Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

作     者：YANG YuCheng UMETSU Jumpei LU Zhi John 

作者机构：MOE Key Lab of Bioinformatics School of Life Sciences Tsinghua University Department of Biological Information Tokyo Institute of TechnologyTokyo 152-8850 Japan 

出 版 物：《Science China(Life Sciences)》 (中国科学（生命科学英文版）)

年 卷 期：2014年第57卷第1期

页      面：22-35页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 08[工学] 09[农学] 071007[理学-遗传学] 0901[农学-作物学] 0836[工学-生物工程] 090102[农学-作物遗传育种] 

基　　金：supported by the National Natural Science Foundation of China(31271402 and 31100601) the National Key Basic Research Program(2012CB316503) 

主　　题：RNA binding protein non-coding RNA UTR RNA structure Saccharomyces cerevisiae 

摘      要：Protein binding is essential to the transport,decay and regulation of almost all RNA ***,the structural preference of protein binding on RNAs and their cellular functions and dynamics upon changing environmental conditions are poorly ***,we integrated various high-throughput data and introduced a computational framework to describe the global interactions between RNA binding proteins(RBPs)and structured RNAs in yeast at single-nucleotide *** found that on average,in terms of percent total lengths,~15%of mRNA untranslated regions(UTRs),~37%of canonical non-coding RNAs(ncRNAs)and^11%of long ncRNAs(lncRNAs)are bound by *** RBP binding sites,in general,tend to occur at single-stranded loops,with evolutionarily conserved signatures,and often facilitate a specific RNA structure conformation in *** found that four nucleotide modifications of tRNA are significantly associated with RBP *** also identified various structural motifs bound by RBPs in the UTRs of mRNAs,associated with localization,degradation and stress ***,we identified200 novel lncRNAs bound by RBPs,and about half of them contain conserved secondary *** present the first ensemble pattern of RBP binding sites in the structured non-coding regions of a eukaryotic genome,emphasizing their structural context and cellular functions.