Evidence map›Paper›PMID 25164756›Full record

ArticleNature2014

Comparative analysis of metazoan chromatin organization.

Joshua W K Ho, Youngsook L Jung, Tao Liu, Burak H Alver, Soohyun Lee, Kohta Ikegami, Kyung-Ah Sohn, Aki Minoda, Michael Y Tolstorukov, Alex Appert and 68 more

Open access · bronzeAbstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 230 papers.

0numbers the graph read from it
0cells of the map it votes in
230citing papers in PubMed
22.1field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

230 citing papers in PubMed, 428 citations in OpenAlex.

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170 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

78 authors at 20 institutions in 8 countries.

Joshua W K Ho1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA [3] [4] Victor Chang Cardiac Research Institute and The University of New South Wales, Sydney, New South Wales 2052, Australia (J.W.K.H.); Department of Biochemistry, University at Buffalo, Buffalo, New York 14203, USA (T.L.); Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA (K.I., T.E.J.); Department of Human Genetics, University of Chicago, Chicago, Illinois 06037, USA (J.D.L.); Division of Genomic Technologies, Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan (A.M.); Department of Genetics, Department of Computer Science, Stanford University, Stanford, California 94305, USA (A.K.); Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA (N.C.R.).
Youngsook L Jung1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA [3].
Tao Liu1] Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, 450 Brookline Avenue, Boston, Massachusetts 02215, USA [3] [4] Victor Chang Cardiac Research Institute and The University of New South Wales, Sydney, New South Wales 2052, Australia (J.W.K.H.); Department of Biochemistry, University at Buffalo, Buffalo, New York 14203, USA (T.L.); Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA (K.I., T.E.J.); Department of Human Genetics, University of Chicago, Chicago, Illinois 06037, USA (J.D.L.); Division of Genomic Technologies, Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan (A.M.); Department of Genetics, Department of Computer Science, Stanford University, Stanford, California 94305, USA (A.K.); Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA (N.C.R.).
Burak H AlverCenter for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Soohyun LeeCenter for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Kohta Ikegami1] Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA [2] Victor Chang Cardiac Research Institute and The University of New South Wales, Sydney, New South Wales 2052, Australia (J.W.K.H.); Department of Biochemistry, University at Buffalo, Buffalo, New York 14203, USA (T.L.); Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA (K.I., T.E.J.); Department of Human Genetics, University of Chicago, Chicago, Illinois 06037, USA (J.D.L.); Division of Genomic Technologies, Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan (A.M.); Department of Genetics, Department of Computer Science, Stanford University, Stanford, California 94305, USA (A.K.); Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA (N.C.R.).
Kyung-Ah Sohn1] Department of Information and Computer Engineering, Ajou University, Suwon 443-749, Korea [2] Systems Biomedical Informatics Research Center, College of Medicine, Seoul National University, Seoul 110-799, Korea.
Aki Minoda1] Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Lab, Berkeley, California 94720, USA [2] Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA [3] Victor Chang Cardiac Research Institute and The University of New South Wales, Sydney, New South Wales 2052, Australia (J.W.K.H.); Department of Biochemistry, University at Buffalo, Buffalo, New York 14203, USA (T.L.); Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA (K.I., T.E.J.); Department of Human Genetics, University of Chicago, Chicago, Illinois 06037, USA (J.D.L.); Division of Genomic Technologies, Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan (A.M.); Department of Genetics, Department of Computer Science, Stanford University, Stanford, California 94305, USA (A.K.); Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA (N.C.R.).
Michael Y Tolstorukov1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.
Alex AppertThe Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
Stephen C J Parker1] National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland 20892, USA [2] National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
Tingting GuDepartment of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA.
Anshul Kundaje1] Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2] Broad Institute, Cambridge, Massachusetts 02141, USA [3] Victor Chang Cardiac Research Institute and The University of New South Wales, Sydney, New South Wales 2052, Australia (J.W.K.H.); Department of Biochemistry, University at Buffalo, Buffalo, New York 14203, USA (T.L.); Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA (K.I., T.E.J.); Department of Human Genetics, University of Chicago, Chicago, Illinois 06037, USA (J.D.L.); Division of Genomic Technologies, Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan (A.M.); Department of Genetics, Department of Computer Science, Stanford University, Stanford, California 94305, USA (A.K.); Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA (N.C.R.).
Nicole C Riddle1] Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA [2] Victor Chang Cardiac Research Institute and The University of New South Wales, Sydney, New South Wales 2052, Australia (J.W.K.H.); Department of Biochemistry, University at Buffalo, Buffalo, New York 14203, USA (T.L.); Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA (K.I., T.E.J.); Department of Human Genetics, University of Chicago, Chicago, Illinois 06037, USA (J.D.L.); Division of Genomic Technologies, Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan (A.M.); Department of Genetics, Department of Computer Science, Stanford University, Stanford, California 94305, USA (A.K.); Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA (N.C.R.).
Eric Bishop1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA.
Thea A EgelhoferDepartment of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA.
Sheng'en Shawn HuDepartment of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China.
Artyom A Alekseyenko1] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Andreas RechtsteinerDepartment of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA.
Dalal Asker1] Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA [2] Food Science and Technology Department, Faculty of Agriculture, Alexandria University, 21545 El-Shatby, Alexandria, Egypt.
Jason A BelskyDepartment of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA.
Sarah K BowmanDepartment of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.
Q Brent ChenDepartment of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.
Ron A-J ChenThe Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
Daniel S Day1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Harvard/MIT Division of Health Sciences and Technology, Cambridge, Massachusetts 02139, USA.
Yan DongThe Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
Andrea C DoseDepartment of Anatomy Physiology and Cell Biology, University of California Davis, Davis, California 95616, USA.
Xikun DuanDepartment of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China.
Charles B EpsteinBroad Institute, Cambridge, Massachusetts 02141, USA.
Sevinc Ercan1] Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA [2] Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA.
Elise A FeingoldNational Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
Francesco FerrariCenter for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Jacob M GarriguesDepartment of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA.
Nils Gehlenborg1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Broad Institute, Cambridge, Massachusetts 02141, USA.
Peter J GoodNational Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
Psalm Haseley1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.
Daniel HeDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA.
Moritz HerrmannThe Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
Michael M HoffmanPrincess Margaret Cancer Centre, Toronto, Ontario M6G 1L7, Canada.
Tess E Jeffers1] Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA [2] Victor Chang Cardiac Research Institute and The University of New South Wales, Sydney, New South Wales 2052, Australia (J.W.K.H.); Department of Biochemistry, University at Buffalo, Buffalo, New York 14203, USA (T.L.); Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA (K.I., T.E.J.); Department of Human Genetics, University of Chicago, Chicago, Illinois 06037, USA (J.D.L.); Division of Genomic Technologies, Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan (A.M.); Department of Genetics, Department of Computer Science, Stanford University, Stanford, California 94305, USA (A.K.); Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA (N.C.R.).
Peter V KharchenkoCenter for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Paulina Kolasinska-ZwierzThe Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
Chitra V Kotwaliwale1] Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA [2] Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.
Nischay Kumar1] Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2] Broad Institute, Cambridge, Massachusetts 02141, USA.
Sasha A Langley1] Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Lab, Berkeley, California 94720, USA [2] Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA.
Erica N LarschanDepartment of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.
Isabel LatorreThe Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
Maxwell W LibbrechtDepartment of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA.
Xueqiu LinDepartment of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China.
Richard Park1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA.
Michael J PazinNational Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
Hoang N Pham1] Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Lab, Berkeley, California 94720, USA [2] Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA [3] Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.
Annette Plachetka1] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
Bo QinDepartment of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China.
Yuri B Schwartz1] Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA [2] Department of Molecular Biology, Umea University, 901 87 Umea, Sweden.
Noam ShoreshBroad Institute, Cambridge, Massachusetts 02141, USA.
Przemyslaw StemporThe Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
Anne VielleThe Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
Chengyang WangDepartment of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China.
Christina M Whittle1] Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA [2] Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.
Huiling Xue1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.
Robert E KingstonDepartment of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.
Ju Han Kim1] Systems Biomedical Informatics Research Center, College of Medicine, Seoul National University, Seoul 110-799, Korea [2] Seoul National University Biomedical Informatics, Division of Biomedical Informatics, College of Medicine, Seoul National University, Seoul 110-799, Korea.
Bradley E Bernstein1] Broad Institute, Cambridge, Massachusetts 02141, USA [2] Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA [3] Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.
Abby F Dernburg1] Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Lab, Berkeley, California 94720, USA [2] Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA [3] Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.
Vincenzo PirrottaDepartment of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA.
Mitzi I Kuroda1] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
William S Noble1] Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA [2] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
Thomas D Tullius1] Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA [2] Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.
Manolis Kellis1] Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2] Broad Institute, Cambridge, Massachusetts 02141, USA.
David M MacAlpineDepartment of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA.
Susan StromeDepartment of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA.
Sarah C R ElginDepartment of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA.
Xiaole Shirley Liu1] Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, 450 Brookline Avenue, Boston, Massachusetts 02215, USA [3] Broad Institute, Cambridge, Massachusetts 02141, USA.
Jason D Lieb1] Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA [2] Victor Chang Cardiac Research Institute and The University of New South Wales, Sydney, New South Wales 2052, Australia (J.W.K.H.); Department of Biochemistry, University at Buffalo, Buffalo, New York 14203, USA (T.L.); Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA (K.I., T.E.J.); Department of Human Genetics, University of Chicago, Chicago, Illinois 06037, USA (J.D.L.); Division of Genomic Technologies, Center for Life Science Technologies, RIKEN, Yokohama 230-0045, Japan (A.M.); Department of Genetics, Department of Computer Science, Stanford University, Stanford, California 94305, USA (A.K.); Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA (N.C.R.).
Julie AhringerThe Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
Gary H Karpen1] Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Lab, Berkeley, California 94720, USA [2] Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA.
Peter J Park1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Informatics Program, Children's Hospital, Boston, Massachusetts 02215, USA.
Brigham and Women's Hospital · USCenter for Systems Biology · USHarvard University · USTongji University · CNUniversity of Cambridge · GBBroad Institute · USNational Institutes of Health · USUniversity of California, Berkeley · USUniversity of California, Santa Cruz · USWellcome/Cancer Research UK Gurdon Institute · GBHoward Hughes Medical Institute · USUniversity of North Carolina at Chapel Hill · USBoston University · USDana-Farber Cancer Institute · USRutgers, The State University of New Jersey · USUniversity of Alabama at Birmingham · USUniversity of Chicago · USWashington University in St. Louis · USAjou University · KRBrown University · US

Funding

Nation Center: Multi-Scale Study- Cellular Networks(RMI)U54CA121852 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI CALIFANO, ANDREA · 2005 to 2015
$37.4M
Training Program in Bioinformatics and Integrative GenomicsT32HG002295 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Peter J Park · 2001 to 2026
$15.8M
Identification of DNA Elements Governing Chromatin Function in C elegansU01HG004270 · NHGRI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI LIEB, JASON D · 2007 to 2011
$9.7M
Genome-Wide Mapping of Chromosomal Proteins in DrosophiliaU01HG004258 · NHGRI · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI KARPEN, GARY H · 2007 to 2011
$9.6M
High-throughput sequencing of chromatin regulatory elementsU54HG004570 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI BERNSTEIN, BRADLEY EVAN · 2007 to 2011
$8.1M
Expanding the catalog of chromatin regulatory elements in the human genomeU54HG006991 · NHGRI · BROAD INSTITUTE, INC. · PI BERNSTEIN, BRADLEY EVAN · 2012 to 2016
$7.9M
EDAC: ENCODE Data Analysis CenterU01HG004695 · NHGRI · EUROPEAN MOLECULAR BIOLOGY LABORATORY · PI BIRNEY, EWAN · 2008 to 2012
$6.4M
Transcription Factor Interactions with NucleosomesR37GM048405 · NIGMS · MASSACHUSETTS GENERAL HOSPITAL · PI KINGSTON, ROBERT · 2009 to 2018
$3.9M
Regulatory Morif Discovery in the Human Genome Using Comparative GenomicsR01HG004037 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI KELLIS, MANOLIS · 2007 to 2015
$3.9M
Computational Biology and Bioinformatics Training ProgramT32GM071340 · NIGMS · DUKE UNIVERSITY · PI MAGWENE, PAUL MITAARI · 2005 to 2020
$3.3M
The Systematic Identification and Analysis of Replication Origins in DrosophilaU01HG004279 · NHGRI · DUKE UNIVERSITY · PI MACALPINE, DAVID M · 2007 to 2011
$2.6M
Establishing coordinate gene regulation during Drosophila dosage compensationR01GM098461 · NIGMS · BROWN UNIVERSITY · PI LARSCHAN, ERICA NICOLE · 2011 to 2016
$2.1M
Howard Hughes Medical InstituteNCI NIH HHS U54 CA121852NCI NIH HHS U54CA121852NHGRI NIH HHS K99 HG006259NHGRI NIH HHS K99HG006259NHGRI NIH HHS R01 HG004037NHGRI NIH HHS T32 HG002295NHGRI NIH HHS U01 HG004258NHGRI NIH HHS U01HG004258NHGRI NIH HHS U01 HG004270NHGRI NIH HHS U01HG004270NHGRI NIH HHS U01 HG004279NHGRI NIH HHS U01HG004279NHGRI NIH HHS U01 HG004695NHGRI NIH HHS U01HG004695NHGRI NIH HHS U54 HG004570NHGRI NIH HHS U54HG004570NHGRI NIH HHS U54 HG006991NIBIB NIH HHS 5RL9EB008539NIBIB NIH HHS RL9 EB008539NIGMS NIH HHS R01 GM098461NIGMS NIH HHS R37 GM048405NIGMS NIH HHS T32 GM071340Wellcome Trust 092096Wellcome Trust 101863Wellcome Trust 54523
6 · The paper itself

Abstract

Genome function is dynamically regulated in part by chromatin, which consists of the histones, non-histone proteins and RNA molecules that package DNA. Studies in Caenorhabditis elegans and Drosophila melanogaster have contributed substantially to our understanding of molecular mechanisms of genome function in humans, and have revealed conservation of chromatin components and mechanisms. Nevertheless, the three organisms have markedly different genome sizes, chromosome architecture and gene organization. On human and fly chromosomes, for example, pericentric heterochromatin flanks single centromeres, whereas worm chromosomes have dispersed heterochromatin-like regions enriched in the distal chromosomal 'arms', and centromeres distributed along their lengths. To systematically investigate chromatin organization and associated gene regulation across species, we generated and analysed a large collection of genome-wide chromatin data sets from cell lines and developmental stages in worm, fly and human. Here we present over 800 new data sets from our ENCODE and modENCODE consortia, bringing the total to over 1,400. Comparison of combinatorial patterns of histone modifications, nuclear lamina-associated domains, organization of large-scale topological domains, chromatin environment at promoters and enhancers, nucleosome positioning, and DNA replication patterns reveals many conserved features of chromatin organization among the three organisms. We also find notable differences in the composition and locations of repressive chromatin. These data sets and analyses provide a rich resource for comparative and species-specific investigations of chromatin composition, organization and function.

Indexed as

AnimalsCaenorhabditis elegansCell LineCentromereChromatinChromatin Assembly and DisassemblyDNA ReplicationDrosophila melanogasterEnhancer Elements, GeneticEpigenesis, GeneticHeterochromatinHistonesHumansMolecular Sequence AnnotationNuclear LaminaNucleosomesChromatinHeterochromatinHistonesNucleosomes

Identifiers

PMID25164756
PMCPMC4227084
OpenAlexW1981516407

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.