小柯机器人

人类和小鼠基因组DNA元件百科全书的拓展工作完成
2020-08-02 23:57
来源：小柯机器人

美国马萨诸塞大学医学院Zhiping Weng等研究小组合作完成人类和小鼠基因组DNA元件百科全书的拓展工作。该研究于2020年7月29日发表于《自然》。

研究人员表示，人类和小鼠基因组包含指定RNA和蛋白质并控制其生成时间、大小和细胞环境的指令。为了更好地描述这些元件，DNA元件百科全书（ENCODE）项目的第三阶段扩展了对细胞和组织库中RNA转录、染色质结构和修饰、DNA甲基化、染色质环化以及转录因子和RNA-结合蛋白的占据分析。
 
研究人员总结了这些工作，这些工作已经产生了5,992个新的实验数据集，包括整个小鼠胚胎发育的系统测定。所有数据都可以通过ENCODE数据门户（https://www.encodeproject.org）获得，包括II期ENCODE和Roadmap Epigenomics数据。通过整合与基因调控相关的选定数据类型，研究人员已经开发了一个包含926,535个人类和339,815个小鼠候选顺式调控元件的数据库，覆盖了它们各自基因组的7.9％和3.4％，并构建了一个基于网络的服务器（SCREEN； http://screen.encodeproject.org），来提供灵活的、用户定义的资源访问。
 
总体而言，ENCODE数据库为科学界提供了广阔的资源，从而更好地了解人类和小鼠基因组的组织和功能。
 
附：英文原文

Title: Expanded encyclopaedias of DNA elements in the human and mouse genomes

Author: Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Charles B. Epstein, Noam Shoresh, Jessika Adrian, Trupti Kawli, Carrie A. Davis, Alexander Dobin, Rajinder Kaul, Jessica Halow, Eric L. Van Nostrand, Peter Freese, David U. Gorkin, Yin Shen, Yupeng He, Mark Mackiewicz, Florencia Pauli-Behn, Brian A. Williams, Ali Mortazavi, Cheryl A. Keller, Xiao-Ou Zhang, Shaimae I. Elhajjajy, Jack Huey, Diane E. Dickel, Valentina Snetkova, Xintao Wei, Xiaofeng Wang, Juan Carlos Rivera-Mulia, Joel Rozowsky, Jing Zhang, Surya B. Chhetri, Jialing Zhang, Alec Victorsen, Kevin P. White, Axel Visel, Gene W. Yeo, Christopher B. Burge, Eric Lcuyer, David M. Gilbert, Job Dekker, John Rinn, Eric M. Mendenhall, Joseph R. Ecker, Manolis Kellis, Robert J. Klein, William S. Noble, Anshul Kundaje, Roderic Guig, Peggy J. Farnham, J. Michael Cherry, Richard M. Myers, Bing Ren, Brenton R. Graveley, Mark B. Gerstein, Len A. Pennacchio, Michael P. Snyder, Bradley E. Bernstein, Barbara Wold, Ross C. Hardison, Thomas R. Gingeras, John A. Stamatoyannopoulos, Zhiping Weng

Issue&Volume: 2020-07-29

Abstract: The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes. The authors summarize the data produced by phase III of the Encyclopedia of DNA Elements (ENCODE) project, a resource for better understanding of the human and mouse genomes.

DOI: 10.1038/s41586-020-2493-4

Source: https://www.nature.com/articles/s41586-020-2493-4

Nature：《自然》，创刊于1869年。隶属于施普林格·自然出版集团，最新IF：69.504
官方网址：http://www.nature.com/
投稿链接：http://www.nature.com/authors/submit_manuscript.html


本期文章：《自然》：Online/在线发表

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