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Updated: Jul 5, 2026

Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase
Published on: April 29, 2010
Promoter-proximal Pol II: when stalling speeds things up
Sergei Nechaev1, Karen Adelman
1Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA. nechaevs@niehs.nih.gov
Gene expression regulation is not just about RNA polymerase II (Pol II) recruitment. Promoter-proximal Pol II stalling during early elongation is a key regulatory step for many genes, especially those involved in development and stimuli response.
Area of Science:
- Molecular Biology
- Genetics
- Gene Regulation
Background:
- Traditionally, gene expression control was attributed mainly to RNA polymerase II (Pol II) recruitment.
- A small number of genes were previously considered exceptions to this rule.
Purpose of the Study:
- To summarize current data on promoter-proximal Pol II stalling.
- To discuss the implications of this regulatory strategy in gene expression control.
Main Methods:
- Genome-wide analyses of Pol II distribution in Drosophila and mammalian systems.
- Review of existing data on Pol II stalling.
Main Results:
- A significant number of genes are regulated after Pol II recruitment, during early transcription elongation.
- Pol II pauses after short RNA synthesis at these genes, with release from the promoter-proximal region being rate-limiting.
- Promoter-proximal Pol II stalling is common in genes related to development and response to stimuli.
Conclusions:
- Promoter-proximal Pol II stalling is a widespread regulatory mechanism, not an exception.
- This mechanism allows for rapid and precise control of gene expression, particularly for developmental and stimulus-responsive genes.
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