Joshua W K Ho 1 , Youngsook L Jung 2 , Tao Liu 3 , Burak H Alver 4 , Soohyun Lee 4 , Kohta Ikegami 5 , Kyung-Ah Sohn 6 , Aki Minoda 7 , Michael Y Tolstorukov 8 , Alex Appert 9 , Stephen C J Parker 10 , Tingting Gu 11 , Anshul Kundaje 12 , Nicole C Riddle 13 , Eric Bishop 14 , Thea A Egelhofer 15 , Sheng'en Shawn Hu 16 , Artyom A Alekseyenko 17 , Andreas Rechtsteiner 15 , Dalal Asker 18 , Jason A Belsky 19 , Sarah K Bowman 20 , Q Brent Chen 21 , Ron A-J Chen 9 , Daniel S Day 22 , Yan Dong 9 , Andrea C Dose 23 , Xikun Duan 16 , Charles B Epstein 24 , Sevinc Ercan 25 , Elise A Feingold 26 , Francesco Ferrari 4 , Jacob M Garrigues 15 , Nils Gehlenborg 27 , Peter J Good 26 , Psalm Haseley 28 , Daniel He 29 , Moritz Herrmann 9 , Michael M Hoffman 30 , Tess E Jeffers 5 , Peter V Kharchenko 4 , Paulina Kolasinska-Zwierz 9 , Chitra V Kotwaliwale 31 , Nischay Kumar 32 , Sasha A Langley 33 , Erica N Larschan 34 , Isabel Latorre 9 , Maxwell W Libbrecht 35 , Xueqiu Lin 16 , Richard Park 14 , Michael J Pazin 26 , Hoang N Pham 36 , Annette Plachetka 17 , Bo Qin 16 , Yuri B Schwartz 37 , Noam Shoresh 24 , Przemyslaw Stempor 9 , Anne Vielle 9 , Chengyang Wang 16 , Christina M Whittle 31 , Huiling Xue 28 , Robert E Kingston 20 , Ju Han Kim 38 , Bradley E Bernstein 39 , Abby F Dernburg 36 , Vincenzo Pirrotta 40 , Mitzi I Kuroda 17 , William S Noble 41 , Thomas D Tullius 42 , Manolis Kellis 32 , David M MacAlpine 19 , Susan Strome 15 , Sarah C R Elgin 11 , Xiaole Shirley Liu 43 , Jason D Lieb 5 , Julie Ahringer 9 , Gary H Karpen 33 , Peter J Park 44
Aug 28 2014
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.