@article {393276, title = {Comparative analysis of metazoan chromatin organization.}, journal = {Nature}, volume = {512}, number = {7515}, year = {2014}, month = {2014 Aug 28}, pages = {449-52}, 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 {\textquoteright}arms{\textquoteright}, 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. }, keywords = {Animals, Caenorhabditis elegans, Cell Line, Centromere, Chromatin, Chromatin Assembly and Disassembly, DNA Replication, Drosophila melanogaster, Enhancer Elements, Genetic, Epigenesis, Genetic, Heterochromatin, Histones, Humans, Molecular Sequence Annotation, Nuclear Lamina, Nucleosomes, Promoter Regions, Genetic, Species Specificity}, issn = {1476-4687}, doi = {10.1038/nature13415}, author = {Ho, Joshua W K* and Jung, Youngsook L* and Liu, Tao* and Alver, Burak Han and Lee, Soohyun and Ikegami, Kohta and Sohn, Kyung-Ah and Minoda, Aki and Tolstorukov, Michael Y and Appert, Alex and Parker, Stephen C J and Gu, Tingting and Kundaje, Anshul and Riddle, Nicole C and Bishop, Eric P and Egelhofer, Thea A and Hu, Sheng{\textquoteright}en Shawn and Alekseyenko, Artyom A and Rechtsteiner, Andreas and Asker, Dalal and Belsky, Jason A and Bowman, Sarah K and Chen, Q Brent and Chen, Ron A-J and Day, Daniel S and Dong, Yan and Dose, Andrea C and Duan, Xikun and Epstein, Charles B and Ercan, Sevinc and Feingold, Elise A and Ferrari, Francesco and Garrigues, Jacob M and Gehlenborg, Nils and Good, Peter J and Haseley, Psalm and He, Daniel and Herrmann, Moritz and Hoffman, Michael M and Jeffers, Tess E and Kharchenko, Peter V and Kolasinska-Zwierz, Paulina and Kotwaliwale, Chitra V and Kumar, Nischay and Langley, Sasha A and Larschan, Erica N and Latorre, Isabel and Libbrecht, Maxwell W and Lin, Xueqiu and Park, Richard and Pazin, Michael J and Pham, Hoang N and Plachetka, Annette and Qin, Bo and Schwartz, Yuri B and Shoresh, Noam and Stempor, Przemyslaw and Vielle, Anne and Wang, Chengyang and Whittle, Christina M and Xue, Huiling and Kingston, Robert E and Kim, Ju Han and Bernstein, Bradley E and Dernburg, Abby F and Pirrotta, Vincenzo and Kuroda, Mitzi I and Noble, William S and Tullius, Thomas D and Kellis, Manolis and MacAlpine, David M** and Strome, Susan** and Elgin, Sarah C R** and Liu, Xiaole Shirley** and Lieb, Jason D** and Ahringer, Julie** and Karpen, Gary H** and Park, Peter J**} }