Comparative analysis of metazoan chromatin organization.
Comparative analysis of metazoan chromatin organization.
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DOI：
10.1038/nature13415
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发表时间：
2014-08-28
期刊：
影响因子：
64.8
通讯作者：
Park, Peter J.
中科院分区：
文献类型：
--
作者：
Ho, Joshua W. K.;June, Youngsook L.;Liu, Tao;Alver, Burak H.;Lee, Soohyun;Ikegami, Kohta;Sohn, Kyung-Ah;Minoda, Aki;Tolstorukov, Michael Y.;Appert, Alex;Parker, Stephen C. J.;Gu, Tingting;Kundaje, Anshul;Riddle, Nicole C.;Bishop, Eric;Egelhofer, Thea A.;Hu, Sheng'en Shawn;Alekseyenko, Artyom A.;Rechtsteiner, Andreas;Asker, Dalal;Belsky, Jason A.;Bowmanm, Sarah K.;Chens, Q. Brent;Chen, Ron A. -J.;Day, Daniel S.;Dong, Yan;Dose, Andrea C.;Duan, Xikun;Epstein, Charles B.;Ercan, Sevinc;Feingold, Elise A.;Ferrari, Francesco;Garrigues, Jacob M.;Gehlenborg, Nils;Good, Peter J.;Haseley, Psalm;He, Daniel;Herrmann, Moritz;Hoffman, Michael M.;Jeffers, Tess E.;Kharchenko, Peter V.;Kolasinska-Zwierz, Paulina;Kotwaliwale, Chitra V.;Kumar, Nischay;Langley, Sasha A.;Larschan, Erica N.;Latorre, Isabel;Libbrecht, Maxwell W.;Lin, Xueqiu;Park, Richard;Pazin, Michael J.;Pham, Hoang N.;Plachetka, Annette;Qin, Bo;Schwartz, Yuri B.;Shoresh, Noam;Stempor, Przemyslaw;Vielle, Anne;Wang, Chengyang;Whittle, Christina M.;Xue, Huiling;Kingstonm, Robert E.;Kim, Ju Han;Bernstein, Bradley E.;Dernburg, Abby F.;Pirrotta, Vincenzo;Kuroda, Mitzi I.;Noble, William S.;Tullius, Thomas D.;Kellis, Manolis;MacAlpine, David M.;Strome, Susan;Elgin, Sarah C. R.;Liu, Xiaole Shirley;Lieb, Jason D.;Ahringer, Julie;Karpen, Gary H.;Park, Peter J.
基因组功能部分由染色质动态调节，染色质由组蛋白、非组蛋白和包装DNA的RNA分子组成。对秀丽隐杆线虫和黑腹果蝇的研究极大地促进了我们对人类基因组功能的分子机制的理解，并揭示了染色质组分和机制的保守性。尽管如此，这三种生物的基因组大小、染色体结构和基因组织都有明显不同。例如，在人类和苍蝇染色体上，着丝粒间异染色质位于单个着丝粒的两侧，而蠕虫染色体具有分散的异染色质样区域，富集在远端染色体“臂”中，并且着丝粒沿着它们的长度分布。为了系统地研究跨物种的染色质组织和相关的基因调控，我们从蠕虫、苍蝇和人类的细胞系和发育阶段中生成并分析了大量的全基因组染色质数据集。在这里，我们展示了来自ENCODE和modENCODE联盟的800多个新数据集，使总数超过1，400。比较组蛋白修饰，核纤层相关结构域，大规模拓扑结构域的组织，启动子和增强子的染色质环境，核小体定位和DNA复制模式的组合模式揭示了三种生物体之间的染色质组织的许多保守特征。我们还发现显着的差异，在组成和位置的抑制染色质。这些数据集和分析提供了丰富的资源比较和物种特异性的染色质组成，组织和功能的调查。
Genome function is dynamically regulated in part by chromatin, which consists of the histones, non-histone proteins and RNA molecules that package DNA. Studies inCaenorhabditis elegansandDrosophila melanogasterhave 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.
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影响因子：
64.8
作者：
Ernst, Jason;Kheradpour, Pouya;Mikkelsen, Tarjei S.;Shoresh, Noam;Ward, Lucas D.;Epstein, Charles B.;Zhang, Xiaolan;Wang, Li;Issner, Robbyn;Coyne, Michael;Ku, Manching;Durham, Timothy;Kellis, Manolis;Bernstein, Bradley E.
通讯作者：
Bernstein, Bradley E.
影响因子：
16
作者：
Chandra, Tamir;Kirschner, Kristina;Thuret, Jean-Yves;Pope, Benjamin D.;Ryba, Tyrone;Newman, Scott;Ahmed, Kashif;Samarajiwa, Shamith A.;Salama, Rafik;Carroll, Thomas;Stark, Rory;Janky, Rekin's;Narita, Masako;Xue, Lixiang;Chicas, Agustin;Nunez, Sabrina;Janknecht, Ralf;Hayashi-Takanaka, Yoko;Wilson, Michael D.;Marshall, Aileen;Odom, Duncan T.;Babu, M. Madan;Bazett-Jones, David P.;Tavare, Simon;Edwards, Paul A. W.;Lowe, Scott W.;Kimura, Hiroshi;Gilbert, David M.;Narita, Masashi
通讯作者：
Narita, Masashi
影响因子：
16
作者：
Hou, Chunhui;Li, Li;Qin, Zhaohui S.;Corces, Victor G.
通讯作者：
Corces, Victor G.
影响因子：
64.5
作者：
Towbin, Benjamin D.;Gonzalez-Aguilera, Cristina;Gasser, Susan M.
通讯作者：
Gasser, Susan M.
影响因子：
7
作者：
Liu, Tao;Rechtsteiner, Andreas;Liu, X. Shirley
通讯作者：
Liu, X. Shirley