The DOI matches its Crossref record; 22 of the 27 references it cites were found in a registry or an index.
Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase
Open accessAbstract
When Polymerases Collide: Genomes must be replicated by DNA polymerase and copied by RNA polymerase. The two processes occur concurrently in bacteria and, although the majority of bacterial genes are co-oriented with replication, head-on collisions still occur and can result in double-strand breaks in the genome. Pomerantz and O'Donnell (p. 590 ) show, in vitro, that both Escherichia coli DNA and RNA polymerases grind to a halt when they collide bumper to bumper but that the replication fork remains intact, with the RNA polymerase being shunted off the DNA and out of the way. Mfd, a transcription-repair coupling factor, promotes DNA replication restart probably by rewinding separated DNA stands ahead of the halted transcription complex, promoting its displacement from the DNA.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Transcription-coupled DNA repair: two decades of progress and surprises
Hanawalt, P. C., & Spivak, G. (2008) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2549 · Cited by 1,081
Transcription-Coupled Repair and Human Disease
Hanawalt, P. C. (1994) · Science · doi:10.1126/science.7801121 · Cited by 494
Replication fork reactivation downstream of a blocked nascent leading strand
Heller, R. C., & Marians, K. J. (2006) · Nature · doi:10.1038/nature04329 · Cited by 318
Park, J., Marr, M. T., & Roberts, J. W. (2002) · Cell · doi:10.1016/s0092-8674(02)00769-9 · Cited by 306
McGlynn, P., & Lloyd, R. (2000) · Cell · doi:10.1016/s0092-8674(00)80621-2 · Cited by 288
Head-On Collision Between a DNA Replication Apparatus and RNA Polymerase Transcription Complex
Liu, B., & Alberts, B. (1995) · Science · doi:10.1126/science.7855590 · Cited by 225
Structural Basis for Bacterial Transcription-Coupled DNA Repair
Deaconescu, A. M., Chambers, A. L., Smith, A. J., Nickels, B. E., Hochschild, A., Savery, N. J., & Darst, S. A. (2006) · Cell · doi:10.1016/j.cell.2005.11.045 · Cited by 205
The replisome uses mRNA as a primer after colliding with RNA polymerase
Pomerantz, R. T., & O’Donnell, M. E. (2008) · Nature · doi:10.1038/nature07527 · Cited by 190 · cited 1×
“coli RNAP halted elongation complex was assembled on a biotinylated DNA containing the T7A1 promoter as previously described (9).”
Self-citationReplication fork barriers: pausing for a break or stalling for time?
Labib, K., & Hodgson, B. (2007) · EMBO Reports · doi:10.1038/sj.embor.7400940 · Cited by 182
Yuzhakov, A., Turner, J., & O'Donnell, M. (1996) · Cell · doi:10.1016/s0092-8674(00)80163-4 · Cited by 180
Self-citation
Flagged first, then by citations
5 of the 27 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Items 101–146 of 146
Cameron, A. D. S., Dillon, S. C., Kröger, C., Beran, L., & Dorman, C. J. (2017) · Microbial Genomics · doi:10.1099/mgen.0.000127 · Cited by 11
“In addition to location, gene orientation is also thought to avoid head-on collisions between the moving replication fork complex and transcription complexes, especially in the cases of heavily transcribed genes [34].”
Bacterial pathogen gene regulation: a DNA-structure-centred view of a protein-dominated domain.
Dorman, C., Colgan, A., & Dorman, M. (2016) · Clinical science · doi:10.1042/cs20160024 · Cited by 12
Detection of RNA-DNA association by a proximity ligation-based method
Petruk, S., Fenstermaker, T. K., Black, K. L., Brock, H. W., & Mazo, A. (2016) · Scientific Reports · doi:10.1038/srep27313 · Cited by 14
Whinn, K. S., Xu, Z., Jergic, S., Sharma, N., Spenkelink, L. M., Dixon, N. E., van Oijen, A. M., & Ghodke, H. B. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad186 · Cited by 11
“Therefore, these results suggest that the DnaB helicase remains bound after the replisome encounters the dCas9-cgRNA1-Atto647 roadblock, consistent with previous ensemble in vivo studies (64-66).”
Non‐Canonical Replication Initiation: You’re Fired!
Ravoitytė, B., & Wellinger, R. E. (2017) · Genes · doi:10.3390/genes8020054 · Cited by 11
“Other possibilities include that R-loops cause replication fork collapse and TIR is the result of replication restart of a replisome–RNAP complex [162,163].”
The progression of replication forks at natural replication barriers in live bacteria
Moolman, M. C., Krishnan, S. T., Kerssemakers, J. W. J., de Leeuw, R., Lorent, V., Sherratt, D. J., & Dekker, N. H. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw397 · Cited by 10
“This result is consistent with what has been observed in vitro during a head-on collision of the E. coli replisome and an RNA polymerase (RNAP) (36).”
InfluentialMfd and transcriptional derepression cause genetic diversity in Bacillus subtilis
Eduardo, A. R. (2011) · Frontiers in Bioscience-Elite · doi:10.2741/455 · Cited by 11
“coli without activating the SOS response (35, 36).”
Rep and UvrD Antagonize One Another at Stalled Replication Forks and This Is Exacerbated by SSB
Liu, X., Seet, J. X., Shi, Y., & Bianco, P. R. (2019) · ACS Omega · doi:10.1021/acsomega.8b02375 · Cited by 8
Deaconescu, A. M., & Suhanovsky, M. M. (2016) · Photochemistry and Photobiology · doi:10.1111/php.12661 · Cited by 13
“Factors such as Mfd have roles beyond TCR that stem from their motor protein activity disrupting elongation complexes stalled by various roadblocks, including replication forks (101).”
Transcription and replication: Far relatives make uneasy bedfellows
Hendriks, G., Jansen, J., Mullenders, L., & de Wind, N. (2010) · Cell Cycle · doi:10.4161/cc.9.12.11987 · Cited by 10
“coli the replication fork encounters an elongating RNA polymerase head-on, replication progression requires displacement of the RNA polymerase.(9) Unlike in E.”
Embracing Heterogeneity: Challenging the Paradigm of Replisomes as Deterministic Machines
Lewis, J. S., van Oijen, A. M., & Spenkelink, L. M. (2023) · Chemical Reviews · doi:10.1021/acs.chemrev.3c00436 · Cited by 12
Linking transcription with DNA repair, damage tolerance, and genome duplication
McGlynn, P. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1010659107 · Cited by 7
Tran, S., Lebreuilly, L., Cormontagne, D., Samson, S., Tô, T., Stosskopf, M., Dervyn, R., Grießhammer, A., de la Cuesta-Zuluaga, J., Maier, L., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-58282-8 · Cited by 8
“Mfd then stimulates DNA repair by recruiting components of the Nucleotide Excision Repair system 11 – 14 .”
Cooke, M. B., Herman, C., & Sivaramakrishnan, P. (2024) · FEBS Letters · doi:10.1002/1873-3468.15063 · Cited by 8
“Conversely, when dealing with lagging strand blockages (head-on), it appears that replisomes behave as if they were coupled and stall for long periods (on the scale of tens of minutes) [186,190,191].”
RNA polymerase between lesion bypass and DNA repair
Deaconescu, A. M. (2013) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-013-1384-3 · Cited by 10
Transcription–Replication Coordination
Saponaro, M. (2022) · Life · doi:10.3390/life12010108 · Cited by 9
The enigmatic role of Mfd in replication-transcription conflicts in bacteria
Ragheb, M. N., & Merrikh, H. (2019) · DNA repair · doi:10.1016/j.dnarep.2019.102659 · Cited by 10
Sources and consequences of oxidative damage from mitochondria and neurotransmitter signaling
Brennan, A., Arron, S. T., Chou, K.-M., Cunningham, E. P., & Cleaver, J. E. (2016) · Environmental and Molecular Mutagenesis · doi:10.1002/em.21995 · Cited by 9
“Bar represents 20 l. Data was analyzed using one-way ANOVA with Dunnett’s post hoc analysis. or is collision with a replication fork required [Carvalho et al., 2003; Olavarrieta et al., 2002; da Costa et al., 2008; Pomerantz and O’Donnell, 2010]?”
Discontinuous leading-strand synthesis: a stop–start story
Yeeles, J. T. P. (2014) · Biochemical Society Transactions · doi:10.1042/bst20130262 · Cited by 7
Stallings, C. L., & Glickman, M. S. (2011) · Transcription · doi:10.4161/trns.2.1.13628 · Cited by 15
Hallmarks of DNA replication stress responses in Escherichia coli and Bacillus subtilis
Torres, R., Carrasco, B., Ayora, S., & Alonso, J. C. (2025) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaf041 · Cited by 8
“Mfd, a transcription-repair coupling factor, acts as a forward translocase, binds to stalled RNAPs, dislodging them from sites of DNA damage and releasing the truncated transcripts independently of replication (Park et al. 2002 , Pomerantz and O’Donnell 2010 , Le et al. 2018 , Ho et al. 2020 ).”
Wilkins, R. J., & Petermann, E. (2025) · Journal of Cell Science · doi:10.1242/jcs.264148 · Cited by 5
“RNA polymerase (RNAP) removal from DNA allows cells to overcome TRCs (Poli et al., 2016; Pomerantz and O ’ Donnell, 2010), suggesting that the RNAP itself presents a major obstacle to fork progression.”
Davletgildeeva, A. T., & Kuznetsov, N. A. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26146951 · Cited by 5
“The results of several in vitro studies demonstrate that the blockade of the replisome resulting from HO-TRC events does not necessarily lead to its disruption, and replication can be resumed in the presence of certain helping factors, such as T4 Dda helicase and Mfd translocase [23,26].”
RNA Polymerase II is a Polar Roadblock to a Progressing DNA Fork
Kay, T. M., Inman, J. T., Lubkowska, L., Le, T. T., Qian, J., Hall, P. M., Wang, D., Kashlev, M., & Wang, M. D. (2024) · bioRxiv · doi:10.1101/2024.10.11.617674 · Cited by 5
“Ultimately, the stalled Pol II must be moved off the DNA to allow replication progression 16 .”
RNA polymerase II is a polar roadblock to a progressing DNA fork
Kay, T. M., Inman, J. T., Lubkowska, L., Le, T. T., Qian, J., Hall, P. M., Batra, S., Remus, D., Wang, D., Kashlev, M., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-63662-1 · Cited by 11
“Ultimately, the stalled Pol II must be moved off the DNA to allow replication progression 16 .”
Miropolskaya, N., Petushkov, I., Esyunina, D., & Kulbachinskiy, A. V. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.102099 · Cited by 3
Transcription-Mediated Mutagenic Processes
Robleto, E., Martin, H., Vallin, C., Pedraza-Reyes, M., & Yasbin, R. (2013) · doi:10.1007/978-1-4614-6280-4_3 · Cited by 4
Zhang, H.-L., Sun, Y., Saha, S. T., Saha, L. K., Pongor, L. S., Dhall, A., & Pommier, Y. G. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.17.599352 · Cited by 6
“HO-TRC HO-TRC are the most damaging as the transcription and replication machinery must pass across each other 24,25 .”
Single-molecule studies of helicases and translocases in prokaryotic genome-maintenance pathways
Whinn, K. S., van Oijen, A. M., & Ghodke, H. B. (2021) · DNA repair · doi:10.1016/j.dnarep.2021.103229 · Cited by 3
An emerging paradigm in epigenetic marking: coordination of transcription and replication
Fenstermaker, T. K., Petruk, S., & Mazo, A. (2024) · Transcription · doi:10.1080/21541264.2024.2316965 · Cited by 3
“More recent studies utilizing a different reconstituted in vitro system showed that the E. coli replisome is able to displace the T7 bacteriophage transcriptional machinery [56,57].”
S phase R-loop formation is restricted by PrimPol-mediated repriming
Šviković, S., Crisp, A., Tan-Wong, S. M., Guilliam, T. A., Doherty, A., Proudfoot, N., Guilbaud, G., & Sale, J. (2018) · bioRxiv · doi:10.1101/318220 · Cited by 2
Cell Cycle Control: The Restriction Point
Aguda, B. D. (2015) · doi:10.1002/9780470015902.a0005993.pub2 · Cited by 2
Relations Between Replication and Transcription
Castro-Roa, D., & Zenki, N. (2011) · InTech eBooks · doi:10.5772/20880 · Cited by 2
Pomerantz, R. T., & O’Donnell, M. E. (2010) · Transcription · doi:10.4161/trns.1.3.13488 · Cited by 3
Self-citationConcise Overview of Methodologies Employed in the Study of Bacterial DNA Replication
Maciąg-Dorszyńska, M., Morcinek-Orłowska, J., & Barańska, S. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26020446 · Cited by 1
“Head-on encounters between the replication and transcription machineries on the lagging DNA strand can lead to replication fork arrest and genomic instability [19–21].”
Regulation of bacterial transcription elongation
Proshkin, S., & Mironov, A. S. (2011) · Molecular Biology · doi:10.1134/s0026893311020154 · Cited by 1
“Recent studies showed that Mfd facilitates the progress of the replication fork after the replisome collides with head on RNA poly merase [123].”
Sensoy, O., Carvajal-Garcia, J., Boumi, S., & Merrikh, H. (2026) · bioRxiv · doi:10.64898/2026.06.02.729377
“Replication restart from the RNA strand of an RNA:DNA hybrid has been observed both in vitro and in vivo (8, 9, 34).”
Autoinhibition is not a universal feature of transcription-repair coupling factors
Brugger, C., Suhanovsky, M. M., Son, J., & Deaconescu, A. M. (2026) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2026.113280
Zong, Z., Guan, H., Huang, M., & Guo, J. (2026) · Genes & Diseases · doi:10.1016/j.gendis.2026.102066
Sequential eviction of crowded nucleoprotein complexes by the RecBCD molecular motor
Terakawa, T., Redding, S., Silverstein, T., & Greene, E. (2017) · bioRxiv · doi:10.1101/142224
RNAP Secondary‐Channel Interactors in Escherichia Coli: Makers and Breakers of Genome Stability
Sivaramakrishnan, P., & Herman, C. (2016) · doi:10.1002/9781119004813.ch53
TERMINATING REPLICATION AT TERS AT EUKARYOTIC CHROMOSOMES
Niska, J. (2014) · doi:10.13130/niska-joanna_phd2014-03-25
“Mfd, which is the transcription-repair coupling factor, promotes direct restart of the 28 fork (Pomerantz and O'Donnell, 2010).”
WITHDRAWN: Stimulation of the Mycobacterium tuberculosis transcription elongation by MtbMfd.
Prabha, S., China, A., Rao, D., & Nagaraja, V. (2011) · Tuberculosis · doi:10.1016/j.tube.2011.11.002
Rotational manipulation via single-molecule magnetic trapping and gene transcription kinetics
Zhang, Z.-P., Liu, S., Zhang, Y.-Q., Xiong, Y., Han, W.-J., Chen, T.-S., & Wang, S. (2023) · Acta Physica Sinica · doi:10.7498/aps.72.20231089
(2020) · Wiley eBooks · doi:10.1002/9781119309697.ref
Metadata
- Authors
- Pomerantz, R. T., & O’Donnell, M.
- Affiliations
- Howard Hughes Medical Institute (US)
- Corresponding author
- O’Donnell, Mike
- Venue
- Science
- Published
- 2010-01-29
- Volume
- 327
- Issue
- 5965
- Pages
- 590-592
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC2861996
- OpenAlex
- W2086307439
- Cited by
- 150
- References
- 27
- Citations by year
- 2026: 3 · 2025: 7 · 2024: 4 · 2023: 8 · 2022: 7 · 2021: 10 · 2020: 10 · 2019: 4 · 2018: 4 · 2017: 6 · 2016: 15 · 2015: 9 · 2014: 7 · 2013: 17 · 2012: 14
- FWCI
- 7.30
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institute of General Medical Sciences (R01GM038839)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- replication fork restart, replication fork stalling, replisome, transcription-coupled repair, Mfd, Escherichia coli, DNA replication, transcription-replication conflict
- MeSH terms
- Bacterial Proteins, DNA-Directed DNA Polymerase, DNA Repair, DNA Replication, DNA, Bacterial, Escherichia coli, DNA-Directed RNA Polymerases, Templates, Genetic, Transcription Factors, Transcription, Genetic, Escherichia coli Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review