Transcription–replication conflicts: how they occur and how they are resolved

Transcription as a Threat to Genome Integrity

(2016) Hélène Gaillard et al.   Annual Review of Biochemistry

Mec1, INO80, and the PAF1 complex cooperate to limit transcription replication conflicts through RNAPII removal during replication stress

(2016) Jérôme Poli et al.   GENES & DEVELOPMENT

Dissecting the Roles of Divergent and Convergent Transcription in Chromosome Instability

(2016) Nicholas R. Pannunzio et al.   Cell Reports

p53 Maintains Genomic Stability by Preventing Interference between Transcription and Replication

(2016) Constance Qiao Xin Yeo et al.   Cell Reports

The Yin and Yang of R-loop biology

(2015) Lorenzo Costantino et al.   CURRENT OPINION IN CELL BIOLOGY

RPA prevents G-rich structure formation at lagging-strand telomeres to allow maintenance of chromosome ends

(2015) J. Audry et al.   EMBO JOURNAL

tRNA processing defects induce replication stress and Chk2-dependent disruption of piRNA transcription

(2015) A. Molla-Herman et al.   EMBO JOURNAL

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

(2015) Elizabeth A. Hoffman et al.   GENOME RESEARCH

Ccr4-Not and TFIIS Function Cooperatively To Rescue Arrested RNA Polymerase II

(2015) Arnob Dutta et al.   MOLECULAR AND CELLULAR BIOLOGY

The Fanconi Anemia Pathway Maintains Genome Stability by Coordinating Replication and Transcription

(2015) Rebekka A. Schwab et al.   MOLECULAR CELL

BRCA1 Recruitment to Transcriptional Pause Sites Is Required for R-Loop-Driven DNA Damage Repair

(2015) Elodie Hatchi et al.   MOLECULAR CELL

R loops: new modulators of genome dynamics and function

(2015) José M. Santos-Pereira et al.   NATURE REVIEWS GENETICS

Breaking bad: R-loops and genome integrity

(2015) Julie Sollier et al.   TRENDS IN CELL BIOLOGY

Oncogenes create a unique landscape of fragile sites

(2015) Karin Miron et al.   Nature Communications

RECQ5-dependent SUMOylation of DNA topoisomerase I prevents transcription-associated genome instability

(2015) Min Li et al.   Nature Communications

Rad53-Mediated Regulation of Rrm3 and Pif1 DNA Helicases Contributes to Prevention of Aberrant Fork Transitions under Replication Stress

(2015) Silvia Emma Rossi et al.   Cell Reports

The B. subtilis Accessory Helicase PcrA Facilitates DNA Replication through Transcription Units

(2015) Christopher N. Merrikh et al.   PLoS Genetics

The Fanconi Anemia Pathway Protects Genome Integrity from R-loops

(2015) María L. García-Rubio et al.   PLoS Genetics

RECQL5 Controls Transcript Elongation and Suppresses Genome Instability Associated with Transcription Stress

(2014) Marco Saponaro et al.   CELL

Dicer Promotes Transcription Termination at Sites of Replication Stress to Maintain Genome Stability

(2014) Stephane E. Castel et al.   CELL

Temporal separation of replication and transcription during S-phase progression

(2014) Matthieu Meryet-Figuiere et al.   CELL CYCLE

Replication initiation and genome instability: a crossroads for DNA and RNA synthesis

(2014) Jacqueline H. Barlow et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

RNA polymerase II contributes to preventing transcription-mediated replication fork stalls

(2014) I. Felipe-Abrio et al.   EMBO JOURNAL

ATR checkpoint kinase and CRL1 TRCP collaborate to degrade ASF1a and thus repress genes overlapping with clusters of stalled replication forks

(2014) J.-S. Im et al.   GENES & DEVELOPMENT

Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage

(2014) Sarah J. Hill et al.   GENES & DEVELOPMENT

The yeast and human FACT chromatin-reorganizing complexes solve R-loop-mediated transcription-replication conflicts

(2014) E. Herrera-Moyano et al.   GENES & DEVELOPMENT

A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression

(2014) K. Skourti-Stathaki et al.   GENES & DEVELOPMENT

Large transcription units unify copy number variants and common fragile sites arising under replication stress

(2014) Thomas E. Wilson et al.   GENOME RESEARCH

Separation of replication and transcription domains in nucleoli

(2014) E. Smirnov et al.   JOURNAL OF STRUCTURAL BIOLOGY

BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2

(2014) Vaibhav Bhatia et al.   NATURE

Topoisomerase I Plays a Critical Role in Suppressing Genome Instability at a Highly Transcribed G-Quadruplex-Forming Sequence

(2014) Puja Yadav et al.   PLoS Genetics

R-loops Associated with Triplet Repeat Expansions Promote Gene Silencing in Friedreich Ataxia and Fragile X Syndrome

(2014) Matthias Groh et al.   PLoS Genetics

Causes of Genome Instability

(2013) Andrés Aguilera et al.   Annual Review of Genetics

Identification of Early Replicating Fragile Sites that Contribute to Genome Instability

(2013) Jacqueline H. Barlow et al.   CELL

Human RECQL5: Guarding the crossroads of DNA replication and transcription and providing backup capability

(2013) Venkateswarlu Popuri et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

R Loops Are Linked to Histone H3 S10 Phosphorylation and Chromatin Condensation

(2013) Maikel Castellano-Pozo et al.   MOLECULAR CELL

The DNA Replication Program Is Altered at the FMR1 Locus in Fragile X Embryonic Stem Cells

(2013) Jeannine Gerhardt et al.   MOLECULAR CELL

Protein-DNA complexes are the primary sources of replication fork pausing in Escherichia coli

(2013) M. K. Gupta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional control of DNA replication licensing by Myc

(2013) Taras Valovka et al.   Scientific Reports

Eukaryotic Replisome Components Cooperate to Process Histones During Chromosome Replication

(2013) Magdalena Foltman et al.   Cell Reports

Cdc45 Is a Critical Effector of Myc-Dependent DNA Replication Stress

(2013) Seetha V. Srinivasan et al.   Cell Reports

Common Fragile Site Profiling in Epithelial and Erythroid Cells Reveals that Most Recurrent Cancer Deletions Lie in Fragile Sites Hosting Large Genes

(2013) Benoît Le Tallec et al.   Cell Reports

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

(2012) Amaya Alzu et al.   CELL

RNA Polymerase Backtracking in Gene Regulation and Genome Instability

(2012) Evgeny Nudler   CELL

DNA replication through hard-to-replicate sites, including both highly transcribed RNA Pol II and Pol III genes, requires the S. pombe Pfh1 helicase

(2012) N. Sabouri et al.   GENES & DEVELOPMENT

Senataxin, Defective in the Neurodegenerative Disorder Ataxia with Oculomotor Apraxia 2, Lies at the Interface of Transcription and the DNA Damage Response

(2012) O. Yuce et al.   MOLECULAR AND CELLULAR BIOLOGY

Preventing Replication Stress to Maintain Genome Stability: Resolving Conflicts between Replication and Transcription

(2012) Rodrigo Bermejo et al.   MOLECULAR CELL

Coordinated control of replication and transcription by a SAPK protects genomic integrity

(2012) Alba Duch et al.   NATURE

Small-molecule–induced DNA damage identifies alternative DNA structures in human genes

(2012) Raphaël Rodriguez et al.   Nature Chemical Biology

Increased replication initiation and conflicts with transcription underlie Cyclin E-induced replication stress

(2012) R M Jones et al.   ONCOGENE

Double-Strand Break Repair-Independent Role for BRCA2 in Blocking Stalled Replication Fork Degradation by MRE11

(2011) Katharina Schlacher et al.   CELL

DNA Replication through G-Quadruplex Motifs Is Promoted by the Saccharomyces cerevisiae Pif1 DNA Helicase

(2011) Katrin Paeschke et al.   CELL

The Replication Checkpoint Protects Fork Stability by Releasing Transcribed Genes from Nuclear Pores

(2011) Rodrigo Bermejo et al.   CELL

Linking RNA Polymerase Backtracking to Genome Instability in E. coli

(2011) Dipak Dutta et al.   CELL

Guanine repeat-containing sequences confer transcription-dependent instability in an orientation-specific manner in yeast

(2011) Nayun Kim et al.   DNA REPAIR

The Histone Chaperone Facilitates Chromatin Transcription (FACT) Protein Maintains Normal Replication Fork Rates

(2011) Takuya Abe et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Set2-RPB1 Interaction Domain of Human RECQ5 Is Important for Transcription-Associated Genome Stability

(2011) M. Li et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2011) Anne Helmrich et al.   MOLECULAR CELL

Failure of Origin Activation in Response to Fork Stalling Leads to Chromosomal Instability at Fragile Sites

(2011) Efrat Ozeri-Galai et al.   MOLECULAR CELL

Co-directional replication–transcription conflicts lead to replication restart

(2011) Houra Merrikh et al.   NATURE

RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II

(2011) Mikel Zaratiegui et al.   NATURE

Cell-type-specific replication initiation programs set fragility of the FRA3B fragile site

(2011) Anne Letessier et al.   NATURE

Topological constraints impair RNA polymerase II transcription and causes instability of plasmid-borne convergent genes

(2011) María L. García-Rubio et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Ashley K. Tehranchi et al.   CELL

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

(2010) Zeynep Baharoglu et al.   MOLECULAR MICROBIOLOGY

Replication stress checkpoint signaling controls tRNA gene transcription

(2010) Vesna C Nguyen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase

(2010) R. T. Pomerantz et al.   SCIENCE

Co-Orientation of Replication and Transcription Preserves Genome Integrity

(2010) Anjana Srivatsan et al.   PLoS Genetics

Genome-Organizing Factors Top2 and Hmo1 Prevent Chromosome Fragility at Sites of S phase Transcription

(2009) Rodrigo Bermejo et al.   CELL

Non-B DNA structure-induced genetic instability and evolution

(2009) Junhua Zhao et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

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

(2009) Anna Azvolinsky et al.   MOLECULAR CELL

Topoisomerase I suppresses genomic instability by preventing interference between replication and transcription

(2009) Sandie Tuduri et al.   NATURE CELL BIOLOGY

Recql5 Plays an Important Role in DNA Replication and Cell Survival after Camptothecin Treatment

(2008) Yiduo Hu et al.   MOLECULAR BIOLOGY OF THE CELL

Transcription-coupled DNA repair: two decades of progress and surprises

(2008) Philip C. Hanawalt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

An Oncogene-Induced DNA Damage Model for Cancer Development

(2008) T. D. Halazonetis et al.   SCIENCE