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Review
. 2013 Nov 13;113(11):8583-603.
doi: 10.1021/cr400105n. Epub 2013 Aug 6.

RNA polymerase II transcription elongation control

Jiannan Guo  1 , David H Price
Affiliations
Review

RNA polymerase II transcription elongation control

Jiannan Guo et al. Chem Rev. .
No abstract available

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Figures

Figure 1
Figure 1. Creating a nucleosome free region for PIC formation
Top, nucleosome occupancy inhibits promoter sequence recognition. Middle, occupancy of transcription factors (purple) and chromatin remodelers (pink) correlates with the nucleosome free region and promoter DNA is exposed. Bottom, GTFs, Pol II and Mediator form a PIC on the exposed promoter.
Figure 2
Figure 2. Comparison of sequencing based global methods
The diagrams illustrate the basic steps used in determining: A) Pol II or factor occupancy by ChIP-Seq, B) Identities and levels of specific RNAs in a population by RNA-Seq, and the locations of engaged Pol II utilizing C) nuclear run on (NRO) by GRO-Seq, or D) isolation of native elongating transcripts by NET-Seq.
Figure 3
Figure 3. Analysis of Pol II and selected transcription factors by ChIP-Seq
The ChIP-Seq datasets were obtained from published studies carried out by the Young lab on mouse embryonic stem cells., Data were analyzed by Tiandao Li in the Price Lab using published methods. Top) UCSC Genome Browser tracks showing ChIP-Seq results for Pol II, Pol II from cells treated with flavopiridol for 1 hr, Pol II with Ser5 or Ser2 CTD phosphorylation or the indicated factors over three chosen genes illustrate the range of Pol II occupancies found across the genome. For each protein, the heights of all three tracks were held constant and can, therefore, be compared across the different genes. Bottom) Metagene analysis showing the average signal for Pol II and the indicated factors from −600 to +600 from the TSS on 20,000 genes in mouse embryonic stem cells. Backgrounds were subtracted from the datasets before they were normalized.
Figure 4
Figure 4. Promoter proximal paused Pol II
The diagram depicts Pol II that is paused under the control of factors including DSIF, NELF, Gdown1, the proposed Gdown1 Negative Accessory Factor (GNAF), and TFIIS. TFIIF and TTF2 are blocked by Gdown1 at this stage, and Pol II is phosphorylated on Ser5 (illustrated as S5-P). The kinase module of Mediator, blocks entry of the next Pol II and facilitates CTD phosphorylation. The general activator and the acetylated chromatin binding protein BRD4 are also depicted although they are not active at this point.
Figure 5
Figure 5. The productive elongation complex
P-TEFb is recruited by BRD4 and triggers the transition into productive elongation. DSIF is phosphorylated turning it into a productive elongation factor and NELF is removed from the elongation complex. The CTD becomes phosphorylated on Ser2, which promotes mRNA processing. Components of SEC and Paf1C interact with both Pol II and Mediator. TFIIS facilitates release of the paused polymerase into productive elongation.
Figure 6
Figure 6. Reversible interaction of P-TEFb and HEXIM with the 7SK snRNP
The diagram depicts 7SK RNA (red line) with the indicated bound proteins before (Top) and after (Bottom) release of P-TEFb. The change in the shape of 7SK RNA represents the conformational change that occurs after release of P-TEFb which causes HEXIM to be ejected. BRD4 is known to cause the release of P-TEFb, but the re-sequestration of P-TEFb requires, as of yet, unknown activities.
Figure 7
Figure 7. Coupling of RNA processing with transcription and the influence of CTD phosphorylation
The diagram depicts Pol II at different stages of elongation across an average gene. The 7 amino acid repeat in the CTD is illustrated such that white circles are unphosphorylated and red circles are phosphorylated. Changes in the phosphorylation of the CTD and their influence on the indicated processing machineries are indicated.
Figure 8
Figure 8. Pol II termination pathways in yeast and human
The heptad repeat in the CTD is illustrated such that white circles are unphosphorylated and red circles are phosphorylated residues. Yeast Pol II can undergo termination mediated by the Nrd1/Nab3/Sen1 complex, which recognizes sequence elements in the transcript. In human, promoter proximal paused Pol II can be terminated by TTF2 unless Gdown1 is present. Once either yeast or human elongation complexes pass a Poly(A) signal and the nascent transcript is cleaved, termination is facilitated by the degradation of the nascent transcript by Rat1 in yeast or its homolog Xrn2 in human. A conformational change of the elongation complex and Pcf11 also promote termination.
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References

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