小柯机器人

科学家绘制出人类RNA结合蛋白的大规模结合图谱
2020-08-02 23:53

美国加州大学圣迭戈分校Gene W. Yeo等研究人员合作绘制出人类RNA结合蛋白的大规模结合图谱。相关论文发表在2020年7月29日出版的《自然》杂志上。

研究人员报道了人类基因组中被RNA结合蛋白(RBP)识别的RNA元素数据集,这是DNA元素百科全书(ENCODE)项目第三阶段的一部分。这类调控元件仅在转录为RNA后才起作用,因为它们充当RBP的结合位点,控制RBP的转录后过程,例如剪接、切割和聚腺苷酸化,以及mRNA的编辑、定位、稳定性和翻译。研究人员描述了K562和HepG2细胞中大量人类RBP识别的RNA元件图谱和表征。
 
五种检测方法的综合分析确定了体内RNA和染色质上的RBP结合位点、RBP的体外结合偏好、RBP结合位点的功能以及RBP的亚细胞定位,从而产生了1223个重复的356个RBP数据集。研究人员描述了整个转录组中RBP结合的光谱以及这些相互作用与RNA生物学各个方面之间的联系,包括RNA稳定性、剪接调控和RNA定位。通过增加大量与RBP相互作用的功能元件,这些数据扩展了人类基因组中编码的功能元件目录。
 
据介绍,许多蛋白质通过与基因组中编码的特定区域结合来调节基因的表达。
 
附:英文原文

Title: A large-scale binding and functional map of human RNA-binding proteins

Author: Eric L. Van Nostrand, Peter Freese, Gabriel A. Pratt, Xiaofeng Wang, Xintao Wei, Rui Xiao, Steven M. Blue, Jia-Yu Chen, Neal A. L. Cody, Daniel Dominguez, Sara Olson, Balaji Sundararaman, Lijun Zhan, Cassandra Bazile, Louis Philip Benoit Bouvrette, Julie Bergalet, Michael O. Duff, Keri E. Garcia, Chelsea Gelboin-Burkhart, Myles Hochman, Nicole J. Lambert, Hairi Li, Michael P. McGurk, Thai B. Nguyen, Tsultrim Palden, Ines Rabano, Shashank Sathe, Rebecca Stanton, Amanda Su, Ruth Wang, Brian A. Yee, Bing Zhou, Ashley L. Louie, Stefan Aigner, Xiang-Dong Fu, Eric Lcuyer, Christopher B. Burge, Brenton R. Graveley, Gene W. Yeo

Issue&Volume: 2020-07-29

Abstract: Many proteins regulate the expression of genes by binding to specific regions encoded in the genome1. Here we introduce a new data set of RNA elements in the human genome that are recognized by RNA-binding proteins (RBPs), generated as part of the Encyclopedia of DNA Elements (ENCODE) project phase III. This class of regulatory elements functions only when transcribed into RNA, as they serve as the binding sites for RBPs that control post-transcriptional processes such as splicing, cleavage and polyadenylation, and the editing, localization, stability and translation of mRNAs. We describe the mapping and characterization of RNA elements recognized by a large collection of human RBPs in K562 and HepG2 cells. Integrative analyses using five assays identify RBP binding sites on RNA and chromatin in vivo, the in vitro binding preferences of RBPs, the function of RBP binding sites and the subcellular localization of RBPs, producing 1,223 replicated data sets for 356 RBPs. We describe the spectrum of RBP binding throughout the transcriptome and the connections between these interactions and various aspects of RNA biology, including RNA stability, splicing regulation and RNA localization. These data expand the catalogue of functional elements encoded in the human genome by the addition of a large set of elements that function at the RNA level by interacting with RBPs. A combination of five assays is used to produce a catalogue of RNA elements to which RNA-binding proteins bind in human cells.

DOI: 10.1038/s41586-020-2077-3

Source: https://www.nature.com/articles/s41586-020-2077-3

Nature:《自然》,创刊于1869年。隶属于施普林格·自然出版集团,最新IF:43.07
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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