Scientific Publications

Comparative analysis of metazoan chromatin organization.

Publication TypeJournal Article
AuthorsHo, JW, Jung YL, Liu T., Alver BH, Lee S., Ikegami K., Sohn KA, Minoda A., Tolstorukov MY, Appert A., Parker SC, Gu T., Kundaje A., Riddle NC, Bishop E., Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A., Asker D., Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y., Dose AC, Duan X., Epstein CB, Ercan S., Feingold EA, Ferrari F., Garrigues JM, Gehlenborg N., Good PJ, Haseley P., He D., Herrmann M., Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P., Kotwaliwale CV, Kumar N., Langley SA, Larschan EN, Latorre I., Libbrecht MW, Lin X., Park R., Pazin MJ, Pham HN, Plachetka A., Qin B., Schwartz YB, Shoresh N., Stempor P., Vielle A., Wang C., Whittle CM, Xue H., Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V., Kuroda MI, Noble WS, Tullius TD, Kellis M., MacAlpine DM, Strome S., Elgin SC, Liu XS, Lieb JD, Ahringer J., Karpen GH, and Park PJ
AbstractGenome 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.
Year of Publication2014
JournalNature
Volume512
Issue7515
Pages449-52
Date Published (YYYY/MM/DD)2014/08/28
ISSN Number0028-0836
DOI10.1038/nature13415
PubMedhttp://www.ncbi.nlm.nih.gov/pubmed/25164756?dopt=Abstract