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	Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae
	YANG YuCheng ; UMETSU Jumpei ; LU Zhi John ; YANG YuCheng ; UMETSU Jumpei ; LU Zhi John
	2016-03-30 ; 2016-03-30
关键词	RNA binding protein non-coding RNA UTR RNA structure Saccharomyces cerevisiae Q78
其他题名	Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae
中文摘要	Protein binding is essential to the transport,decay and regulation of almost all RNA molecules.However,the structural preference of protein binding on RNAs and their cellular functions and dynamics upon changing environmental conditions are poorly understood.Here,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 resolution.We 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 proteins.The 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 vivo.We found that four nucleotide modifications of tRNA are significantly associated with RBP binding.We also identified various structural motifs bound by RBPs in the UTRs of mRNAs,associated with localization,degradation and stress responses.Moreover,we identified>200 novel lncRNAs bound by RBPs,and about half of them contain conserved secondary structures.We 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.; Protein binding is essential to the transport, decay and regulation of almost all RNA molecules. However, the structural pref- erence of protein binding on RNAs and their cellular functions and dynamics upon changing environmental conditions are poorly understood. Here, 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 resolution. We 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 proteins. The 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 vivo. We found that four nucleotide modifications of tRNA are significantly associated with RBP binding. We also identified various structural motifs bound by RBPs in the UTRs of mRNAs, associated with localization, degradation and stress responses. Moreover, we identified >200 novel lncRNAs bound by RBPs, and about half of them contain conserved secondary structures. We present the first ensemble pattern of RBP binding sites in the structured non-coding regions of a eu- karyotic genome, emphasizing their structural context and cellular functions.
语种	英语 ; 英语
内容类型	期刊论文
源URL	[http://ir.lib.tsinghua.edu.cn/ir/item.do?handle=123456789/148430]
专题	清华大学
推荐引用方式 GB/T 7714	YANG YuCheng,UMETSU Jumpei,LU Zhi John,et al. Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae[J],2016, 2016.
APA	YANG YuCheng,UMETSU Jumpei,LU Zhi John,YANG YuCheng,UMETSU Jumpei,&LU Zhi John.(2016).Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae..
MLA	YANG YuCheng,et al."Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae".(2016).

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