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Breaking barriers to transcription elongation

Key Points

  • Many RNA polymerase II (Pol II)-transcribed genes are regulated at the level of transcription elongation, which has three main stages: promoter escape, promoter-proximal pausing, and productive elongation.

  • Immediately following transcription initiation, the transcription complex is unstable. Promoter escape is the earliest step in transcription elongation during which the transcription complex breaks its contacts with promoter-bound factors and simultaneously tightens its grip on the nascent RNA.

  • The combined results from several recent studies have identified potential protein–nucleic acid interactions, as well as mechanisms, that are instrumental in the completion of promoter escape by Pol II.

  • Promoter-proximal pausing might provide a checkpoint before committing to productive elongation, and provides a highly dynamic regulatory step in Pol II transcription. There are several key factors (including DSIF, NELF and P-TEFb) that are thought to be important for transcription regulation during early Pol II elongation.

  • Several elongation factors also facilitate productive elongation by Pol II through the gene by directly altering its elongation properties or by affecting chromatin structure.

  • The main constituent of chromatin is the nucleosome, and the obstacle that nucleosomes pose to transcription elongation must be overcome.

  • The histone components of nucleosomes can be modified covalently, or the nucleosome can be altered structurally, to facilitate transcription. There are several elongation factors known to be important for the covalent and structural modification of nucleosomes.

Abstract

Hundreds of protein factors participate in transcription and its regulation in eukaryotes. Many of these proteins regulate specific genes by targeting upstream promoter regions, whereas a smaller but mechanistically diverse set of factors functions at most genes during RNA polymerase II (Pol II) elongation. These elongation factors can affect mRNA production at particular stages and in different ways during transcription. Some factors act directly on Pol II, whereas others manipulate the chromatin environment.

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Figure 1: Promoter escape and the formation of an early elongation complex.
Figure 2: Promoter-proximal pausing and escape to productive elongation.
Figure 3: The typical histone modification pattern of an active gene.
Figure 4: Nucleosome remodelling and disassembly/reassembly enzymes.

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Acknowledgements

We thank K. Adelman, D. Luse, D. Reinberg and J. Roberts for critical comments on the manuscript, and colleagues who provided manuscripts prior to publication. We apologize to investigators whose work is not cited or is indirectly cited due to space limitations. This effort was supported by the National Institutes of Health.

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DATABASES

Saccharomyces Genome Database

Asf1

Cdc73

Chd1

Ctr9

Eaf3

Hos2

Leo1

Paf1

Rtf1

Set2

FURTHER INFORMATION

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Glossary

Promoter escape

Describes the transitions that must take place for Pol II to become a stable elongation complex in eukaryotic transcription, and involves ATP-dependent structural remodelling of the ITC and conformational changes within the polymerase.

Decondensed

Refers to chromatin that is less compact in structure and more accessible to various DNA and histone-interacting factors.

Promoter clearance

Often used interchangeably with the term promoter escape, but also refers to post-promoter-escape events during which Pol II becomes prone to backtracking and arrest, but the transcript is resistant to dissociation from the polymerase.

Abortive initiation

The tendency of Pol II to continually synthesize and release short RNA products without disengaging the template DNA.

Switch domain

A series of protein loops within the Pol II active site that stabilize the RNA–DNA hybrid. The switch domains are thought to induce conformational changes in Pol II on interacting with the hybrid.

B-finger

Refers to the N-terminal 'finger' domain of TFIIB that protrudes through the RNA-exit tunnel and into the active site of Pol II where it has important roles in transcription-start-site selection and promoter escape.

Transcript slippage

Occurs when the initial RNA transcript unpairs from the DNA template and rehybridizes upstream so that a longer RNA transcript is produced.

Peptidyl-prolyl isomerases

Enzymes that modify the conformation of peptides by catalysing the cis/trans isomerization of prolines.

Transcription bubble

The unwound portion of the DNA (usually 10 bp) that indicates the location of transcription complexes.

Backtracking

Movement of Pol II back along the DNA template, which results in misalignment of the 3′ end of the RNA with the active site. These complexes might be competent for further elongation if the polymerase moves forward again, but are susceptible to arrest.

Arrest

An event in which backtracked transcription complexes that are elongation incompetent cannot move forward without the aid of accessory factors.

Transcriptional pausing

An event in which the forward movement of elongation-competent transcription complexes is temporarily blocked owing to template sequence, regulatory factors or both. The RNA remains aligned with the active site.

Transcriptional stalling

Temporary blocking of the elongation of elongation complexes that can include both paused and arrested RNA polymerases.

UV-crosslinking and chromatin immunoprecipitation

(UV ChIP). A method developed to analyse specific interactions between protein and DNA in vivo using UV crosslinking and antibody-mediated purification of specific proteins and their associated DNA.

Polytene chromosomes

Giant chromosomes that arise from rounds of chromosome replication without cell division, in which the resulting chromatids remain aligned and their substructure, including active genes, is easily visualized by light microscopy.

Capping enzyme

Enzyme with RNA-triphosphatase and RNA-guanyltransferase activity, which adds a guanosine to the RNA 5′ end during cap formation through a 5′ to 5′ triphosphate linkage. Capping enzyme comprises one polypeptide in metazoans and two polypeptides in yeast.

Processivity

A measure of the number of nucleotide additions per transcription-initiation event.

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Saunders, A., Core, L. & Lis, J. Breaking barriers to transcription elongation. Nat Rev Mol Cell Biol 7, 557–567 (2006). https://doi.org/10.1038/nrm1981

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