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The ?70 region 1.2 regulates promoter escape by unwinding DNA downstream of the transcription start site.

ABSTRACT: The mechanisms of abortive synthesis and promoter escape during initiation of transcription are poorly understood. Here, we show that, after initiation of RNA synthesis, non-specific interaction of ?(70) region 1.2, present in all ?(70) family factors, with the non-template strand around position -4 relative to the transcription start site facilitates unwinding of the DNA duplex downstream of the transcription start site. This leads to stabilization of short RNA products and allows their extension, i.e. promoter escape. We show that this activity of ?(70) region 1.2 is assisted by the ?-lobe domain, but does not involve the ?'-rudder or the ?'-switch-2, earlier proposed to participate in promoter escape. DNA sequence independence of this function of ?(70) region 1.2 suggests that it may be conserved in all ?(70) family factors. Our results indicate that the abortive nature of initial synthesis is caused, at least in part, by failure to open the downstream DNA by the ?-lobe and ? region 1.2.

SUBMITTER: Bochkareva A

PROVIDER: S-EPMC3632114 | biostudies-other | 2013 Apr

REPOSITORIES: biostudies-other

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The σ70 region 1.2 regulates promoter escape by unwinding DNA downstream of the transcription start site.

Bochkareva Aleksandra A Zenkin Nikolay N

Nucleic acids research 20130220 8

The mechanisms of abortive synthesis and promoter escape during initiation of transcription are poorly understood. Here, we show that, after initiation of RNA synthesis, non-specific interaction of σ(70) region 1.2, present in all σ(70) family factors, with the non-template strand around position -4 relative to the transcription start site facilitates unwinding of the DNA duplex downstream of the transcription start site. This leads to stabilization of short RNA products and allows their extensi ...[more]

PMID: 23430153

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Project description:BackgroundThe translation start site plays an important role in the control of translation efficiency of eukaryotic mRNAs. The recognition of the start AUG codon by eukaryotic ribosomes is considered to depend on its nucleotide context. However, the fraction of eukaryotic mRNAs with the start codon in a suboptimal context is relatively large. It may be expected that mRNA should possess some features providing efficient translation, including the proper recognition of a translation start site. It has been experimentally shown that a downstream hairpin located in certain positions with respect to start codon can compensate in part for the suboptimal AUG context and also increases translation from non-AUG initiation codons. Prediction of such a compensatory hairpin may be useful in the evaluation of eukaryotic mRNA translation properties.ResultsWe evaluated interdependency between the start codon context and mRNA secondary structure at the CDS beginning: it was found that a suboptimal start codon context significantly correlated with higher base pairing probabilities at positions 13 - 17 of CDS of human and mouse mRNAs. It is likely that the downstream hairpins are used to enhance translation of some mammalian mRNAs in vivo. Thus, we have developed a tool, AUG_hairpin, to predict local stem-loop structures located within the defined region at the beginning of mRNA coding part. The implemented algorithm is based on the available published experimental data on the CDS-located stem-loop structures influencing the recognition of upstream start codons.ConclusionAn occurrence of a potential secondary structure downstream of start AUG codon in a suboptimal context (or downstream of a potential non-AUG start codon) may provide researchers with a testable assumption on the presence of additional regulatory signal influencing mRNA translation initiation rate and the start codon choice. AUG_hairpin, which has a convenient Web-interface with adjustable parameters, will make such an evaluation easy and efficient.

Dataset Information

The ?70 region 1.2 regulates promoter escape by unwinding DNA downstream of the transcription start site.

Publications

The σ70 region 1.2 regulates promoter escape by unwinding DNA downstream of the transcription start site.

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