Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals.
Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals.
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DOI：
10.1101/gr.130559.111
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发表时间：
2012-05
期刊：
影响因子：
7
通讯作者：
Akimitsu N
中科院分区：
文献类型：
--
作者：
Tani H;Mizutani R;Salam KA;Tano K;Ijiri K;Wakamatsu A;Isogai T;Suzuki Y;Akimitsu N
哺乳动物基因组产生大量的非编码RNA（ncRNA）。然而，大多数ncRNA的功能尚不清楚，需要新的技术来区分功能性ncRNA。对mRNA的研究表明，每种mRNA的半衰期与其生理功能密切相关，提高了ncRNA的RNA稳定性反映其功能的可能性。在这项研究中，我们首先通过开发一种新的全基因组方法确定了HeLa Tet-off（TO）细胞中11，052种mRNA和1418种ncRNA的半衰期，我们将其命名为5′-溴尿苷免疫沉淀追踪-深度测序分析（BRIC-seq）。该方法涉及用5′-溴尿苷脉冲标记内源性RNA，并使用多方面深度测序测量RNA水平随时间的持续下降。通过分析RNA半衰期与功能类别之间的关系，我们发现具有长半衰期（t1/2 ≥ 4 h）的RNA包含显著比例的ncRNA，以及参与管家功能的mRNA，而具有短半衰期（t1/2 < 4 h）的RNA包括已知的调节性ncRNA和调节性mRNA。一组重要的短寿命ncRNA的稳定性受外部刺激如视黄酸处理的调节。特别是，我们确定并表征了几种新的长ncRNA参与细胞增殖的短寿命ncRNA组。我们将这种半衰期短的新型ncRNA命名为短寿命非编码转录物（SLiTs）。我们建议，监测RNA半衰期的策略将提供一个强大的工具，调查迄今为止功能不明的调控RNA。
Mammalian genomes produce huge numbers of noncoding RNAs (ncRNAs). However, the functions of most ncRNAs are unclear, and novel techniques that can distinguish functional ncRNAs are needed. Studies of mRNAs have revealed that the half-life of each mRNA is closely related to its physiological function, raising the possibility that the RNA stability of an ncRNA reflects its function. In this study, we first determined the half-lives of 11,052 mRNAs and 1418 ncRNAs in HeLa Tet-off (TO) cells by developing a novel genome-wide method, which we named 5′-bromo-uridine immunoprecipitation chase–deep sequencing analysis (BRIC-seq). This method involved pulse-labeling endogenous RNAs with 5′-bromo-uridine and measuring the ongoing decrease in RNA levels over time using multifaceted deep sequencing. By analyzing the relationship between RNA half-lives and functional categories, we found that RNAs with a long half-life (t1/2 ≥ 4 h) contained a significant proportion of ncRNAs, as well as mRNAs involved in housekeeping functions, whereas RNAs with a short half-life (t1/2 < 4 h) included known regulatory ncRNAs and regulatory mRNAs. The stabilities of a significant set of short-lived ncRNAs are regulated by external stimuli, such as retinoic acid treatment. In particular, we identified and characterized several novel long ncRNAs involved in cell proliferation from the group of short-lived ncRNAs. We designated this novel class of ncRNAs with a short half-life as Short-Lived noncoding Transcripts (SLiTs). We propose that the strategy of monitoring RNA half-life will provide a powerful tool for investigating hitherto functionally uncharacterized regulatory RNAs.
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影响因子：
64.8
作者：
通讯作者：
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影响因子：
5.3
作者：
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DOI：
10.1073/pnas.0600148103
发表时间：
2006-05-16
影响因子：
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作者：
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通讯作者：
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影响因子：
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作者：
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通讯作者：
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作者：
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