Article

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

ABSTRACT

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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    • "As the RNA polymerase II (RNAP2) machinery departs the TSS and moves into the gene body, further repositioning of nucleosomes would be necessary, but a key question concerns what happens in the underwound region behind the two RNAP2 complexes? One facet of this question is that this promoter orientation is somehow used to regulate gene expression (Wei et al., 2011). Another facet is that this interplay of transcription, torsional stress, and active chromatin can cause genome instability. "
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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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