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2015 ; 12
(7
): 1089-98
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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
PMID26257179
show 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 sequencing. 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 eRNAs derived from active
prototypical 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 correlated with active genes and may prove useful in de
novo enhancer annotation.