Replication Fork Stalling at Natural Impediments

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The Complete Genome Sequence of Escherichia coli K-12

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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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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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ATR: an essential regulator of genome integrity

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R Loops: From Transcription Byproducts to Threats to Genome Stability

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Maintaining genome stability at the replication fork

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Sources of DNA Double-Strand Breaks and Models of Recombinational DNA RepairPreprint

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Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses

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ATM and ATR as therapeutic targets in cancer

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Collisions between Replication and Transcription Complexes Cause Common Fragile Site Instability at the Longest Human Genes

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Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes

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Mechanisms and Consequences of Double‐Strand DNA Break Formation in Chromatin

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Mechanisms of trinucleotide repeat instability during human development

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R-loop-mediated genomic instability is caused by impairment of replication fork progressionPreprint

Gan, W., Guan, Z., Liu, J., Gui, T., Shen, K., Manley, J. L., & Xialu Li, C. (2011) · Genes & Development · doi:10.1101/gad.17010011 · Cited by 459

Hallmarks of DNA replication stress

Saxena, S., & Zou, L. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.05.004 · Cited by 486

Identification of Early Replicating Fragile Sites that Contribute to Genome Instability

Barlow, J. H., Faryabi, R. B., Callén, E., Wong, N., Malhowski, A. J., Chen, H. T., Gutierrez-Cruz, G., Sun, H., McKinnon, P. J., Wright, G. W., et al. (2013) · Cell · doi:10.1016/j.cell.2013.01.006 · Cited by 464

Human mutation rate associated with DNA replication timing

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Non-B DNA structure-induced genetic instability and evolution

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Increased global transcription activity as a mechanism of replication stress in cancer

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G‐quadruplex‐induced instability during leading‐strand replication

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Linking RNA Polymerase Backtracking to Genome Instability in E. coli

Dutta, D., Shatalin, K. Y., Epshtein, V., Gottesman, M. E., & Nudler, E. (2011) · Cell · doi:10.1016/j.cell.2011.07.034 · Cited by 322

Epigenetic Instability due to Defective Replication of Structured DNA

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PCNA on the crossroad of cancer

Stoimenov, I., & Helleday, T. (2009) · Biochemical Society Transactions · doi:10.1042/bst0370605 · Cited by 301

Highly Transcribed RNA Polymerase II Genes Are Impediments to Replication Fork Progression in Saccharomyces cerevisiae

Azvolinsky, A., Giresi, P. G., Lieb, J. D., & Zakian, V. A. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.05.022 · Cited by 285

The impact of replication stress on replication dynamics and DNA damage in vertebrate cells

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A dual function of the CRISPR–Cas system in bacterial antivirus immunity and DNA repair

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The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in vivo

Boubakri, H., de Septenville, A. L., Viguera, E., & Michel, B. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.308 · Cited by 253

The Plastid Genomes of Flowering Plants

Ruhlman, T. A., & Jansen, R. K. (2014) · Methods in molecular biology · doi:10.1007/978-1-62703-995-6_1 · Cited by 253

Fragile sites in cancer: more than meets the eye

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Senataxin Associates with Replication Forks to Protect Fork Integrity across RNA-Polymerase-II-Transcribed Genes

Alzu, A., Bermejo, R., Begnis, M., Lucca, C., Piccini, D., Carotenuto, W., Saponaro, M., Brambati, A., Cocito, A., Foiani, M., et al. (2012) · Cell · doi:10.1016/j.cell.2012.09.041 · Cited by 251

Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist’s perspective

Chowdhury, D. (2013) · Physics Reports · doi:10.1016/j.physrep.2013.03.005 · Cited by 221

Whirly proteins maintain plastid genome stability in Arabidopsis

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Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomesPreprint

Chen, C.-L., Rappailles, A., Duquenne, L., Huvet, M., Guilbaud, G., Farinelli, L., Audit, B., d'Aubenton-Carafa, Y., Arnéodo, A., Hyrien, O., et al. (2010) · Genome Research · doi:10.1101/gr.098947.109 · Cited by 221

Nuclear Deformation Causes DNA Damage by Increasing Replication Stress

Shah, P., Hobson, C. M., Cheng, S., Colville, M. J., Paszek, M. J., Superfine, R., & Lammerding, J. (2020) · Current Biology · doi:10.1016/j.cub.2020.11.037 · Cited by 213

Dual Roles of Poly(dA:dT) Tracts in Replication Initiation and Fork Collapse

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Co-Orientation of Replication and Transcription Preserves Genome Integrity

Srivatsan, A., Tehranchi, A. K., MacAlpine, D. M., & Wang, J. D. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000810 · Cited by 194

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

Co-directional replication–transcription conflicts lead to replication restart

Merrikh, H., Machón, C., Grainger, W. H., Grossman, A. D., & Soultanas, P. (2011) · Nature · doi:10.1038/nature09758 · Cited by 187

Plasmid DNA vaccine vector design: Impact on efficacy, safety and upstream production

Williams, J. A., Carnes, A. E., & Hodgson, C. P. (2009) · Biotechnology Advances · doi:10.1016/j.biotechadv.2009.02.003 · Cited by 186

Replication Stress-Induced Genome Instability: The Dark Side of Replication Maintenance by Homologous Recombination

Carr, A. M., & Lambert, S. (2013) · Journal of Molecular Biology · doi:10.1016/j.jmb.2013.04.023 · Cited by 201

FANCD2 Facilitates Replication through Common Fragile Sites

Madireddy, A., Kosiyatrakul, S. T., Boisvert, R. A., Herrera‐Moyano, E., García-Rubio, M. L., Gerhardt, J., Vuono, E. A., Owen, N. M., Yan, Z., Olson, S. B., et al. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.09.017 · Cited by 174

The Intra-S Phase Checkpoint Targets Dna2 to Prevent Stalled Replication Forks from Reversing

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Rep Provides a Second Motor at the Replisome to Promote Duplication of Protein-Bound DNA

Guy, C. P., Atkinson, J., Gupta, M. K., Mahdi, A. A., Gwynn, E. J., Rudolph, C. J., Moon, P. B., van Knippenberg, I. C., Cadman, C. J., Dillingham, M. S., et al. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.11.009 · Cited by 163

R-loop generation during transcription: Formation, processing and cellular outcomes

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Mechanisms and implications of transcription blockage by guanine-rich DNA sequences

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Clusters of Nucleotide Substitutions and Insertion/Deletion Mutations Are Associated with Repeat Sequences

McDonald, M. J., Wang, W.-C., Huang, H., & Leu, J. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1000622 · Cited by 153

Replication-dependent instability at (CTG)•(CAG) repeat hairpins in human cells

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The Transcription Factor DksA Prevents Conflicts between DNA Replication and Transcription Machinery

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The Interplay between G-quadruplex and Transcription

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Accelerated gene evolution through replication–transcription conflicts

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Oxidative Stress Induces Telomere Dysfunction and Senescence by Replication Fork Arrest

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Mechanisms of structural chromosomal rearrangement formation

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DNA triplet repeat expansion and mismatch repair

Iyer, R. R., Pluciennik, A., Napierala, M., & Wells, R. D. (2015) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060614-034010 · Cited by 130

Determinants of G quadruplex‐induced epigenetic instability in REV1‐deficient cells

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Replication Stress, DNA Damage, Inflammatory Cytokines and Innate Immune Response

Ragu, S., Matos-Rodrigues, G. E., & López, B. S. (2020) · Genes · doi:10.3390/genes11040409 · Cited by 131

Double-strand break repair in bacteria: a view fromBacillus subtilis

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DNA Damage Response and Immune Defense

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Genomic instability and DNA damage responses in progeria arising from defective maturation of prelamin A

Musich, P. R., & Zou, Y. (2009) · Aging · doi:10.18632/aging.100012 · Cited by 117

Transcription termination maintains chromosome integrity

Washburn, R. S., & Gottesman, M. E. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1009564108 · Cited by 117

Involvement of xeroderma pigmentosum group A (XPA) in progeria arising from defective maturation of prelamin A

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Mechanisms of rDNA Copy Number Maintenance

Nelson, J. O., Watase, G. J., Warsinger-Pepe, N., & Yamashita, Y. M. (2019) · Trends in Genetics · doi:10.1016/j.tig.2019.07.006 · Cited by 120

Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome

Guiblet, W. M., Cremona, M. A., Harris, R. S., Chen, D., Eckert, K. A., Chiaromonte, F., Huang, Y.-F., & Makova, K. D. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1269 · Cited by 115

Replication Fork Reversal after Replication–Transcription Collision

de Septenville, A. L., Duigou, S., Boubakri, H., & Michel, B. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002622 · Cited by 113

Proliferating Cell Nuclear Antigen (PCNA) Regulates Primordial Follicle Assembly by Promoting Apoptosis of Oocytes in Fetal and Neonatal Mouse Ovaries

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Multiple roles of DNA2 nuclease/helicase in DNA metabolism, genome stability and human diseases

Zheng, L., Meng, Y., Campbell, J. L., & Shen, B. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1101 · Cited by 113

At the Beginning of the End and in the Middle of the Beginning: Structure and Maintenance of Telomeric DNA Repeats and Interstitial Telomeric Sequences

Aksenova, A. Y., & Mirkin, S. M. (2019) · Genes · doi:10.3390/genes10020118 · Cited by 114

Identifying G-Quadruplex-DNA-Disrupting Small Molecules

Mitteaux, J., Lejault, P., Wojciechowski, F., Joubert, A., Boudon, J., Desbois, N., Gros, C. P., Hudson, R. H. E., Boulé, J.-B., Granzhan, A., et al. (2021) · Journal of the American Chemical Society · doi:10.1021/jacs.1c04426 · Cited by 111

DNA Sequences That Interfere with Transcription: Implications for Genome Function and Stability

Belotserkovskii, B. P., Mirkin, S. M., & Hanawalt, P. C. (2013) · Chemical Reviews · doi:10.1021/cr400078y · Cited by 103

Targeting DNA damage and repair: Embracing the pharmacological era for successful cancer therapy

Aziz, K., Nowsheen, S., Pantelias, G. E., Iliakis, G. E., Gorgoulis, V. G., & Georgakilas, A. G. (2011) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2011.11.010 · Cited by 107

R‐loop formation during S phase is restricted by PrimPol‐mediated repriming

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Impediments to replication fork movement: stabilisation, reactivation and genome instability

Lambert, S., & Carr, A. M. (2013) · Chromosoma · doi:10.1007/s00412-013-0398-9 · Cited by 117

Structure and repair of replication-coupled DNA breaks

Pavani, R., Tripathi, V., Vrtis, K. B., Zong, D., Chari, R., Callén, E., Pankajam, A. V., Zhen, G., Matos-Rodrigues, G. E., Yang, J., et al. (2024) · Science · doi:10.1126/science.ado3867 · Cited by 97

Replication fork instability and the consequences of fork collisions from rereplicationPreprint

Alexander, J. L., & Orr‐Weaver, T. L. (2016) · Genes & Development · doi:10.1101/gad.288142.116 · Cited by 104

Local and global functions of Timeless and Tipin in replication fork protection

Leman, A. R., & Noguchi, E. (2012) · Cell Cycle · doi:10.4161/cc.21989 · Cited by 99

Overcoming natural replication barriers: differential helicase requirements

Anand, R., Shah, K., Niu, H., Sung, P., Mirkin, S. M., & Freudenreich, C. H. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr836 · Cited by 92

The conflict between DNA replication and transcription

McGlynn, P., Savery, N. J., & Dillingham, M. S. (2012) · Molecular Microbiology · doi:10.1111/j.1365-2958.2012.08102.x · Cited by 92

The role of fork stalling and DNA structures in causing chromosome fragility

Kaushal, S., & Freudenreich, C. H. (2018) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22721 · Cited by 95

Recovery of Arrested Replication Forks by Homologous Recombination Is Error-Prone

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Stalled replication forks within heterochromatin require ATRX for protection

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G-quadruplex-interacting compounds alter latent DNA replication and episomal persistence of KSHV

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Human telomeres replicate using chromosome-specific, rather than universal, replication programs

Drosopoulos, W. C., Kosiyatrakul, S. T., Yan, Z., Calderano, S. G., & Schildkraut, C. L. (2012) · The Journal of Cell Biology · doi:10.1083/jcb.201112083 · Cited by 88

Break-seq reveals hydroxyurea-induced chromosome fragility as a result of unscheduled conflict between DNA replication and transcriptionPreprint

Hoffman, E. A., McCulley, A., Haarer, B. K., Arnak, R., & Feng, W. (2015) · Genome Research · doi:10.1101/gr.180497.114 · Cited by 86

Is RecG a general guardian of the bacterial genome?

Rudolph, C. J., Upton, A. L., Briggs, G. S., & Lloyd, R. G. (2010) · DNA repair · doi:10.1016/j.dnarep.2009.12.014 · Cited by 83

Cooperation of RAD51 and RAD54 in regression of a model replication fork

Bugreev, D. V., Rossi, M. J., & Mazin, A. V. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1139 · Cited by 85

Transcription leads to pervasive replisome instability in bacteria

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Whither the replisome: Emerging perspectives on the dynamic nature of the DNA replication machinery

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DNA structure and the Werner protein modulate human DNA polymerase delta-dependent replication dynamics within the common fragile site FRA16D

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Pif1-family helicases cooperatively suppress widespread replication-fork arrest at tRNA genes

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Rad3ATR Decorates Critical Chromosomal Domains with γH2A to Protect Genome Integrity during S-Phase in Fission Yeast

Rozenzhak, S., Mejía-Ramírez, E., Williams, J. S., Schaffer, L., Hammond, J. A., Head, S. R., & Russell, P. R. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001032 · Cited by 79

Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error ratePreprint

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