Interplay between DNA supercoiling and transcription elongation

doi:10.4161/trns.28636

. 2014;5(3):e28636.

doi: 10.4161/trns.28636.

Interplay between DNA supercoiling and transcription elongation

Jie Ma¹, Michelle Wang

Affiliations

PMID: 25764330
PMCID: PMC4215170
DOI: 10.4161/trns.28636

Interplay between DNA supercoiling and transcription elongation

Jie Ma et al. Transcription. 2014.

. 2014;5(3):e28636.

doi: 10.4161/trns.28636.

Authors

Jie Ma¹, Michelle Wang

Affiliation

¹ a Department of Physics, Laboratory of Atomic and Solid State Physics; Cornell University; Ithaca, NY.

PMID: 25764330
PMCID: PMC4215170
DOI: 10.4161/trns.28636

Abstract

Transcription-coupled DNA supercoiling has been shown to be an important regulator of transcription that is broadly present in the cell. Here we review experimental work which shows that RNA polymerase is a powerful torsional motor that can alter DNA topology and structure, and DNA supercoiling in turn directly affects transcription elongation.

Keywords: DNA supercoiling; E. coli RNA polymerase; angular optical trap; single molecule; torque; torsional motor; transcription; twin supercoiled domain model.

PubMed Disclaimer

Figures

None — **Figure 1.** Examples of regulatory roles of transcription-coupled DNA supercoiling. (A) (−) supercoiling facilitates promoter coupling and divergent transcription. (B) (−) supercoiling contributes to the melting of the same promoter and encourages subsequent transcription. (C) (−) supercoiling promotes the formation of an R-Loop (extensive RNA-DNA hybrid). (D) Accumulated (−) supercoiling upstream and (+) supercoiling downstream can cause RNAP to stall. (E) (−) supercoiling upstream facilitates the formation of non-B DNA structures which can attract regulatory proteins. (F) (+) supercoiling downstream can destabilize nucleosome structures and (−) supercoiling upstream can facilitate the re-assembly of nucleosome.

See this image and copyright information in PMC

Cited by

Chromatinization Modulates Topoisomerase II Processivity.
Lee J, Wu M, Inman JT, Singh G, Park SH, Lee JH, Fulbright RM, Hong Y, Jeong J, Berger JM, Wang MD. Lee J, et al. bioRxiv [Preprint]. 2023 Oct 4:2023.10.03.560726. doi: 10.1101/2023.10.03.560726. bioRxiv. 2023. Update in: Nat Commun. 2023 Oct 27;14(1):6844. doi: 10.1038/s41467-023-42600-z PMID: 37873421 Free PMC article. Updated. Preprint.
RBM22 regulates RNA polymerase II 5' pausing, elongation rate, and termination by coordinating 7SK-P-TEFb complex and SPT5.
Du X, Qin W, Yang C, Dai L, San M, Xia Y, Zhou S, Wang M, Wu S, Zhang S, Zhou H, Li F, He F, Tang J, Chen JY, Zhou Y, Xiao R. Du X, et al. Genome Biol. 2024 Apr 19;25(1):102. doi: 10.1186/s13059-024-03242-6. Genome Biol. 2024. PMID: 38641822 Free PMC article.
AIRE in context: Leveraging chromatin plasticity to trigger ectopic gene expression.
Kaiser C, Bradu A, Gamble N, Caldwell JA, Koh AS. Kaiser C, et al. Immunol Rev. 2022 Jan;305(1):59-76. doi: 10.1111/imr.13026. Epub 2021 Sep 20. Immunol Rev. 2022. PMID: 34545959 Free PMC article. Review.
Creation and resolution of non-B-DNA structural impediments during replication.
Mellor C, Perez C, Sale JE. Mellor C, et al. Crit Rev Biochem Mol Biol. 2022 Aug;57(4):412-442. doi: 10.1080/10409238.2022.2121803. Epub 2022 Sep 28. Crit Rev Biochem Mol Biol. 2022. PMID: 36170051 Free PMC article.
Ligand-dependent enhancer activation regulated by topoisomerase-I activity.
Puc J, Kozbial P, Li W, Tan Y, Liu Z, Suter T, Ohgi KA, Zhang J, Aggarwal AK, Rosenfeld MG. Puc J, et al. Cell. 2015 Jan 29;160(3):367-80. doi: 10.1016/j.cell.2014.12.023. Epub 2015 Jan 22. Cell. 2015. PMID: 25619691 Free PMC article.

See all "Cited by" articles

References

1. Liu LF, Wang JC. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci U S A. 1987;84:7024–7. doi: 10.1073/pnas.84.20.7024. - DOI - PMC - PubMed
1. Koster DA, Crut A, Shuman S, Bjornsti M-A, Dekker NH. Cellular strategies for regulating DNA supercoiling: a single-molecule perspective. Cell. 2010;142:519–30. doi: 10.1016/j.cell.2010.08.001. - DOI - PMC - PubMed
1. Wu H-Y, Shyy SH, Wang JC, Liu LF. Transcription generates positively and negatively supercoiled domains in the template. Cell. 1988;53:433–40. doi: 10.1016/0092-8674(88)90163-8. - DOI - PubMed
1. Tsao Y-P, Wu H-Y, Liu LF. Transcription-driven supercoiling of DNA: direct biochemical evidence from in vitro studies. Cell. 1989;56:111–8. doi: 10.1016/0092-8674(89)90989-6. - DOI - PubMed
1. Krasilnikov AS, Podtelezhnikov A, Vologodskii A, Mirkin SM. Large-scale effects of transcriptional DNA supercoiling in vivo. J Mol Biol. 1999;292:1149–60. doi: 10.1006/jmbi.1999.3117. - DOI - PubMed

Publication types

Actions

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions

Substances

Actions
Actions

LinkOut - more resources

Full Text Sources
Other Literature Sources
- The Lens - Patent Citations Database
- scite Smart Citations

[1] Liu LF, Wang JC. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci U S A. 1987;84:7024–7. doi: 10.1073/pnas.84.20.7024. - DOI - PMC - PubMed

[2] Liu LF, Wang JC. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci U S A. 1987;84:7024–7. doi: 10.1073/pnas.84.20.7024. - DOI - PMC - PubMed

[3] Koster DA, Crut A, Shuman S, Bjornsti M-A, Dekker NH. Cellular strategies for regulating DNA supercoiling: a single-molecule perspective. Cell. 2010;142:519–30. doi: 10.1016/j.cell.2010.08.001. - DOI - PMC - PubMed

[4] Koster DA, Crut A, Shuman S, Bjornsti M-A, Dekker NH. Cellular strategies for regulating DNA supercoiling: a single-molecule perspective. Cell. 2010;142:519–30. doi: 10.1016/j.cell.2010.08.001. - DOI - PMC - PubMed

[5] Wu H-Y, Shyy SH, Wang JC, Liu LF. Transcription generates positively and negatively supercoiled domains in the template. Cell. 1988;53:433–40. doi: 10.1016/0092-8674(88)90163-8. - DOI - PubMed

[6] Wu H-Y, Shyy SH, Wang JC, Liu LF. Transcription generates positively and negatively supercoiled domains in the template. Cell. 1988;53:433–40. doi: 10.1016/0092-8674(88)90163-8. - DOI - PubMed

[7] Tsao Y-P, Wu H-Y, Liu LF. Transcription-driven supercoiling of DNA: direct biochemical evidence from in vitro studies. Cell. 1989;56:111–8. doi: 10.1016/0092-8674(89)90989-6. - DOI - PubMed

[8] Tsao Y-P, Wu H-Y, Liu LF. Transcription-driven supercoiling of DNA: direct biochemical evidence from in vitro studies. Cell. 1989;56:111–8. doi: 10.1016/0092-8674(89)90989-6. - DOI - PubMed

[9] Krasilnikov AS, Podtelezhnikov A, Vologodskii A, Mirkin SM. Large-scale effects of transcriptional DNA supercoiling in vivo. J Mol Biol. 1999;292:1149–60. doi: 10.1006/jmbi.1999.3117. - DOI - PubMed

[10] Krasilnikov AS, Podtelezhnikov A, Vologodskii A, Mirkin SM. Large-scale effects of transcriptional DNA supercoiling in vivo. J Mol Biol. 1999;292:1149–60. doi: 10.1006/jmbi.1999.3117. - DOI - PubMed

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Interplay between DNA supercoiling and transcription elongation

Affiliation

Interplay between DNA supercoiling and transcription elongation

Authors

Affiliation

Abstract

Figures

Similar articles

Cited by

References

Publication types

MeSH terms

Substances

LinkOut - more resources

Full Text Sources

Other Literature Sources