Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes.
Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes.
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DOI：
10.1016/j.celrep.2015.07.033
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发表时间：
2015-08-18
期刊：
影响因子：
8.8
通讯作者：
Ruthenburg AJ
中科院分区：
文献类型：
--
作者：
Werner MS;Ruthenburg AJ
据报道，许多长链非编码rna （lncRNAs）通过募集染色质修饰子或桥接远端增强元件到基因启动子来调节转录。然而，这些调控模式的普遍性以及数千种未被研究的人类lncrna的染色质附着机制仍不清楚。为了解决这些问题，我们进行了严格的核分离与RNA-seq相结合。我们提供了人类染色质相关lncRNAs的全基因组鉴定，并证明RNAPII将RNA粘附到染色质上是一种普遍的附着机制。我们还发现了数千种富含染色质的rna (cherna)，它们与已知的lncrna具有相同的分子特性。尽管cherna的产生与源于活性增强子的非编码rna不同，但其与邻近蛋白编码基因的表达密切相关。这项工作为核RNA组织提供了一个更新的框架，其中包括具有增强子样特性的大量染色质相关转录物群体，并且可能在从头增强子注释中证明是有用的。
A number of long noncoding RNAs (lncRNAs) have been reported to regulate transcription via recruitment of chromatin-modifiers or bridging distal enhancer elements to gene promoters. However, the generality of these modes of regulation and the mechanisms of chromatin attachment for thousands of unstudied human lncRNAs remain unclear. To address these questions, we performed stringent nuclear fractionation coupled to RNA-seq. We provide genome-wide identification of human chromatin-associated lncRNAs, and demonstrate tethering of RNA to chromatin by RNAPII is a pervasive mechanism of attachment. We also uncovered thousands of chromatin-enriched RNAs (cheRNAs) that share molecular properties with known lncRNAs. Although distinct from noncoding RNAs derived from active enhancers, the production of cheRNAs is strongly correlated with the expression of neighboring protein-coding genes. This work provides an updated framework for nuclear RNA organization that includes a large chromatin-associated transcript population with enhancer-like properties, and may prove useful in de novo enhancer annotation.
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影响因子：
64.8
作者：
Ernst, Jason;Kheradpour, Pouya;Mikkelsen, Tarjei S.;Shoresh, Noam;Ward, Lucas D.;Epstein, Charles B.;Zhang, Xiaolan;Wang, Li;Issner, Robbyn;Coyne, Michael;Ku, Manching;Durham, Timothy;Kellis, Manolis;Bernstein, Bradley E.
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通讯作者：
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影响因子：
48
作者：
Cloonan, Nicole;Forrest, Alistair R. R.;Grimmond, Sean M.
通讯作者：
Grimmond, Sean M.