Comparative analysis of metazoan chromatin organization.

Published

Journal Article

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.

Full Text

Duke Authors

Cited Authors

  • Ho, JWK; Jung, YL; Liu, T; Alver, BH; Lee, S; Ikegami, K; Sohn, K-A; Minoda, A; Tolstorukov, MY; Appert, A; Parker, SCJ; 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-J; 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, SCR; Liu, XS; Lieb, JD; Ahringer, J; Karpen, GH; Park, PJ

Published Date

  • August 28, 2014

Published In

Volume / Issue

  • 512 / 7515

Start / End Page

  • 449 - 452

PubMed ID

  • 25164756

Pubmed Central ID

  • 25164756

Electronic International Standard Serial Number (EISSN)

  • 1476-4687

Digital Object Identifier (DOI)

  • 10.1038/nature13415

Language

  • eng

Conference Location

  • England