小柯机器人

英国伯明翰大学Ferenc Müller等研究人员合作绘制出斑马鱼顺式调节元件的功能分层和发育动力学多组学图谱。该研究于2022年7月4日在线发表于国际一流学术期刊《自然—遗传学》。

据研究人员介绍，斑马鱼是研究胚胎发育和模拟人类疾病的常用生物体，到目前为止，它还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，研究人员成立了国际DANIO-CODE联盟，并创建了一个中央存储库来存储和处理斑马鱼的发育功能基因组数据。这个数据协调中心（https://danio-code.zfin.org）结合了总共1802组未发表的和重新分析过的已发表的基因组数据，研究人员用这些数据来改进现有的注释并显示其在实验设计中的效用。研究人员在整个发育过程中确定了超过14万个顺式调控元件，包括具有取决于其在时间和空间上的活性的不同特征的类别。研究人员划定了在子代基因组激活期间活跃的调控元件，和在器官发育期间活跃的调控元件之间的不同距离拓扑结构和染色质特征。

最后，研究人员在斑马鱼和小鼠之间匹配了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效用扩展到哺乳动物。

附：英文原文

Title: Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

Author: Baranasic, Damir, Hrtenhuber, Matthias, Balwierz, Piotr J., Zehnder, Tobias, Mukarram, Abdul Kadir, Nepal, Chirag, Vrnai, Csilla, Hadzhiev, Yavor, Jimenez-Gonzalez, Ada, Li, Nan, Wragg, Joseph, DOrazio, Fabio M., Relic, Dorde, Pachkov, Mikhail, Daz, Noelia, Hernndez-Rodrguez, Benjamn, Chen, Zelin, Stoiber, Marcus, Dong, Michal, 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, apiski, 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., Gmez-Skarmeta, Jos Luis, Onichtchouk, Daria, Brown, Ben James, Bogdanovic, Ozren, van Nimwegen, Erik, Westerfield, Monte, Wardle, Fiona C., Daub, Carsten O., Lenhard, Boris, Mller, Ferenc

Issue&Volume: 2022-07-04

Abstract: 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 Our data coordination center ( https://danio-code.zfin.org ) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design.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.

DOI: 10.1038/s41588-022-01089-w

Source: https://www.nature.com/articles/s41588-022-01089-w

Nature Genetics：《自然—遗传学》，创刊于1992年。隶属于施普林格·自然出版集团，最新IF：41.307
官方网址：https://www.nature.com/ng/
投稿链接：https://mts-ng.nature.com/cgi-bin/main.plex