Active chromatin and noncoding RNAs: An intimate relationship

Stanford University, Stanford, California, United States
Current opinion in genetics & development (Impact Factor: 7.57). 12/2011; 22(2):172-8. DOI: 10.1016/j.gde.2011.11.002
Source: PubMed


Eukaryotic genomes are packaged into chromatin, where diverse histone modifications can demarcate chromatin domains that facilitate or block gene expression. While silent chromatin has been associated with long noncoding RNAs (lncRNAs) for some time, new studies suggest that noncoding RNAs also modulate the active chromatin state. Divergent, antisense, and enhancer-like intergenic noncoding RNAs can either activate or repress gene expression by altering histone H3 lysine 4 methylation. An emerging class of enhancer-like lncRNAs may link chromosome structure to chromatin state and establish active chromatin domains. The confluence of several new technologies promises to rapidly expand this fascinating topic of investigation.

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Available from: Ryan Alexander Flynn
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    • "In addition, a large fraction of TSS-proximal transcriptional expenditure is dedicated to the production of unstable non-coding RNAs that are subject to RNA exosomemediated degradation (PROMPTs, uaRNAs, xTSS-RNAs) (Flynn et al., 2011; Pefanis et al., 2014; Preker et al., 2008). Although the characteristics of these new RNA species may overlap, it is abundantly clear that these non-coding RNAs function in the regulation of transcription initiation and transcription elongation by various mechanisms, including control of RNA polII pausing and recruitment of chromatin modification factors (Flynn and Chang, 2012; Reyes-Turcu and Grewal, 2012; Shin et al., 2013). "
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    • "lncRNAs are able to activate or repress gene expression at multiple levels through diverse mechanisms. For example, lncRNAs can recruit repressive (e.g., PRC2) and activating (e.g., the Trithorax group) chromatin modifiers at the DNA level much like molecular scaffolds , leading to regulation of target gene expression [26] [27] [28] [29]. At the RNA level, lncRNAs play a role in post-transcriptional events during gene expression and contribute to splicing, mRNA translation and mRNA degradation [30] [31] [32] [33]. "
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    • "It has been proposed that active enhancers may also be promoters regulating noncoding RNA expression in addition to their enhancer function [30,31]. Recent studies propose that eRNAs bind transcriptional co-activators and chromatin modifying complexes, mediate chromatin looping of enhancer elements with promoters in cis, and provide a structural scaffold for factors that regulate chromatin and gene expression [25,26,29]. Alternatively, the eRNAs might result from collisions of RNAPII with genomic regions or RNAPII interactions during long distance looping of enhancers to promoters [32]. "
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