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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Mechanism of Replicative DNA Polymerase Delta Pausing and a Potential Role for DNA Polymerase Kappa in Common Fragile Site Replication

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DNA-damage accumulation and replicative arrest in Hutchinson–Gilford progeria syndrome

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Generic plasmid DNA production platform incorporating low metabolic burden seed‐stock and fed‐batch fermentation processes

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DNA replication stress: from molecular mechanisms to human disease

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A recurrent cancer-associated substitution in DNA polymerase ε produces a hyperactive enzyme

Xing, X., Kane, D. P., Bulock, C. R., Moore, E. A., Sharma, S., Chabes, A., & Shcherbakova, P. V. (2019) · Nature Communications · doi:10.1038/s41467-018-08145-2 · Cited by 67

Genome-wide high-resolution mapping of mitotic DNA synthesis sites and common fragile sites by direct sequencing

Ji, F., Liao, H., Pan, S. D., Ouyang, L., Jia, F., Fu, Z., Zhang, F., Geng, X., Wang, X., Li, T., et al. (2020) · Cell Research · doi:10.1038/s41422-020-0357-y · Cited by 65

The Human Specialized DNA Polymerases and Non-B DNA: Vital Relationships to Preserve Genome Integrity

Boyer, A.-S., Grgurević, S., Cazaux, C., & Hoffmann, J. (2013) · Journal of Molecular Biology · doi:10.1016/j.jmb.2013.09.022 · Cited by 74

p97 Promotes a Conserved Mechanism of Helicase Unloading during DNA Cross-Link Repair

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Nuclease dead Cas9 is a programmable roadblock for DNA replication

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Interference Between DNA Replication and Transcription as a Cause of Genomic Instability

Lin, Y., & Pasero, P. (2012) · Current Genomics · doi:10.2174/138920212799034767 · Cited by 58

Replication stress and genome rearrangements: lessons from yeast models

Lambert, S., & Carr, A. M. (2012) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2012.11.009 · Cited by 64

RecG Directs DNA Synthesis during Double-Strand Break Repair

Azeroglu, B., Mawer, J. S. P., Cockram, C. A., White, M. A., Hasan, A. M. M., Filatenkova, M., & Leach, D. R. F. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1005799 · Cited by 60

H3K4 methylation at active genes mitigates transcription-replication conflicts during replication stress

Chong, S. Y., Cutler, S., Lin, J., Tsai, C.-H., Tsai, H., Biggins, S., Tsukiyama, T., Lo, Y., & Kao, C.-F. (2020) · Nature Communications · doi:10.1038/s41467-020-14595-4 · Cited by 60

RNA polymerase mutations that facilitate replication progression in the rep uvrD recF mutant lacking two accessory replicative helicases

Baharoglu, Z., Lestini, R., Duigou, S., & Michel, B. (2010) · Molecular Microbiology · doi:10.1111/j.1365-2958.2010.07208.x · Cited by 59

S1-END-seq reveals DNA secondary structures in human cells

Matos-Rodrigues, G. E., van Wietmarschen, N., Wu, W., Tripathi, V., Koussa, N. C., Pavani, R., Nathan, W. J., Callén, E., Belinky, F., Mohammed, A., et al. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.08.007 · Cited by 63

Emerging roles of CST in maintaining genome stability and human disease

Stewart, J. A. (2018) · Frontiers in bioscience · doi:10.2741/4661 · Cited by 59

The end protection problem—an unexpected twist in the tail

Ruis, P., & Boulton, S. J. (2021) · Genes & Development · doi:10.1101/gad.344044.120 · Cited by 57

PRIMPOL ready, set, reprime!

Tirman, S., Cybulla, E., Quinet, A., Meroni, A., & Vindigni, A. (2020) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2020.1841089 · Cited by 60

Shaping the landscape of theEscherichia colichromosome: replication-transcription encounters in cells with an ectopic replication origin

Ivanova, D., Taylor, T. S., Smith, S. L., Dimude, J. U., Upton, A. L., Mehrjouy, M. M., Skovgaard, O., Sherratt, D. J., Retkutė, R., & Rudolph, C. J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv704 · Cited by 57

Historical perspective on the DNA damage response

Hanawalt, P. C. (2015) · DNA repair · doi:10.1016/j.dnarep.2015.10.001 · Cited by 63

Dynamic Evolution of Euchromatic Satellites on the X Chromosome in Drosophila melanogaster and the simulans Clade

Sproul, J. S., Khost, D. E., Eickbush, D. G., Negm, S., Wei, X., Wong, I., & Larracuente, A. M. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa078 · Cited by 54

Acute inactivation of the replicative helicase in human cells triggers MCM8–9-dependent DNA synthesisPreprint

Natsume, T., Nishimura, K., Minocherhomji, S., Bhowmick, R., Hickson, I. D., & Kanemaki, M. T. (2017) · Genes & Development · doi:10.1101/gad.297663.117 · Cited by 55

Chaperoning HMGA2 Protein Protects Stalled Replication Forks in Stem and Cancer Cells

Yu, H., Lim, H. H., Tjokro, N. O., Sathiyanathan, P., Natarajan, S., Chew, T. W., Klonisch, T. C., Goodman, S. D., Surana, U., & Dröge, P. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.01.014 · Cited by 56

Strategic role of the ubiquitin-dependent segregase p97 (VCP or Cdc48) in DNA replication

Ramadan, K., Halder, S., Wiseman, K., & Vaz, B. (2016) · Chromosoma · doi:10.1007/s00412-016-0587-4 · Cited by 56

Roles of human POLD1 and POLD3 in genome stability

Tumini, E., Barroso, S. I., Calero, C. P., & Aguilera, A. (2016) · Scientific Reports · doi:10.1038/srep38873 · Cited by 56

Template-switching during replication fork repair in bacteria

Lovett, S. T. (2017) · DNA repair · doi:10.1016/j.dnarep.2017.06.014 · Cited by 56

Bacterial global regulators DksA/ppGpp increase fidelity of transcription

Roghanian, M., Zenkin, N., & Yuzenkova, Y. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv003 · Cited by 54

Interactions of small molecules with DNA junctions

McQuaid, K. T., Pipier, A., Cardin, C. J., & Monchaud, D. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1043 · Cited by 54

Homeostatic regulation of meiotic DSB formation by ATM/ATR

Cooper, T. J., Wardell, K., Garcia, V., & Neale, M. J. (2014) · Experimental Cell Research · doi:10.1016/j.yexcr.2014.07.016 · Cited by 54

Regulation of DNA Replication through Natural Impediments in the Eukaryotic Genome

Gadaleta, M. C., & Noguchi, E. (2017) · Genes · doi:10.3390/genes8030098 · Cited by 64

Cobalt and nickel impair DNA metabolism by the oxidative stress independent pathway

Kumar, V., Mishra, R. K., Kaur, G., & Dutta, D. (2017) · Metallomics · doi:10.1039/c7mt00231a · Cited by 54

Endogenous DNA Double-Strand Breaks during DNA Transactions: Emerging Insights and Methods for Genome-Wide Profiling

Bouwman, B. A. M., & Crosetto, N. (2018) · Genes · doi:10.3390/genes9120632 · Cited by 65

Interaction of Rep and DnaB on DNA

Atkinson, J., Gupta, M. K., & McGlynn, P. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq975 · Cited by 53

Ctf4 Prevents Genome Rearrangements by Suppressing DNA Double-Strand Break Formation and Its End Resection at Arrested Replication Forks

Sasaki, M., & Kobayashi, T. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.04.020 · Cited by 52

DNA ADP-Ribosylation Stalls Replication and Is Reversed by RecF-Mediated Homologous Recombination and Nucleotide Excision Repair

Lawarée, E., Jankevicius, G., Cooper, C., Ahel, I., Uphoff, S., & Tang, C. M. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.01.014 · Cited by 54

Cohesin Causes Replicative DNA Damage by Trapping DNA Topological Stress

Minchell, N. E., Keszthelyi, A., & Baxter, J. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.03.013 · Cited by 54

The human intra-S checkpoint response to UVC-induced DNA damage

Kaufmann, W. K. (2009) · Carcinogenesis · doi:10.1093/carcin/bgp230 · Cited by 56

Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli

Kumar, A., Beloglazova, N. G., Bundalovic-Torma, C., Phanse, S., Deineko, V., Gagarinova, A. G., Musso, G. A., Vlasblom, J., Lemak, S., Hooshyar, M., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2015.12.060 · Cited by 51

Ribosomal DNA stability is supported by many ‘buffer genes’—introduction to the Yeast rDNA Stability Database

Kobayashi, T., & Sasaki, M. (2017) · FEMS Yeast Research · doi:10.1093/femsyr/fox001 · Cited by 54

Genome-wide mapping of individual replication fork velocities using nanopore sequencing

Theulot, B., Lacroix, L., Arbona, J., Millot, G. A., Jean, É., Cruaud, C., Pellet, J., Proux, F., Hennion, M., Engelen, S., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31012-0 · Cited by 51

Establishment of a replication fork barrier following induction of DNA binding in mammalian cells

Beuzer, P., Quivy, J., & Almouzni, G. (2014) · Cell Cycle · doi:10.4161/cc.28627 · Cited by 53

A single‐molecule approach to DNA replication in E scherichia coli cells demonstrated that DNA polymerase III is a major determinant of fork speed

Pham, T. M., Tan, K. W., Sakumura, Y., Okumura, K., Maki, H., & Akiyama, M. T. (2013) · Molecular Microbiology · doi:10.1111/mmi.12386 · Cited by 51

Nuclear architecture, chromosome domains and genetic damage

Folle, G. A. (2007) · Mutation Research/Reviews in Mutation Research · doi:10.1016/j.mrrev.2007.08.005 · Cited by 53

R-loop and diseases: the cell cycle matters

Xu, Y., Jiao, Y., Liu, C., Miao, R., Liu, C., Wang, Y., Ma, C., & Liu, J. (2024) · Molecular Cancer · doi:10.1186/s12943-024-02000-3 · Cited by 49

Embryonic Stem Cells License a High Level of Dormant Origins to Protect the Genome against Replication Stress

Ge, X. Q., Han, J., Cheng, E.-C., Yamaguchi, S., Shima, N., Thomas, J., & Lin, H. (2015) · Stem Cell Reports · doi:10.1016/j.stemcr.2015.06.002 · Cited by 47

Nucleoid occlusion prevents cell division during replication fork arrest in Bacillus subtilis

Bernard, R., Marquis, K. A., & Rudner, D. Z. (2010) · Molecular Microbiology · doi:10.1111/j.1365-2958.2010.07369.x · Cited by 52

DNA polymerase kappa produces interrupted mutations and displays polar pausing within mononucleotide microsatellite sequences

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Allele-specific analysis of DNA replication origins in mammalian cells

Bartholdy, B., Mukhopadhyay, R., Lajugie, J., Aladjem, M. I., & Bouhassira, E. E. (2015) · Nature Communications · doi:10.1038/ncomms8051 · Cited by 49

Direct Evidence for the Formation of Precatenanes during DNA Replication

Cebrián, J., Castán, A., Martínez, V., Kadomatsu-Hermosa, M. J., Parra, C., Fernández-Nestosa, M. J., Schaerer, C. E., Hernández, P., Krimer, D. B., & Schvartzman, J. B. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.642272 · Cited by 51

Altered Replication in Human Cells Promotes DMPK (CTG) n · (CAG) n Repeat Instability

Liu, G., Chen, X., Gao, Y., Lewis, T., Barthelemy, J., & Leffak, M. (2012) · Molecular and Cellular Biology · doi:10.1128/mcb.06727-11 · Cited by 49

ATR maintains chromosomal integrity during postnatal cerebellar neurogenesis and is required for medulloblastoma formation

Lang, P. Y., Nanjangud, G. J., Sokolsky‐Papkov, M., Shaw, C., Hwang, D., Parker, J. S., Kabanov, A. V., & Gershon, T. R. (2016) · Development · doi:10.1242/dev.139022 · Cited by 46

Complementary roles of Pif1 helicase and single stranded DNA binding proteins in stimulating DNA replication through G-quadruplexes

Sparks, M. A., Singh, S. P., Burgers, P., & Galletto, R. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz608 · Cited by 47

DNA Junction Ligands Trigger DNA Damage and Are Synthetic Lethal with DNA Repair Inhibitors in Cancer Cells

Duskova, K., Lejault, P., Benchimol, É., Guillot, R., Britton, S., Granzhan, A., & Monchaud, D. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.9b11150 · Cited by 46

A novel mechanistic spectrum underlies glaucoma-associated chromosome 6p25 copy number variation

Chanda, B., Asai-Coakwell, M., Ye, M., Mungall, A. J. J., Barrow, M., Dobyns, W. B., Behesti, H., Sowden, J. C., Carter, N. P., Walter, M. A., et al. (2008) · Human Molecular Genetics · doi:10.1093/hmg/ddn238 · Cited by 47

AID Induces Double-Strand Breaks at Immunoglobulin Switch Regions and c-MYC Causing Chromosomal Translocations in Yeast THO Mutants

Ruiz, J. F., Gómez‐González, B., & Aguilera, A. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002009 · Cited by 46

Time for remodeling: SNF2-family DNA translocases in replication fork metabolism and human disease

Joseph, S. A., Taglialatela, A., Leuzzi, G., Huang, J., Cuella-Martin, R., & Ciccia, A. (2020) · DNA repair · doi:10.1016/j.dnarep.2020.102943 · Cited by 48

Replication Fork Stalling and Checkpoint Activation by a PKD1 Locus Mirror Repeat Polypurine-Polypyrimidine (Pu-Py) Tract

Liu, G., Myers, S. L., Chen, X., Bissler, J. J., Sinden, R. R., & Leffak, M. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.402503 · Cited by 46

Contributions of the specialised DNA polymerases to replication of structured DNA

Wickramasinghe, C. M., Arzouk, H., Frey, A., Maiter, A., & Sale, J. E. (2015) · DNA repair · doi:10.1016/j.dnarep.2015.01.004 · Cited by 46

Comparative chloroplast genomics of the genus Taxodium

Duan, H., Guo, J., Xuan, L., Wang, Z., Li, M., Yin, Y., & Yang, Y. (2020) · BMC Genomics · doi:10.1186/s12864-020-6532-1 · Cited by 45

Human subtelomeric copy number gains suggest a DNA replication mechanism for formation: beyond breakage–fusion–bridge for telomere stabilization

Yatsenko, S. A., Hixson, P. M., Roney, E. K., Scott, D. A., Schaaf, C. P., Ng, Y., Palmer, R., Fisher, R. B., Patel, A., Cheung, S. W., et al. (2012) · Human Genetics · doi:10.1007/s00439-012-1216-9 · Cited by 44

Disruption of PCNA-lamins A/C interactions by prelamin A induces DNA replication fork stalling

Cobb, A. M., Murray, T. V., Warren, D. T., Liu, Y., & Shanahan, C. M. (2016) · Nucleus · doi:10.1080/19491034.2016.1239685 · Cited by 41

The Dark Side of UV-Induced DNA Lesion Repair

Strzałka, W., Zgłobicki, P., Kowalska, E., Bażant, A., Dziga, D., & Banaś, A. K. (2020) · Genes · doi:10.3390/genes11121450 · Cited by 48

Replication stress induces specific enrichment of RECQ1 at common fragile sites FRA3B and FRA16D

Lu, X., Parvathaneni, S., Hara, T., Lal, A., & Sharma, S. (2013) · Molecular Cancer · doi:10.1186/1476-4598-12-29 · Cited by 43

Triplex structures induce DNA double strand breaks via replication fork collapse in NER deficient cells

Tiwari, M. K., Adaku, N., Peart, N. J., & Rogers, F. A. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw515 · Cited by 42

Filling gaps in translesion DNA synthesis in human cells

Quinet, A., Lerner, L. K., Martins, D. J., & Menck, C. F. M. (2018) · Mutation Research/Genetic Toxicology and Environmental Mutagenesis · doi:10.1016/j.mrgentox.2018.02.004 · Cited by 46

Effect of static magnetic field on DNA synthesis: The interplay between DNA chirality and magnetic field left‐right asymmetry

Yang, X., Li, Z., Polyakova, T., Dejneka, A., Zablotskii, V., & Zhang, X. (2020) · FASEB BioAdvances · doi:10.1096/fba.2019-00045 · Cited by 42

Human PIF1 helicase supports DNA replication and cell growth under oncogenic-stress

Gagou, M. E., Ganesh, A. N., Phear, G. A., Robinson, D. A., Petermann, E., Cox, A., & Meuth, M. (2014) · Oncotarget · doi:10.18632/oncotarget.2501 · Cited by 42

The complete mitogenomes of Calameuta filiformis (Eversmann, 1847) and Calameuta idolon (Rossi, 1794) (Hymenoptera: Cephidae): The remarkable features of the elongated A+T rich region in Cephini

Korkmaz, E. M., Budak, M., Ördek, M. N., & Başıbüyük, H. H. (2015) · Gene · doi:10.1016/j.gene.2015.10.050 · Cited by 41

Replication–Transcription Conflicts: A Perpetual War on the Chromosome

Browning, K. R., & Merrikh, H. (2024) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-030222-115809 · Cited by 41

The hidden side of unstable DNA repeats: Mutagenesis at a distance

Shah, K., & Mirkin, S. M. (2015) · DNA repair · doi:10.1016/j.dnarep.2015.04.020 · Cited by 42

Replication stalling and heteroduplex formation within CAG/CTG trinucleotide repeats by mismatch repair

Viterbo, D., Michoud, G., Mosbach, V., Dujon, B., & Richard, G. (2016) · DNA repair · doi:10.1016/j.dnarep.2016.03.002 · Cited by 39

Non-B DNA Secondary Structures and Their Resolution by RecQ Helicases

Sharma, S. (2011) · Journal of Nucleic Acids · doi:10.4061/2011/724215 · Cited by 43

Plasmid pSM19035, a model to study stable maintenance in Firmicutes

Lioy, V. S., Pratto, F., de la Hoz, A. B., Ayora, S., & Alonso, J. C. (2010) · Plasmid · doi:10.1016/j.plasmid.2010.04.002 · Cited by 40

Single-Stranded Annealing Induced by Re-Initiation of Replication Origins Provides a Novel and Efficient Mechanism for Generating Copy Number Expansion via Non-Allelic Homologous Recombination

Finn, K. J., & Li, J. J. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003192 · Cited by 43

Break-Induced Replication Requires DNA Damage-Induced Phosphorylation of Pif1 and Leads to Telomere Lengthening

Vasianovich, Y., Harrington, L. A., & Makovets, S. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004679 · Cited by 40

From R-Loops to G-Quadruplexes: Emerging New Threats for the Replication Fork

Maffia, A., Ranise, C., & Sabbioneda, S. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21041506 · Cited by 40

Transcription and replication

Poveda, A., Clech, M. L., & Pasero, P. (2010) · Transcription · doi:10.4161/trns.1.2.12665 · Cited by 40

The Replication Stress Response on a Narrow Path Between Genomic Instability and Inflammation

Técher, H., & Pasero, P. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.702584 · Cited by 37

Spontaneous de novo germline mutations in humans and mice: rates, spectra, causes and consequences

Ohno, M. (2018) · Genes & Genetic Systems · doi:10.1266/ggs.18-00015 · Cited by 38

New Insights into the Functions of Transcription Factors that Bind the RNA Polymerase Secondary Channel

Zenkin, N., & Yuzenkova, Y. (2015) · Biomolecules · doi:10.3390/biom5031195 · Cited by 38

Non-B DNA-forming Sequences and WRN Deficiency Independently Increase the Frequency of Base Substitution in Human Cells

Bacolla, A., Wang, G., Jain, A., Chuzhanova, N. A., Cer, R. Z., Collins, J., Cooper, D. N., Bohr, V. A., & Vásquez, K. M. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.176636 · Cited by 37

The repair of G-quadruplex-induced DNA damage

van Kregten, M., & Tijsterman, M. (2014) · Experimental Cell Research · doi:10.1016/j.yexcr.2014.08.038 · Cited by 38

A Recombination Hot Spot in HIV-1 Contains Guanosine Runs That Can Form a G-quartet Structure and Promote Strand Transfer in Vitro

Shen, W., Gao, L., Balakrishnan, M., & Bambara, R. A. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.055368 · Cited by 38

Pif1 removes a Rap1-dependent barrier to the strand displacement activity of DNA polymerase δ

Koc, K. N., Singh, S. P., Stodola, J. L., Burgers, P., & Galletto, R. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw181 · Cited by 38

Plastid Genomes of Flowering Plants: Essential Principles

Ruhlman, T. A., & Jansen, R. K. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1472-3_1 · Cited by 37

Roles of DNA helicases in the maintenance of genome integrity

Bochman, M. L. (2014) · Molecular & Cellular Oncology · doi:10.4161/23723548.2014.963429 · Cited by 38

Molecular Traffic Jams on DNA

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Replication Restart after Replication-Transcription Conflicts Requires RecA in Bacillus subtilis

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