Replication Fork Stalling at Natural Impediments

A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes

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The Complete Genome Sequence of Escherichia coli K-12

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DNA Repair and Mutagenesis

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Comprehensive Identification of Cell Cycle–regulated Genes of the YeastSaccharomyces cerevisiaeby Microarray Hybridization

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Escherichia Coli and Salmonella: Typhimurium Cellular and Molecular Biology

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Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome

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A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes. The Huntington's Disease Collaborative Research Group.

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The human mutator gene homolog MSH2 and its association with hereditary nonpolyposis colon cancer

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Friedreich's Ataxia: Autosomal Recessive Disease Caused by an Intronic GAA Triplet Repeat Expansion

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Molecular basis of myotonic dystrophy: Expansion of a trinucleotide (CTG) repeat at the 3′ end of a transcript encoding a protein kinase family member

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Impediment of Replication Forks by Long Non-coding RNA Provokes Chromosomal Rearrangements by Error-Prone Restart

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CRISPR-Directed Gene Editing Catalyzes Precise Gene Segment Replacement In Vitro Enabling a Novel Method for Multiplex Site-Directed Mutagenesis

Sansbury, B. M., Wagner, A. M., Tarcic, G., Barth, S., Nitzan, E., Goldfus, R., Vidne, M., & Kmiec, E. B. (2019) · The CRISPR Journal · doi:10.1089/crispr.2018.0054 · Cited by 16

Deletion formation mutations in plasmid expression vectors are unfavored by runaway amplification conditions and differentially selected under kanamycin stress

Oliveira, P. H., Prazeres, D. M. F., & Monteiro, G. A. (2009) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2009.08.002 · Cited by 16

Stringent response processes suppress DNA damage sensitivity caused by deficiency in full‐length translation initiation factor 2 or PriA helicase

Madison, K. E., Jones‐Foster, E. N., Vogt, A., Turner, S. K., North, S. H., & Nakai, H. (2014) · Molecular Microbiology · doi:10.1111/mmi.12538 · Cited by 16

The Role of Replication Clamp-Loader Protein HolC of Escherichia coli in Overcoming Replication/Transcription Conflicts

Cooper, D. L., Harada, T., Tamazi, S., Ferrazzoli, A. E., & Lovett, S. T. (2021) · mBio · doi:10.1128/mbio.00184-21 · Cited by 16

The replication-transcription conflict

Soultanas, P. (2011) · Transcription · doi:10.4161/trns.2.3.15908 · Cited by 15

Mycobacterium tuberculosis RecG binds and unwinds model DNA substrates with a preference for Holliday junctions

Zegeye, E. D., Balasingham, S. V., Laerdahl, J. K., Homberset, H., & Tønjum, T. (2012) · Microbiology · doi:10.1099/mic.0.058693-0 · Cited by 15

DNA flap creation by the RarA/MgsA protein ofEscherichia coli

Stanage, T. H., Page, A. N., & Cox, M. M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1322 · Cited by 15

Genetic instability is prevented by Mrc1‐dependent spatio‐temporal separation of replicative and repair activities of homologous recombination

Prado, F. (2014) · BioEssays · doi:10.1002/bies.201300161 · Cited by 17

CarD

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Involvement of transcription-coupled repair factor Mfd and DNA helicase UvrD in mutational processes in Pseudomonas putida

Ukkivi, K., & Kivisaar, M. (2018) · DNA repair · doi:10.1016/j.dnarep.2018.09.011 · Cited by 15

Too Much of a Good Thing: How Ectopic DNA Replication Affects Bacterial Replication Dynamics

Syeda, A., Dimude, J. U., Skovgaard, O., & Rudolph, C. J. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00534 · Cited by 17

Genetic instabilities of (CCTG)·(CAGG) and (ATTCT)·(AGAAT) disease‐associated repeats reveal multiple pathways for repeat deletion

Edwards, S. F., Hashem, V. I., Klysik, E. A., & Sinden, R. R. (2009) · Molecular Carcinogenesis · doi:10.1002/mc.20534 · Cited by 16

Essential Domains ofSchizosaccharomyces pombeRad8 Required for DNA Damage Response

Ding, L., & Forsburg, S. L. (2014) · G3 Genes Genomes Genetics · doi:10.1534/g3.114.011346 · Cited by 14

Challenges in the Application of Synthetic Biology Toward Synthesis of Commodity Products by Cyanobacteria via “Direct Conversion”

Du, W., Caicedo-Burbano, P., Hellingwerf, K. J., & dos Santos, F. B. (2018) · Advances in experimental medicine and biology · doi:10.1007/978-981-13-0854-3_1 · Cited by 14

Bacillus subtilis RarA Acts as a Positive RecA Accessory Protein

Romero, H., Serrano, E., Hernández-Tamayo, R., Carrasco, B., Cárdenas, P. P., Ayora, S., Graumann, P. L., & Alonso, J. C. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00092 · Cited by 12

The fragility of a structurally diverse duplication block triggers recurrent genomic amplification

Suzuki, R., Murata, M. M., Manguso, N., Watanabe, T., Mouakkad, L., Igari, F., Rahman, M. M., Qu, Y., Cui, X., Giuliano, A. E., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1136 · Cited by 13

Deregulation of the Replisome Factor MCMBP Prompts Oncogenesis in Colorectal Carcinomas through Chromosomal Instability

Quimbaya, M., Raspé, E., Denecker, G., Craene, B. D., Roelandt, R., Declercq, W., Sagaert, X., Veylder, L. D., & Berx, G. (2014) · Neoplasia · doi:10.1016/j.neo.2014.07.011 · Cited by 14

Validation of Bacterial Replication Termination Models Using Simulation of Genomic Mutations

Kono, N., Arakawa, K., & Tomita, M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034526 · Cited by 14

Molecular Highways—Navigating Collisions of DNA Motor Proteins

Le, T. T., & Wang, M. D. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.08.006 · Cited by 15

Bacillus subtilis PcrA Helicase Removes Trafficking Barriers

Álamo, M. M., Carrasco, B., Torres, R., & Alonso, J. C. (2021) · Cells · doi:10.3390/cells10040935 · Cited by 14

Driving past four-stranded snags

Mirkin, S. M. (2013) · Nature · doi:10.1038/nature12244 · Cited by 14

Mechanism of regulation of ‘chromosome kissing’ induced by Fob1 and its physiological significancePreprint

Choudhury, M., Zzaman, S., Jiang, J. C., Jazwinski, S. M., & Bastia, D. (2015) · Genes & Development · doi:10.1101/gad.260844.115 · Cited by 15

Plastid Genome Stability and Repair

Zampini, É., Truche, S., Lepage, É., Tremblay‐Belzile, S., & Brisson, N. (2017) · Wiley eBooks · doi:10.1002/9781118647110.ch7 · Cited by 13

Lambda exonuclease digestion of CGG trinucleotide repeats

Conroy, R., Koretsky, A. P., & Moreland, J. (2009) · European Biophysics Journal · doi:10.1007/s00249-009-0502-5 · Cited by 13

Distinct roles of structure-specific endonucleases EEPD1 and Metnase in replication stress responses

Sharma, N., Speed, M. C., Allen, C., Maranon, D. G., Williamson, E. A., Singh, S., Hromas, R., & Nickoloff, J. A. (2020) · NAR Cancer · doi:10.1093/narcan/zcaa008 · Cited by 13

Regulation of Structure-Specific Endonucleases in Replication Stress

Kim, S. M., & Forsburg, S. L. (2018) · Genes · doi:10.3390/genes9120634 · Cited by 13

Transcription in cyanobacteria: a distinctive machinery and putative mechanisms

Riaz-Bradley, A. (2019) · Biochemical Society Transactions · doi:10.1042/bst20180508 · Cited by 13

Assessment of genome stability in various breeds of cattle

Wójcik, E., & Szostek, M. (2019) · PLoS ONE · doi:10.1371/journal.pone.0217799 · Cited by 13

Stochasticity of replication forks’ speeds plays a key role in the dynamics of DNA replication

Yousefi, R., & Rowicka, M. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007519 · Cited by 11

Defining Genetic Factors That Modulate Intergenerational CAG Repeat Instability inDrosophila melanogaster

Jung, J., van Jaarsveld, M. T. M., Shieh, S.-Y., Xu, K., & Bonini, N. M. (2010) · Genetics · doi:10.1534/genetics.110.121418 · Cited by 13

R/G-band boundaries: Genomic instability and human disease

Watanabe, Y., & Maekawa, M. (2013) · Clinica Chimica Acta · doi:10.1016/j.cca.2013.02.011 · Cited by 12

The abundance of Fob1 modulates the efficiency of rRFBs to stall replication forks

Castán, A., Hernández, P., Krimer, D. B., & Schvartzman, J. B. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx655 · Cited by 12

Proteasome-dependent degradation of replisome components regulates faithful DNA replication

Roseaulin, L., Noguchi, C., & Noguchi, E. (2013) · Cell Cycle · doi:10.4161/cc.25692 · Cited by 12

Modulation of DNA damage tolerance in E scherichia coli recG and ruv strains by mutations affecting PriB , the ribosome and RNA polymerase

Mahdi, A. A., Briggs, G. S., & Lloyd, R. G. (2012) · Molecular Microbiology · doi:10.1111/mmi.12010 · Cited by 12

DNA replication timing reveals genome-wide features of transcription and fragility

Berkemeier, F., Cook, P. R., & Boemo, M. A. (2025) · Nature Communications · doi:10.1038/s41467-025-59991-w · Cited by 13

Single-molecule visualization of stalled replication-fork rescue by the Escherichia coli Rep helicase

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

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

Coordination and Substitution of DNA Polymerases in Response to Genomic Obstacles

Trakselis, M. A., Cranford, M. T., & Chu, A. M. (2017) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.7b00190 · Cited by 11

Genome-Wide Distribution of Nascent Transcripts in Sperm DNA, Products of a Late Wave of General Transcription

Kianmehr, L., Khazali, H., Rajabi‐Maham, H., Sharifi‐Zarchi, A., Cuzin, F., & Rassoulzadegan, M. (2019) · Cells · doi:10.3390/cells8101196 · Cited by 9

Insights into the Function of Regulatory RNAs in Bacteria and Archaea

Fard, E. S., Taghvimi, S., Kichi, Z. A., Weber, C., Shabaninejad, Z., Taheri‐Anganeh, M., Khatami, S. H., Mousavi, P., Movahedpour, A., & Natarelli, L. (2021) · International Journal of Translational Medicine · doi:10.3390/ijtm1030024 · Cited by 11

Enhanced polymerase activity permits efficient synthesis by cancer-associated DNA polymerase ϵ variants at low dNTP levels

Barbari, S. R., Beach, A. K., Markgren, J. G., Parkash, V., Moore, E. A., Johansson, E., & Shcherbakova, P. V. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac602 · Cited by 11

The impact of managed care on substance abuse treatment: a problem in need of solution. A report of the American Society of Addiction Medicine.

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Replication fork progression is paused in two large chromosomal zones flanking the DNA replication origin in Escherichia coli

Akiyama, M. T., Oshima, T., Chumsakul, O., Ishikawa, S., & Maki, H. (2016) · Genes to Cells · doi:10.1111/gtc.12388 · Cited by 10

Eukaryotic Replication Barriers: How, Why and Where Forks Stall

Jacob, Z., Emma, L. B., & Ramsay, J. (2011) · InTech eBooks · doi:10.5772/20383 · Cited by 10

Mutation at a distance caused by homopolymeric guanine repeats in Saccharomyces cerevisiae

McDonald, M. J., Yu, Y.-H., Guo, J.-F., Chong, S. Y., Kao, C.-F., & Leu, J. (2016) · Science Advances · doi:10.1126/sciadv.1501033 · Cited by 10

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

In vitro reconstitution of DNA replication initiated by genetic recombination: a T4 bacteriophage model for a type of DNA synthesis important for all cells

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Overcoming diverse homologous recombinations and single chimeric guide RNA competitive inhibition enhances Cas9‐based cyclical multiple genes coediting in filamentous fungi

Miao, Y., Xia, Y., Kong, Y., Zhu, H., Mei, H., Li, P., Feng, H., Xun, W., Xu, Z., Zhang, N., et al. (2021) · Environmental Microbiology · doi:10.1111/1462-2920.15477 · Cited by 10

A redundancy of processes that cause replication fork stalling enhances recombination at two distinct sites in yeast rDNA

Mayán, M. D., Martínez-Robles, M. L., Hernández, P., Schvartzman, J. B., & Krimer, D. B. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06278.x · Cited by 10

Studying essential DNA metabolism proteins in Xenopus egg extract

Sannino, V., Kolinjivadi, A. M., Baldi, G., & Costanzo, V. (2016) · The International Journal of Developmental Biology · doi:10.1387/ijdb.160103vc · Cited by 9

Mutation Rate and Spectrum of the Silkworm in Normal and Temperature Stress Conditions

Han, M., Ren, J., Guo, H., Tong, X., Hu, H., Lu, K., Dai, Z., & Dai, F. (2023) · Genes · doi:10.3390/genes14030649 · Cited by 9

DEK oncoprotein participates in heterochromatin replication via SUMO-dependent nuclear bodies

Pierzyńska‐Mach, A., Czada, C., Vogel, C., Gwosch, E., Osswald, X., Bartoschek, D., Diaspro, A., Kappes, F., & Ferrando‐May, E. (2023) · Journal of Cell Science · doi:10.1242/jcs.261329 · Cited by 9

Bacillus subtilis RarA acts at the interplay between replication and repair-by-recombination

Romero, H., Torres, R., Hernández-Tamayo, R., Carrasco, B., Ayora, S., Graumann, P. L., & Alonso, J. C. (2019) · DNA repair · doi:10.1016/j.dnarep.2019.03.010 · Cited by 10

Modeling diseases of noncoding unstable repeat expansions using mutant pluripotent stem cells

Yanovsky‐Dagan, S. (2015) · World Journal of Stem Cells · doi:10.4252/wjsc.v7.i5.823 · Cited by 10

When transcription goes on Holliday: Double Holliday junctions block RNA polymerase II transcription in vitro

Pipathsouk, A., Belotserkovskii, B. P., & Hanawalt, P. C. (2016) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2016.12.002 · Cited by 10

A Double-Strand Break Does Not Promote Neisseria gonorrhoeae Pilin Antigenic Variation

Prister, L. L., Xu, J., & Seifert, H. S. (2019) · Journal of Bacteriology · doi:10.1128/jb.00256-19 · Cited by 9

Guanine quadruplexes and their roles in molecular processes

Mishra, S., Kota, S., Chaudhary, R., & Misra, H. S. (2021) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2021.1926417 · Cited by 9

Transcription near arrested DNA replication forks triggers ribosomal DNA copy number changes

Sasaki, M., & Kobayashi, T. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf014 · Cited by 6

A Sequence within the Varicella-Zoster Virus (VZV) OriS Is a Negative Regulator of DNA Replication and Is Bound by a Protein Complex Containing the VZV ORF29 Protein

Khalil, M. I., Arvin, A. M., Jones, J. O., & Ruyechan, W. T. (2011) · Journal of Virology · doi:10.1128/jvi.05501-11 · Cited by 8

Repeat RNAs associate with replication forks and post-replicative DNA

Gylling, H. M., González‐Aguilera, C., Smith, M. A., Kaczorowski, D. C., Groth, A., & Lund, A. H. (2020) · RNA · doi:10.1261/rna.074757.120 · Cited by 8

DNA repair during regeneration in Ambystoma mexicanum

García‐Lepe, U. O., Cruz‐Ramírez, A., & Bermúdez‐Cruz, R. M. (2020) · Developmental Dynamics · doi:10.1002/dvdy.276 · Cited by 11

SSB Facilitates Fork-Substrate Discrimination by the PriA DNA Helicase

Tan, H. Y., & Bianco, P. R. (2021) · ACS Omega · doi:10.1021/acsomega.1c00722 · Cited by 8

Blm helicase facilitates rapid replication of repetitive DNA sequences in early Drosophila development

Ruchert, J. M., Brady, M. M., McMahan, S., Lacey, K. J., Latta, L. C., Sekelsky, J. J., & Stoffregen, E. P. (2021) · Genetics · doi:10.1093/genetics/iyab169 · Cited by 8

Bacillus subtilis RecA, DisA, and RadA/Sms Interplay Prevents Replication Stress by Regulating Fork Remodeling

Torres, R., & Alonso, J. C. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.766897 · Cited by 8

Differential efficacies of Cas nucleases on microsatellites involved in human disorders and associated off-target mutations

Poggi, L., Emmenegger, L., Descorps‐Declère, S., Dumas, B., & Richard, G. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab569 · Cited by 8

Why Do Centromeres Evolve So Fast: BIR Replication, Hypermutation, Transposition, and Molecular-DrivePreprint

Rice, W. R. (2020) · Preprints.org · doi:10.20944/preprints202012.0669.v1 · Cited by 8

A TRilogy of ATR’s Non-Canonical Roles Throughout the Cell Cycle and Its Relation to Cancer

Joo, Y. K., Ramírez, C. D., & Kabeche, L. (2024) · Cancers · doi:10.3390/cancers16203536 · Cited by 8

C9orf72 hexanucleotide repeat allele tagging SNPs: Associations with ALS risk and longevity

Kaivola, K., Pirinen, M., Laaksovirta, H., Jansson, L., Rautila, O. S., Launes, J., Hokkanen, L., Lahti, J. M. T., Eriksson, J. G., Strandberg, T. E., et al. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1087098 · Cited by 7

A local ATR-dependent checkpoint pathway is activated by a site-specific replication fork block in human cells

Ahmed‐Seghir, S., Jalan, M., Grimsley, H. E., Sharma, A., Twayana, S., Kosiyatrakul, S. T., Thompson, C. M., Schildkraut, C. L., & Powell, S. N. (2023) · eLife · doi:10.7554/elife.87357.3 · Cited by 7

Preserving the Replication Fork in Response to Nucleotide Starvation: Evading the Replication Fork Collapse Point

Sarah, A. T., & Susan, L. (2013) · InTech eBooks · doi:10.5772/51393 · Cited by 7

Genetic interactions among homologous recombination mutants in Candida albicans

Bellido, A., Andaluz, E., Gómez‐Raja, J., Alvarez, A. M., & Larriba, G. (2014) · Fungal Genetics and Biology · doi:10.1016/j.fgb.2014.10.016 · Cited by 9

Deep statistical modelling of nanopore sequencing translocation times reveals latent non-B DNA structures

Hosseini, M., Palmer, A., Manka, W., Grady, P. G. S., Patchigolla, V. S. P., Bi, J., O'Neill, R. J. W., Chi, Z., & Aguiar, D. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad220 · Cited by 7

Joint Efforts of Replicative Helicase and SSB Ensure Inherent Replicative Tolerance of G‐Quadruplex

Guo, L., Bao, Y., Zhao, Y., Ren, Z., Bi, L., Zhang, X., Liu, C., Hou, X., Wang, M. D., & Sun, B. (2023) · Advanced Science · doi:10.1002/advs.202307696 · Cited by 10

Unraveling the Mysteries of Aging Through a Hutchinson–Gilford Progeria Syndrome Model

Serio, R. N. (2011) · Rejuvenation Research · doi:10.1089/rej.2010.1088 · Cited by 7

Mutation Landscape of Base Substitutions, Duplications, and Deletions in the Representative Current Cholera Pandemic Strain

Wei, W., Xiong, L., Ye, Y., Du, M., Gao, Y., Zhang, K.-Y., Jin, Y.-T., Yang, Z., Wong, P.-C., Lau, S. K. P., et al. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy151 · Cited by 7

Mutations in the insulator protein Suppressor of Hairy wing induce genome instability

Hsu, S.-J., Stow, E. C., Simmons, J. R., Wallace, H. A., Lopez, A. A., Stroud, S., & Labrador, M. (2020) · Chromosoma · doi:10.1007/s00412-020-00743-8 · Cited by 7

The Replication of Frataxin Gene Is Assured by Activation of Dormant Origins in the Presence of a GAA-Repeat Expansion

Stevanoni, M., Palumbo, E., & Russo, A. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006201 · Cited by 7

Single-molecule binding characterization of primosomal protein PriA involved in replication restart

Lee, T.-Y., Li, Y.-C., Lin, M.-G., Hsiao, C., & Li, H. (2021) · Physical Chemistry Chemical Physics · doi:10.1039/d1cp00638j · Cited by 6

DNA replication-associated lesions: importance in early tumorigenesis and cancer therapy

Petermann, E., & Helleday, T. (2007) · Biochemical Society Transactions · doi:10.1042/bst0351352 · Cited by 6

Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes

Lin, C.-H., Lian, C.-Y., Hsiung, C. A., & Chen, F. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-s9-s19 · Cited by 6

Up-regulated PIF1 predicts poor clinical outcomes and correlates with low immune infiltrates in clear cell renal cell carcinoma

Cai, T., Wang, N., Meng, P., Sun, W., & Cui, Y. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2022.1058040 · Cited by 6

Methods for the Detection of DNA Damage

Firsanov, D., Solovjeva, L., Mikhailov, V. M., & Svetlova, M. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-803309-8.00037-9 · Cited by 6

The shared ancestry between the C9orf72 hexanucleotide repeat expansion and intermediate-length alleles using haplotype sharing trees and HAPTK

Rautila, O. S., Kaivola, K., Rautila, H., Hokkanen, L., Launes, J., Strandberg, T. E., Laaksovirta, H., Palmio, J., & Tienari, P. J. (2024) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2023.12.019 · Cited by 5

Overcoming natural replication barriers formed by DNA structures and the role of repositioning to the nuclear periphery

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A nuclear orthologue of the dNTP triphosphohydrolase SAMHD1 controls dNTP homeostasis and genomic stability in Trypanosoma brucei

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