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Review
. 2008 Apr;18(2):130-6.
doi: 10.1016/j.gde.2007.12.008. Epub 2008 Feb 20.

The Transition From Transcriptional Initiation to Elongation

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Free PMC article
Review

The Transition From Transcriptional Initiation to Elongation

Joseph T Wade et al. Curr Opin Genet Dev. .
Free PMC article

Abstract

Transcription is the first step in gene expression, and its regulation underlies multicellular development and the response to environmental changes. Most studies of transcriptional regulation have focused on the recruitment of RNA polymerase to promoters. However, recent work has shown that, for many promoters, post-recruitment steps in transcriptional initiation are likely to be rate limiting. The rate at which RNA polymerase transitions from transcriptional initiation to elongation varies dramatically between promoters and between organisms and is the target of multiple regulatory proteins that can function to both repress and activate transcription.

Figures

Figure 1
Figure 1. Steps in transcription initiation
A. Steps in transcription initiation in eubacteria.

Preinitiation closed complex formation at the promoter by RNAP holoenzyme (containing a σ factor).

DNA is unwound around the transcription start site to form an open complex.

Abortive synthesis of 2–15 nt RNAs requiring DNA “scrunching”.

Promoter escape is typically associated with loss of σ factor.

B. Steps in transcription initiation in eukaryotes.

Preinitiation complex formation at the promoter with Pol II and general transcription factors.

DNA is unwound around the transcription start site to form an open complex.

Abortive synthesis of 2–3 nt RNAs.

Promoter escape is associated with release of most general transcription factors and with phosphorylation at Serine 5 of the C-terminal domain of the largest Pol II subunit (red circle). In some eukaryotes Pol II pauses after synthesis of 20–50 nt RNAs.

Escape from promoter-proximal pauses is associated with phosphorylation at Serine 2 of the C-terminal domain of the largest Pol II subunit (green circle) by pTEFb.

Figure 2
Figure 2. Possible profiles of ChIP signal for RNAP
The graph shows 3 possible ChIP profiles for RNAP across a gene. In all cases RNAP associates with promoter DNA sequences at an equivalent level. In case (1) the ChIP signal is constant throughout the promoter and coding sequence, indicating rapid transition of RNAP from initiation to elongation. In case (2) the ChIP signal is reduced within the coding sequence as compared to the promoter, although ChIP signal in the coding sequence is above background. This indicates that some or all RNAP complexes transition slowly from initiation to elongation. As ChIP measures a population of cells it is impossible to determine whether all RNAP complexes transition at the same rate. In case (3) the ChIP signal is only present at the promoter. This indicates “poised” RNAP at the promoter, i.e. RNAP that is unable to make the transition from initiation to elongation. If the peak of RNAP ChIP signal is downstream of the transcription start site this indicates that RNAP is paused in early elongation. In all cases a Traveling Ratio (TR) can be calculated as the ratio of coding sequence signal (C) to promoter signal (P). Hence, TR can be used as an measure of the rate of transition from initiation to elongation at a given promoter.

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