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Deprecated: Implicit conversion from float 245.2 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Cell+Rep 2015 ; 12 (7): 1089-98 Nephropedia Template TP
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Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes #MMPMID26257179
Werner MS; Ruthenburg AJ
Cell Rep 2015[Aug]; 12 (7): 1089-98 PMID26257179show ga
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.