Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.
Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.
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斑马鱼顺式调控元件的功能分层和发育动态的多组图谱。
DOI：
10.1038/s41588-022-01089-w
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发表时间：
2022-07
期刊：
影响因子：
30.8
通讯作者：
Muller, Ferenc
中科院分区：
文献类型：
--
作者：
Baranasic, Damir;Hortenhuber, Matthias;Balwierz, Piotr J.;Zehnder, Tobias;Mukarram, Abdul Kadir;Nepal, Chirag;Varnai, Csilla;Hadzhiev, Yavor;Jimenez-Gonzalez, Ada;Li, Nan;Wragg, Joseph;D'Orazio, Fabio M.;Relic, Dorde;Pachkov, Mikhail;Diaz, Noelia;Hernandez-Rodriguez, Benjamin;Chen, Zelin;Stoiber, Marcus;Dong, Michael;Stevens, Irene;Ross, Samuel E.;Eagle, Anne;Martin, Ryan;Obasaju, Oluwapelumi;Rastegar, Sepand;McGarvey, Alison C.;Kopp, Wolfgang;Chambers, Emily;Wang, Dennis;Kim, Hyejeong R.;Acemel, Rafael D.;Naranjo, Silvia;Lapinski, Maciej;Chong, Vanessa;Mathavan, Sinnakaruppan;Peers, Bernard;Sauka-Spengler, Tatjana;Vingron, Martin;Carninci, Piero;Ohler, Uwe;Lacadie, Scott Allen;Burgess, Shawn M.;Winata, Cecilia;van Eeden, Freek;Vaquerizas, Juan M.;Luis Gomez-Skarmeta, Jose;Onichtchouk, Daria;Brown, Ben James;Bogdanovic, Ozren;van Nimwegen, Erik;Westerfield, Monte;Wardle, Fiona C.;Daub, Carsten O.;Lenhard, Boris;Muller, Ferenc
斑马鱼是一种用于研究胚胎发育和模拟人类疾病的流行生物，迄今为止缺乏类似于其他动物模型的系统功能注释程序。为了解决这个问题，我们成立了国际DANIO-CODE联盟，并创建了一个中央存储库来存储和处理斑马鱼发育功能基因组数据。我们的数据协调中心（https：danio-code.zfin.org）结合了总共1，802组未发表和重新分析的已发表基因组数据，我们使用这些数据来改进现有的注释并显示其在实验设计中的实用性。我们在整个发育过程中鉴定了超过140，000种顺式调控元件，包括具有不同特征的类别，这些特征取决于它们在时间和空间上的活性。我们描绘了不同的距离拓扑结构和染色质功能之间的调控元件在合子基因组激活和那些活跃在器官发生。最后，我们匹配了斑马鱼和小鼠之间的调控元件和表观基因组景观，并预测了它们之间超越序列相似性的功能关系，从而将斑马鱼发育基因组学的实用性扩展到哺乳动物。DANIO-CODE联盟利用大规模多组学数据集来改进斑马鱼基因组注释。他们在整个发育过程中鉴定了约140，000个顺式调控元件，并与小鼠调控景观进行了比较。
Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals. The DANIO-CODE consortium leverages a large-scale multiomic dataset to improve zebrafish genome annotation. They identify ~140,000 cis-regulatory elements throughout development and perform a comparison with the mouse regulatory landscape.
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影响因子：
64.8
作者：
Dixon JR;Jung I;Selvaraj S;Shen Y;Antosiewicz-Bourget JE;Lee AY;Ye Z;Kim A;Rajagopal N;Xie W;Diao Y;Liang J;Zhao H;Lobanenkov VV;Ecker JR;Thomson JA;Ren B
通讯作者：
Ren B
影响因子：
13.6
作者：
Chen, Zelin;Omori, Yoshihiro;Burgess, Shawn M.
通讯作者：
Burgess, Shawn M.
DOI：
10.1073/pnas.0807297105
发表时间：
2008-09-30
影响因子：
11.1
作者：
Anderson, Ericka L.;Baltus, Andrew E.;Page, David C.
通讯作者：
Page, David C.
影响因子：
7
作者：
Engstrom, Par G.;Sui, Shannan J. Ho;Lenhard, Boris
通讯作者：
Lenhard, Boris
影响因子：
14.9
作者：
Clement, Yves;Torbey, Patrick;Crollius, Hugues Roest
通讯作者：
Crollius, Hugues Roest