinki, Finland
| | - Wing-Kin Sung
- Genome Institute Singapore (GIS), A*STAR, 60 Biopolis St, #02-01 Genome, 138672, Singapore
| | - Chrysanti Murad
- Microbiology Department, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Jianmin Ma
- Bioinformatics Institute (BII), A*STAR, 30 Biopolis St, #07-01 Matrix, 138671, Singapore
| | - Martin L Hibberd
- Genome Institute Singapore (GIS), A*STAR, 60 Biopolis St, #02-01 Genome, 138672, Singapore
| | - Christopher W Wong
- Genome Institute Singapore (GIS), A*STAR, 60 Biopolis St, #02-01 Genome, 138672, Singapore
| | - Eric A F Simões
- University of Colorado School of Medicine, 13001 E 17th Place, Aurora, CO 80045, USA; Center for Global Health, Colorado School of Public Health, and Children's Hospital Colorado, 13001 E 17th Place, Aurora, CO 80045, USA
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3
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Utami KH, Hillmer AM, Aksoy I, Chew EGY, Teo ASM, Zhang Z, Lee CWH, Chen PJ, Seng CC, Ariyaratne PN, Rouam SL, Soo LS, Yousoof S, Prokudin I, Peters G, Collins F, Wilson M, Kakakios A, Haddad G, Menuet A, Perche O, Tay SKH, Sung KWK, Ruan X, Ruan Y, Liu ET, Briault S, Jamieson RV, Davila S, Cacheux V. Detection of chromosomal breakpoints in patients with developmental delay and speech disorders. PLoS One 2014; 9:e90852. [PMID: 24603971 PMCID: PMC3946304 DOI: 10.1371/journal.pone.0090852] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 02/04/2014] [Indexed: 01/25/2023] Open
Abstract
Delineating candidate genes at the chromosomal breakpoint regions in the apparently balanced chromosome rearrangements (ABCR) has been shown to be more effective with the emergence of next-generation sequencing (NGS) technologies. We employed a large-insert (7-11 kb) paired-end tag sequencing technology (DNA-PET) to systematically analyze genome of four patients harbouring cytogenetically defined ABCR with neurodevelopmental symptoms, including developmental delay (DD) and speech disorders. We characterized structural variants (SVs) specific to each individual, including those matching the chromosomal breakpoints. Refinement of these regions by Sanger sequencing resulted in the identification of five disrupted genes in three individuals: guanine nucleotide binding protein, q polypeptide (GNAQ), RNA-binding protein, fox-1 homolog (RBFOX3), unc-5 homolog D (C.elegans) (UNC5D), transmembrane protein 47 (TMEM47), and X-linked inhibitor of apoptosis (XIAP). Among them, XIAP is the causative gene for the immunodeficiency phenotype seen in the patient. The remaining genes displayed specific expression in the fetal brain and have known biologically relevant functions in brain development, suggesting putative candidate genes for neurodevelopmental phenotypes. This study demonstrates the application of NGS technologies in mapping individual gene disruptions in ABCR as a resource for deciphering candidate genes in human neurodevelopmental disorders (NDDs).
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Affiliation(s)
- Kagistia H. Utami
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Axel M. Hillmer
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore
| | - Irene Aksoy
- Stem Cells and Developmental Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Elaine G. Y. Chew
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore
| | - Audrey S. M. Teo
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore
| | - Zhenshui Zhang
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore
| | - Charlie W. H. Lee
- Computational and Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Pauline J. Chen
- Computational and Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Chan Chee Seng
- Scientific & Research Computing, Genome Institute of Singapore, Singapore, Singapore
| | - Pramila N. Ariyaratne
- Computational and Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Sigrid L. Rouam
- Computational and Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Lim Seong Soo
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Saira Yousoof
- Eye and Developmental Genetics Research, The Children’s Hospital at Westmead, Children’s Medical Research Institute and Save Sight Institute, Sydney, New South Wales, Australia
- Disciplines of Paediatrics and Child Health and Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Ivan Prokudin
- Eye and Developmental Genetics Research, The Children’s Hospital at Westmead, Children’s Medical Research Institute and Save Sight Institute, Sydney, New South Wales, Australia
- Disciplines of Paediatrics and Child Health and Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Gregory Peters
- Department of Cytogenetics, The Children’s Hospital at Westmead, Sydney, New South Wales, Australia
| | - Felicity Collins
- Department of Clinical Genetics, The Children’s Hospital at Westmead, Sydney, New South Wales, Australia
| | - Meredith Wilson
- Department of Clinical Genetics, The Children’s Hospital at Westmead, Sydney, New South Wales, Australia
| | - Alyson Kakakios
- Department of Immunology, The Children’s Hospital at Westmead, Sydney, New South Wales, Australia
| | | | - Arnaud Menuet
- Service de Genetique INEM UMR7355 CNRS-University, Centre Hospitalier Régional d’Orléans, Orléans, France
| | - Olivier Perche
- Service de Genetique INEM UMR7355 CNRS-University, Centre Hospitalier Régional d’Orléans, Orléans, France
| | - Stacey Kiat Hong Tay
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ken W. K. Sung
- Computational and Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Xiaoan Ruan
- Genome Technology and Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Yijun Ruan
- Genome Technology and Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Edison T. Liu
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore
| | - Sylvain Briault
- Service de Genetique INEM UMR7355 CNRS-University, Centre Hospitalier Régional d’Orléans, Orléans, France
| | - Robyn V. Jamieson
- Eye and Developmental Genetics Research, The Children’s Hospital at Westmead, Children’s Medical Research Institute and Save Sight Institute, Sydney, New South Wales, Australia
| | - Sonia Davila
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Valere Cacheux
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
- * E-mail:
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4
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Lee VJ, Yap J, Cook AR, Chen MI, Tay JK, Tan BH, Loh JP, Chew SW, Koh WH, Lin R, Cui L, Lee CWH, Sung WK, Wong CW, Hibberd ML, Kang WL, Seet B, Tambyah PA. Oseltamivir ring prophylaxis for containment of 2009 H1N1 influenza outbreaks. N Engl J Med 2010; 362:2166-74. [PMID: 20558367 DOI: 10.1056/nejmoa0908482] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND From June 22 through June 25, 2009, four outbreaks of infection with the pandemic influenza A (H1N1) virus occurred in Singapore military camps. We report the efficacy of ring chemoprophylaxis (geographically targeted containment by means of prophylaxis) with oseltamivir to control outbreaks of 2009 H1N1 influenza in semiclosed environments. METHODS All personnel with suspected infection were tested and clinically isolated if infection was confirmed. In addition, we administered postexposure ring chemoprophylaxis with oseltamivir and segregated the affected military units to contain the spread of the virus. All personnel were screened three times weekly both for virologic infection, by means of nasopharyngeal swabs and reverse-transcriptase-polymerase-chain-reaction assay with sequencing, and for clinical symptoms, by means of questionnaires. RESULTS A total of 1175 personnel were at risk across the four sites, with 1100 receiving oseltamivir prophylaxis. A total of 75 personnel (6.4%) were infected before the intervention, and 7 (0.6%) after the intervention. There was a significant reduction in the overall reproductive number (the number of new cases attributable to the index case), from 1.91 (95% credible interval, 1.50 to 2.36) before the intervention to 0.11 (95% credible interval, 0.05 to 0.20) after the intervention. Three of the four outbreaks showed a significant reduction in the rate of infection after the intervention. Molecular analysis revealed that all four outbreaks were derived from the New York lineage of the 2009 H1N1 virus and that cases within each outbreak were due to transmission rather than unrelated episodes of infection. Of the 816 personnel treated with oseltamivir who were surveyed, 63 (7.7%) reported mild, nonrespiratory side effects of the drug, with no severe adverse events. CONCLUSIONS Oseltamivir ring chemoprophylaxis, together with prompt identification and isolation of infected personnel, was effective in reducing the impact of outbreaks of 2009 H1N1 influenza in semiclosed settings.
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Affiliation(s)
- Vernon J Lee
- Biodefence Centre, Ministry of Defence, Department of Epidemiology and Public Health, National University of Singapore.
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5
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Sung WK, Lu Y, Lee CWH, Zhang D, Ronaghi M, Lee CGL. Deregulated direct targets of the hepatitis B virus (HBV) protein, HBx, identified through chromatin immunoprecipitation and expression microarray profiling. J Biol Chem 2009; 284:21941-21954. [PMID: 19439406 DOI: 10.1074/jbc.m109.014563] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The hepatitis B-X (HBx) protein is strongly associated with hepatocellular carcinoma. It is implicated not to directly cause cancer but to play a role in hepatocellular carcinoma as a co-factor. The oncogenic potential of HBx primarily lies in its interaction with transcriptional regulators resulting in aberrant gene expression and deregulated cellular pathways. Utilizing ultraviolet irradiation to simulate a tumor-initiating event, we integrated chip-based chromatin immunoprecipitation (ChIP-chip) with expression microarray profiling and identified 184 gene targets directly deregulated by HBx. One-hundred forty-four transcription factors interacting with HBx were computationally inferred. We experimentally validated that HBx interacts with some of the predicted transcription factors (pTF) as well as the promoters of the deregulated target genes of these pTFs. Significantly, we demonstrated that the pTF interacts with the promoters of the deregulated HBx target genes and that deregulation by HBx of these HBx target genes carrying the pTF consensus sequences can be reversed using pTF small interfering RNAs. The roles of these deregulated direct HBx target genes and their relevance in cancer was inferred via querying against biogroup/cancer-related microarray databases using web-based NextBio(TM) software. Six pathways, including the Jak-STAT pathway, were predicted to be significantly deregulated when HBx binds indirectly to direct target gene promoters. In conclusion, this study represents the first ever demonstration of the utilization of ChIP-chip to identify deregulated direct gene targets from indirect protein-DNA binding as well as transcriptional factors directly interacting with HBx. Increased knowledge of the gene/transcriptional factor targets of HBx will enhance our understanding of the role of HBx in hepatocellular carcinogenesis and facilitate the design of better strategies in combating hepatitis B virus-associated hepatocellular carcinoma.
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Affiliation(s)
- Wing-Kin Sung
- Departments of Computer Science, Singapore 119077, Singapore; Genome Institute of Singapore, Singapore 138672, Singapore
| | - Yiwei Lu
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Charlie W H Lee
- Departments of Computer Science, Singapore 119077, Singapore; Genome Institute of Singapore, Singapore 138672, Singapore
| | - Dongwei Zhang
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore 169610, Singapore; Biochemistry, National University of Singapore, Singapore 119077, Singapore
| | - Mostafa Ronaghi
- Department of Biochemistry, Stanford Genome Technology Center, Stanford University, Stanford, California 94305
| | - Caroline G L Lee
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore 169610, Singapore; Biochemistry, National University of Singapore, Singapore 119077, Singapore; Duke-NUS Graduate Medical School, Singapore 169547, Singapore
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6
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Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SCJ, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CWH, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JNS, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PIW, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VVB, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007; 447:799-816. [PMID: 17571346 PMCID: PMC2212820 DOI: 10.1038/nature05874] [Citation(s) in RCA: 3782] [Impact Index Per Article: 222.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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7
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Zeller KI, Zhao X, Lee CWH, Chiu KP, Yao F, Yustein JT, Ooi HS, Orlov YL, Shahab A, Yong HC, Fu Y, Weng Z, Kuznetsov VA, Sung WK, Ruan Y, Dang CV, Wei CL. Global mapping of c-Myc binding sites and target gene networks in human B cells. Proc Natl Acad Sci U S A 2006; 103:17834-9. [PMID: 17093053 PMCID: PMC1635161 DOI: 10.1073/pnas.0604129103] [Citation(s) in RCA: 401] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The protooncogene MYC encodes the c-Myc transcription factor that regulates cell growth, cell proliferation, cell cycle, and apoptosis. Although deregulation of MYC contributes to tumorigenesis, it is still unclear what direct Myc-induced transcriptomes promote cell transformation. Here we provide a snapshot of genome-wide, unbiased characterization of direct Myc binding targets in a model of human B lymphoid tumor using ChIP coupled with pair-end ditag sequencing analysis (ChIP-PET). Myc potentially occupies > 4,000 genomic loci with the majority near proximal promoter regions associated frequently with CpG islands. Using gene expression profiles with ChIP-PET, we identified 668 direct Myc-regulated gene targets, including 48 transcription factors, indicating that Myc is a central transcriptional hub in growth and proliferation control. This first global genomic view of Myc binding sites yields insights of transcriptional circuitries and cis regulatory modules involving Myc and provides a substantial framework for our understanding of mechanisms of Myc-induced tumorigenesis.
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Affiliation(s)
- Karen I. Zeller
- *Department of Medicine and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | | | | | | | - Fei Yao
- Genome Institute of Singapore, Singapore 138672
| | - Jason T. Yustein
- *Department of Medicine and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | | | | | - Atif Shahab
- Bioinformatics Institute, Singapore 138671; and
| | | | - YuTao Fu
- Bioinformatics Program, Boston University, Boston, MA 02115
| | - Zhiping Weng
- Bioinformatics Program, Boston University, Boston, MA 02115
| | | | | | - Yijun Ruan
- Genome Institute of Singapore, Singapore 138672
| | - Chi V. Dang
- *Department of Medicine and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- To whom correspondence may be addressed. E-mail:
or
| | - Chia-Lin Wei
- Genome Institute of Singapore, Singapore 138672
- To whom correspondence may be addressed. E-mail:
or
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8
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Loh YH, Wu Q, Chew JL, Vega VB, Zhang W, Chen X, Bourque G, George J, Leong B, Liu J, Wong KY, Sung KW, Lee CWH, Zhao XD, Chiu KP, Lipovich L, Kuznetsov VA, Robson P, Stanton LW, Wei CL, Ruan Y, Lim B, Ng HH. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet 2006; 38:431-40. [PMID: 16518401 DOI: 10.1038/ng1760] [Citation(s) in RCA: 1797] [Impact Index Per Article: 99.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Accepted: 02/06/2006] [Indexed: 02/06/2023]
Abstract
Oct4 and Nanog are transcription factors required to maintain the pluripotency and self-renewal of embryonic stem (ES) cells. Using the chromatin immunoprecipitation paired-end ditags method, we mapped the binding sites of these factors in the mouse ES cell genome. We identified 1,083 and 3,006 high-confidence binding sites for Oct4 and Nanog, respectively. Comparative location analyses indicated that Oct4 and Nanog overlap substantially in their targets, and they are bound to genes in different configurations. Using de novo motif discovery algorithms, we defined the cis-acting elements mediating their respective binding to genomic sites. By integrating RNA interference-mediated depletion of Oct4 and Nanog with microarray expression profiling, we demonstrated that these factors can activate or suppress transcription. We further showed that common core downstream targets are important to keep ES cells from differentiating. The emerging picture is one in which Oct4 and Nanog control a cascade of pathways that are intricately connected to govern pluripotency, self-renewal, genome surveillance and cell fate determination.
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Affiliation(s)
- Yuin-Han Loh
- Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672
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