title: Comparative analysis of metazoan chromatin organization.
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.
authors.affiliation: 1] 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.).
authors.forename: Joshua W K
authors.initials: JW
authors.lastname: Ho
authors.affiliation: 1] 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].
authors.forename: Youngsook L
authors.initials: YL
authors.lastname: Jung
authors.affiliation: 1] 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.).
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.affiliation: Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Burak H
authors.initials: BH
authors.lastname: Alver
authors.affiliation: Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Soohyun
authors.initials: S
authors.lastname: Lee
authors.affiliation: 1] 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.).
authors.forename: Kohta
authors.initials: K
authors.lastname: Ikegami
authors.affiliation: 1] 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.
authors.forename: Kyung-Ah
authors.initials: KA
authors.lastname: Sohn
authors.affiliation: 1] 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.).
authors.forename: Aki
authors.initials: A
authors.lastname: Minoda
authors.affiliation: 1] 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.
authors.forename: Michael Y
authors.initials: MY
authors.lastname: Tolstorukov
authors.affiliation: The Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
authors.forename: Alex
authors.initials: A
authors.lastname: Appert
authors.affiliation: 1] 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.
authors.forename: Stephen C J
authors.initials: SC
authors.lastname: Parker
authors.affiliation: Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA.
authors.forename: Tingting
authors.initials: T
authors.lastname: Gu
authors.affiliation: 1] 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.).
authors.forename: Anshul
authors.initials: A
authors.lastname: Kundaje
authors.affiliation: 1] 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.).
authors.forename: Nicole C
authors.initials: NC
authors.lastname: Riddle
authors.affiliation: 1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Bishop
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA.
authors.forename: Thea A
authors.initials: TA
authors.lastname: Egelhofer
authors.affiliation: Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China.
authors.forename: Sheng'en Shawn
authors.initials: SS
authors.lastname: Hu
authors.affiliation: 1] 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.
authors.forename: Artyom A
authors.initials: AA
authors.lastname: Alekseyenko
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA.
authors.forename: Andreas
authors.initials: A
authors.lastname: Rechtsteiner
authors.affiliation: 1] 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.
authors.forename: Dalal
authors.initials: D
authors.lastname: Asker
authors.affiliation: Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA.
authors.forename: Jason A
authors.initials: JA
authors.lastname: Belsky
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.
authors.forename: Sarah K
authors.initials: SK
authors.lastname: Bowman
authors.affiliation: Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.
authors.forename: Q Brent
authors.initials: QB
authors.lastname: Chen
authors.affiliation: The Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
authors.forename: Ron A-J
authors.initials: RA
authors.lastname: Chen
authors.affiliation: 1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Harvard/MIT Division of Health Sciences and Technology, Cambridge, Massachusetts 02139, USA.
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Day
authors.affiliation: The Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
authors.forename: Yan
authors.initials: Y
authors.lastname: Dong
authors.affiliation: Department of Anatomy Physiology and Cell Biology, University of California Davis, Davis, California 95616, USA.
authors.forename: Andrea C
authors.initials: AC
authors.lastname: Dose
authors.affiliation: Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China.
authors.forename: Xikun
authors.initials: X
authors.lastname: Duan
authors.affiliation: Broad Institute, Cambridge, Massachusetts 02141, USA.
authors.forename: Charles B
authors.initials: CB
authors.lastname: Epstein
authors.affiliation: 1] 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.
authors.forename: Sevinc
authors.initials: S
authors.lastname: Ercan
authors.affiliation: National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Elise A
authors.initials: EA
authors.lastname: Feingold
authors.affiliation: Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Francesco
authors.initials: F
authors.lastname: Ferrari
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA.
authors.forename: Jacob M
authors.initials: JM
authors.lastname: Garrigues
authors.affiliation: 1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Broad Institute, Cambridge, Massachusetts 02141, USA.
authors.forename: Nils
authors.initials: N
authors.lastname: Gehlenborg
authors.affiliation: National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Good
authors.affiliation: 1] 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.
authors.forename: Psalm
authors.initials: P
authors.lastname: Haseley
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: He
authors.affiliation: The Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
authors.forename: Moritz
authors.initials: M
authors.lastname: Herrmann
authors.affiliation: Princess Margaret Cancer Centre, Toronto, Ontario M6G 1L7, Canada.
authors.forename: Michael M
authors.initials: MM
authors.lastname: Hoffman
authors.affiliation: 1] 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.).
authors.forename: Tess E
authors.initials: TE
authors.lastname: Jeffers
authors.affiliation: Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Peter V
authors.initials: PV
authors.lastname: Kharchenko
authors.affiliation: The Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
authors.forename: Paulina
authors.initials: P
authors.lastname: Kolasinska-Zwierz
authors.affiliation: 1] Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA [2] Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.
authors.forename: Chitra V
authors.initials: CV
authors.lastname: Kotwaliwale
authors.affiliation: 1] Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2] Broad Institute, Cambridge, Massachusetts 02141, USA.
authors.forename: Nischay
authors.initials: N
authors.lastname: Kumar
authors.affiliation: 1] 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.
authors.forename: Sasha A
authors.initials: SA
authors.lastname: Langley
authors.affiliation: Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.
authors.forename: Erica N
authors.initials: EN
authors.lastname: Larschan
authors.affiliation: The Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
authors.forename: Isabel
authors.initials: I
authors.lastname: Latorre
authors.affiliation: Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Maxwell W
authors.initials: MW
authors.lastname: Libbrecht
authors.affiliation: Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China.
authors.forename: Xueqiu
authors.initials: X
authors.lastname: Lin
authors.affiliation: 1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Park
authors.affiliation: National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Pazin
authors.affiliation: 1] 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.
authors.forename: Hoang N
authors.initials: HN
authors.lastname: Pham
authors.affiliation: 1] 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.
authors.forename: Annette
authors.initials: A
authors.lastname: Plachetka
authors.affiliation: Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Qin
authors.affiliation: 1] Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA [2] Department of Molecular Biology, Umea University, 901 87 Umea, Sweden.
authors.forename: Yuri B
authors.initials: YB
authors.lastname: Schwartz
authors.affiliation: Broad Institute, Cambridge, Massachusetts 02141, USA.
authors.forename: Noam
authors.initials: N
authors.lastname: Shoresh
authors.affiliation: The Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
authors.forename: Przemyslaw
authors.initials: P
authors.lastname: Stempor
authors.affiliation: The Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
authors.forename: Anne
authors.initials: A
authors.lastname: Vielle
authors.affiliation: Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China.
authors.forename: Chengyang
authors.initials: C
authors.lastname: Wang
authors.affiliation: 1] Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA [2] Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.
authors.forename: Christina M
authors.initials: CM
authors.lastname: Whittle
authors.affiliation: 1] 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.
authors.forename: Huiling
authors.initials: H
authors.lastname: Xue
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Kingston
authors.affiliation: 1] 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.
authors.forename: Ju Han
authors.initials: JH
authors.lastname: Kim
authors.affiliation: 1] 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.
authors.forename: Bradley E
authors.initials: BE
authors.lastname: Bernstein
authors.affiliation: 1] 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.
authors.forename: Abby F
authors.initials: AF
authors.lastname: Dernburg
authors.affiliation: Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA.
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Pirrotta
authors.affiliation: 1] 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.
authors.forename: Mitzi I
authors.initials: MI
authors.lastname: Kuroda
authors.affiliation: 1] 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.
authors.forename: William S
authors.initials: WS
authors.lastname: Noble
authors.affiliation: 1] Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA [2] Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Tullius
authors.affiliation: 1] Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2] Broad Institute, Cambridge, Massachusetts 02141, USA.
authors.forename: Manolis
authors.initials: M
authors.lastname: Kellis
authors.affiliation: Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA.
authors.forename: David M
authors.initials: DM
authors.lastname: MacAlpine
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA.
authors.forename: Susan
authors.initials: S
authors.lastname: Strome
authors.affiliation: Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA.
authors.forename: Sarah C R
authors.initials: SC
authors.lastname: Elgin
authors.affiliation: 1] 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.
authors.forename: Xiaole Shirley
authors.initials: XS
authors.lastname: Liu
authors.affiliation: 1] 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.).
authors.forename: Jason D
authors.initials: JD
authors.lastname: Lieb
authors.affiliation: The Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
authors.forename: Julie
authors.initials: J
authors.lastname: Ahringer
authors.affiliation: 1] 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.
authors.forename: Gary H
authors.initials: GH
authors.lastname: Karpen
authors.affiliation: 1] 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.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Park
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000166:cytology* / Q000235:genetics*; D002460:Cell Line; D002503:Centromere / Q000235:genetics / Q000378:metabolism; D002843:Chromatin / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D042002:Chromatin Assembly and Disassembly / Q000235:genetics; D004261:DNA Replication / Q000235:genetics; D004331:Drosophila melanogaster / Q000166:cytology* / Q000235:genetics*; D004742:Enhancer Elements, Genetic / Q000235:genetics; D044127:Epigenesis, Genetic; D006570:Heterochromatin / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D006657:Histones / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D058977:Molecular Sequence Annotation; D034881:Nuclear Lamina / Q000378:metabolism; D009707:Nucleosomes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic / Q000235:genetics; D013045:Species Specificity
chemical_list: D002843:Chromatin; D006570:Heterochromatin; D006657:Histones; D009707:Nucleosomes