Joshua W. K. Ho^1,2*†, Youngsook L. Jung^1,2*, Tao Liu^3,4*†, Burak H. Alver¹, Soohyun Lee¹, Kohta Ikegami^5†, Kyung-Ah Sohn^6,7, Aki Minoda^8,9†, Michael Y. Tolstorukov^1,2,10, Alex Appert¹¹, Stephen C. J. Parker^12,13, Tingting Gu¹⁴, Anshul Kundaje^15,16†, Nicole C. Riddle^14†, Eric Bishop^1,17, Thea A. Egelhofer¹⁸, Sheng’en Shawn Hu¹⁹, Artyom A. Alekseyenko^2,20, Andreas Rechtsteiner¹⁸, Dalal Asker^21,22, Jason A. Belsky²³, Sarah K. Bowman¹⁰, Q. Brent Chen⁵, Ron A.-J. Chen¹¹,Daniel S. Day^1,24, Yan Dong11, ndrea C. Dose²⁵, Xikun Duan¹⁹, Charles B. Epstein16, Sevinc Ercan^5,26, Elise A. Feingold¹³, Francesco Ferrari¹, Jacob M. Garrigues¹⁸, Nils Gehlenborg^1,16, Peter J. Good¹³, Psalm Haseley^1,2, Daniel He⁹, Moritz Herrmann¹¹,Michael M. Hoffman²⁷, Tess E. Jeffers^5†, Peter V. Kharchenko¹, Paulina Kolasinska-Zwierz¹¹, Chitra V. Kotwaliwale^9,28, Nischay Kumar^15,16, Sasha A. Langley^8,9, Erica N. Larschan²⁹, Isabel Latorre¹¹, Maxwell W. Libbrecht³⁰, Xueqiu Lin¹⁹, Richard Park^1,17, Michael J. Pazin¹³, Hoang N. Pham^8,9,28, Annette Plachetka^2,20, Bo Qin¹⁹, Yuri B. Schwartz^21,31, NoamShoresh¹⁶, Przemyslaw Stempor¹¹, Anne Vielle¹¹, Chengyang Wang¹⁹, Christina M. Whittle^9,28, Huiling Xue^1,2, Robert E. Kingston¹⁰, Ju Han Kim^7,32, Bradley E. Bernstein^16,28,33, Abby F. Dernburg^8,9,28, Vincenzo Pirrotta²¹, Mitzi I. Kuroda^2,20,WilliamS. Noble^30,34, Thomas D. Tullius^17,35, Manolis Kellis^15,16, David M. MacAlpine²³, Susan Strome¹⁸, Sarah C. R. Elgin¹⁴, Xiaole Shirley Liu^3,4,16, Jason D. Lieb^5†, Julie Ahringer¹¹, Gary H. Karpen^8,9 & Peter J. Park^1,2,36

¹Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA. ²Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA. ³Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA. ⁴Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, 450 Brookline Avenue, Boston, Massachusetts 02215, USA. ⁵Department of Biology and Carolina Center for GenomeSciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA. ⁶Department of Information and Computer Engineering, Ajou University, Suwon 443-749, Korea. ⁷Systems Biomedical Informatics Research Center, College of Medicine, Seoul National University, Seoul 110-799, Korea. ⁸Department of Genome Dynamics, Life Sciences Division, Lawrence Berkeley National Lab, Berkeley, California 94720, USA. ⁹Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA. ¹⁰Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA. ¹¹The Gurdon Institute and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK. ¹²National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland 20892, USA. ¹³National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA. ¹⁴Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA. ¹⁵Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. ¹⁶Broad Institute, Cambridge, Massachusetts 02141, USA. ¹⁷Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA. ¹⁸Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA. ¹⁹Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai 200092, China. ²⁰Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. ²¹Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NewJersey 08854, USA. ²²Food Science and Technology Department, Faculty of Agriculture, Alexandria University,21545El-Shatby, Alexandria, Egypt. ²³Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA. ²⁴Harvard/MIT Division of Health Sciences and Technology, Cambridge, Massachusetts 02139, USA. ²⁵Department of Anatomy Physiology and Cell Biology, University of California Davis, Davis, California 95616, USA. ²⁶Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA. ²⁷Princess Margaret Cancer Centre, Toronto, Ontario M6G 1L7, Canada. ²⁸Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA. ²⁹Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA. ³⁰Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA. ³¹Department of Molecular Biology, Umea University, 901 87 Umea, Sweden. ³²Seoul National University Biomedical Informatics, Division of Biomedical Informatics, College of Medicine, Seoul National University, Seoul 110-799, Korea. ³³Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA. ³⁴Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA. ³⁵Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA. ³⁶Informatics Program, Children’s Hospital, Boston, Massachusetts 02215, USA. ^†Present addresses: 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.).
^*These authors contributed equally to this work.

Correspondence to: David M. MacAlpine or Susan Strome or Sarah C. R. Elgin or Xiaole Shirley Liu or Jason D. Lieb or Julie Ahringer or Gary H. Karpen or Peter J. Park
 
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^{1, 2, 3}. 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^{4, 5}. 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.