Comparative analysis of metazoan chromatin organization
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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | en_US |
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American Association for the Advancement of Science (AAAS)
2016
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| Online Access: | http://hdl.handle.net/1721.1/100728 |
| _version_ | 1826217504851099648 |
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| author | Kundaje, Anshul Kumar, Nischay Kellis, Manolis Day, Daniel S. |
| author2 | Harvard University--MIT Division of Health Sciences and Technology |
| author_facet | Harvard University--MIT Division of Health Sciences and Technology Kundaje, Anshul Kumar, Nischay Kellis, Manolis Day, Daniel S. |
| author_sort | Kundaje, Anshul |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T17:04:38Z |
| format | Article |
| id | mit-1721.1/100728 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T17:04:38Z |
| publishDate | 2016 |
| publisher | American Association for the Advancement of Science (AAAS) |
| record_format | dspace |
| spelling | mit-1721.1/1007282022-09-29T23:32:13Z Comparative analysis of metazoan chromatin organization Kundaje, Anshul Kumar, Nischay Kellis, Manolis Day, Daniel S. Harvard University--MIT Division of Health Sciences and Technology Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Kundaje, Anshul Kumar, Nischay Kellis, Manolis Day, Daniel S. 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. National Science Foundation (U.S.) (1122374) 2016-01-06T17:44:57Z 2016-01-06T17:44:57Z 2014-08 2013-11 Article http://purl.org/eprint/type/JournalArticle 0028-0836 1476-4687 http://hdl.handle.net/1721.1/100728 Ho, Joshua W. K., Youngsook L. Jung, Tao Liu, Burak H. Alver, Soohyun Lee, Kohta Ikegami, Kyung-Ah Sohn, et al. “Comparative Analysis of Metazoan Chromatin Organization.” Nature 512, no. 7515 (August 27, 2014): 449–452. en_US http://dx.doi.org/10.1038/nature13415 Nature Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported licence http://creativecommons.org/licenses/by-nc-sa/3.0/ application/pdf American Association for the Advancement of Science (AAAS) Nature |
| spellingShingle | Kundaje, Anshul Kumar, Nischay Kellis, Manolis Day, Daniel S. Comparative analysis of metazoan chromatin organization |
| title | Comparative analysis of metazoan chromatin organization |
| title_full | Comparative analysis of metazoan chromatin organization |
| title_fullStr | Comparative analysis of metazoan chromatin organization |
| title_full_unstemmed | Comparative analysis of metazoan chromatin organization |
| title_short | Comparative analysis of metazoan chromatin organization |
| title_sort | comparative analysis of metazoan chromatin organization |
| url | http://hdl.handle.net/1721.1/100728 |
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