Functional consequences of bidirectional promoters

Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Trends in Genetics (Impact Factor: 9.92). 07/2011; 27(7):267-76. DOI: 10.1016/j.tig.2011.04.002
Source: PubMed


Several studies have shown that promoters of protein-coding genes are origins of pervasive non-coding RNA transcription and can initiate transcription in both directions. However, only recently have researchers begun to elucidate the functional implications of this bidirectionality and non-coding RNA production. Increasing evidence indicates that non-coding transcription at promoters influences the expression of protein-coding genes, revealing a new layer of transcriptional regulation. This regulation acts at multiple levels, from modifying local chromatin to enabling regional signal spreading and more distal regulation. Moreover, the bidirectional activity of a promoter is regulated at multiple points during transcription, giving rise to diverse types of transcripts.

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Available from: Vicent Pelechano, Apr 17, 2014
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    • "On the other hand, addition of a short poly(A) tail is also utilized by the RNA exosome during RNA decay, and thus many decay intermediates as well as noncoding transcripts are terminated by a short poly(A) tail (Wyers et al. 2005; Slomovic et al. 2010). Finally, widespread stutter activity of RNA Pol II surrounding transcriptional start and termination sites (Kapranov et al. 2010; Wei et al. 2011) forms a further source of adenylated RNA in the cell. Here we harness the efficiency of Klenow-mediated 3 ′ tagging (Janicke et al. 2012) to measure the dynamics of the adenylated transcriptome. "
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    • "Remarkably, fusing the mRNA capping enzymes to a mutant CTD containing all Ser5 residues replaced by Ala was sufficient to restore viability in fission yeast, revealing that, at least in yeast, the main essential function of CTD Ser5 phosphorylation is recruitment of the capping machinery [28]. A surprising discovery from genome-wide analysis was the finding that many genes that are not being expressed contain Pol II initiation complexes engaged with the promoter and may generate short abortive non-coding RNAs that are reminiscent of cryptic unstable transcripts or CUTs [29] [30]. This is the case for genes regulated at specific development stages or inducible genes that need to rapidly respond to specific stimuli. "
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    • "With all this overabundance, there is a debate raging between those that claim almost any identified transcript and snippet of RNA to be functional (Mattick 2003; Lee et al. 2009; Carninci 2010; Kishore et al. 2010; Clark et al. 2011; Bernstein et al. 2012; Kapranov and St Laurent 2012; Khayrullina et al. 2012; Gebetsberger and Polacek 2013; Mattick and Dinger 2013) and more conservative voices (Brosius 2005c; Huttenhofer et al. 2005; Robinson 2010; van Bakel et al. 2010; Graur et al. 2013). The writer concurs with the argumentation for spurious and stochastic transcripts (Kowalczyk et al. 2012; Jensen et al. 2013; Mudge et al. 2013), especially as many transcription promoters are bidirectional (Seila et al. 2008; Neil et al. 2009; Xu et al. 2009; Wei et al. 2011; Uesaka et al. 2014). Even the yeast Saccharomyces cerevisiae featuring a compact genome abounds with transcriptional noise and erroneous initiation of transcription by RNA polymerase II (Struhl 2007). "
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