Consequences and Resolution of Transcription–Replication Conflicts

Rtt109 slows replication speed by histone N-terminal acetylation

(2021) Nelly Frenkel et al.   GENOME RESEARCH

RNF168 regulates R-loop resolution and genomic stability in BRCA1/2-deficient tumors

(2021) Parasvi S. Patel et al.   JOURNAL OF CLINICAL INVESTIGATION

Persistence of RNA transcription during DNA replication delays duplication of transcription start sites until G2/M

(2021) Jianming Wang et al.   Cell Reports

Topological stress is responsible for the detrimental outcomes of head-on replication-transcription conflicts

(2021) Kevin S. Lang et al.   Cell Reports

The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts

(2021) Aleix Bayona-Feliu et al.   NATURE GENETICS

ARID1A regulates R-loop associated DNA replication stress

(2021) Shuhe Tsai et al.   PLoS Genetics

Determinants of Replication-Fork Pausing at tRNA Genes in Saccharomyces cerevisiae

(2020) Rani Yeung et al.   GENETICS

SF3B1 mutations induce R-loop accumulation and DNA damage in MDS and leukemia cells with therapeutic implications

(2020) Shalini Singh et al.   LEUKEMIA

Negative supercoil at gene boundaries modulates gene topology

(2020) Yathish Jagadheesh Achar et al.   NATURE

Chromatin fibers stabilize nucleosomes under torsional stress

(2020) Artur Kaczmarczyk et al.   Nature Communications

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

(2020) Shin Yen Chong et al.   Nature Communications

Sen1 Is Recruited to Replication Forks via Ctf4 and Mrc1 and Promotes Genome Stability

(2020) Rowin Appanah et al.   Cell Reports

UAP56/DDX39B is a major cotranscriptional RNA–DNA helicase that unwinds harmful R loops genome-wide

(2020) Carmen Pérez-Calero et al.   GENES & DEVELOPMENT

Chromatin replication and epigenetic cell memory

(2020) Kathleen R. Stewart-Morgan et al.   NATURE CELL BIOLOGY

A distinct role for recombination repair factors in an early cellular response to transcription–replication conflicts

(2020) Xin Shao et al.   NUCLEIC ACIDS RESEARCH

High-resolution mapping of mitotic DNA synthesis regions and common fragile sites in the human genome through direct sequencing

(2020) Morgane Macheret et al.   CELL RESEARCH

ATAD5 restricts R-loop formation through PCNA unloading and RNA helicase maintenance at the replication fork

(2020) Sangin Kim et al.   NUCLEIC ACIDS RESEARCH

Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites

(2020) Alexy Promonet et al.   Nature Communications

Genome-wide R-loop analysis defines unique roles for DDX5, XRN2, and PRMT5 in DNA/RNA hybrid resolution

(2020) Oscar D Villarreal et al.   Life Science Alliance

Replisome bypass of transcription complexes and R-loops

(2020) Jan-Gert Brüning et al.   NUCLEIC ACIDS RESEARCH

Inheritance of Histone (H3/H4): A Binary Choice?

(2020) Nicole J. Francis et al.   TRENDS IN BIOCHEMICAL SCIENCES

BRD4 prevents the accumulation of R-loops and protects against transcription–replication collision events and DNA damage

(2020) Fred C. Lam et al.   Nature Communications

BRD4 Prevents R-Loop Formation and Transcription-Replication Conflicts by Ensuring Efficient Transcription Elongation

(2020) Drake S. Edwards et al.   Cell Reports

TonEBP recognizes R-loops and initiates m6A RNA methylation for R-loop resolution

(2020) Hyun Je Kang et al.   NUCLEIC ACIDS RESEARCH

Replisome bypass of a protein-based R-loop block by Pif1

(2020) Grant D. Schauer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

WDR82/PNUTS-PP1 Prevents Transcription-Replication Conflicts by Promoting RNA Polymerase II Degradation on Chromatin

(2020) Helga B. Landsverk et al.   Cell Reports

Structural insight into nucleosome transcription by RNA polymerase II with elongation factors

(2019) Haruhiko Ehara et al.   SCIENCE

Direct removal of RNA polymerase barriers to replication by accessory replicative helicases

(2019) Michelle Hawkins et al.   NUCLEIC ACIDS RESEARCH

R-Loops as Cellular Regulators and Genomic Threats

(2019) Madzia P. Crossley et al.   MOLECULAR CELL

Transcription-mediated replication hindrance: a major driver of genome instability

(2019) Belén Gómez-González et al.   GENES & DEVELOPMENT

Transcription Restart Establishes Chromatin Accessibility after DNA Replication

(2019) Kathleen R. Stewart-Morgan et al.   MOLECULAR CELL

FANCM limits ALT activity by restricting telomeric replication stress induced by deregulated BLM and R-loops

(2019) Bruno Silva et al.   Nature Communications

Histone Recycling by FACT and Spt6 during Transcription Prevents the Scrambling of Histone Modifications

(2019) Célia Jeronimo et al.   Cell Reports

Control of DNA replication timing in the 3D genome

(2019) Claire Marchal et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The nucleosome core particle remembers its position through DNA replication and RNA transcription

(2019) Gavin Schlissel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Depletion of the MFAP1/SPP381 Splicing Factor Causes R-Loop-Independent Genome Instability

(2019) Irene Salas-Armenteros et al.   Cell Reports

Functional Analysis of the Replication Fork Proteome Identifies BET Proteins as PCNA Regulators

(2019) Sarah R. Wessel et al.   Cell Reports

Origins of DNA replication

(2019) Babatunde Ekundayo et al.   PLoS Genetics

R Loops: From Physiological to Pathological Roles

(2019) Tatiana García-Muse et al.   CELL

Fork Cleavage-Religation Cycle and Active Transcription Mediate Replication Restart after Fork Stalling at Co-transcriptional R-Loops

(2019) Nagaraja Chappidi et al.   MOLECULAR CELL

N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells

(2019) Abdulkadir Abakir et al.   NATURE GENETICS

ATAD5 promotes replication restart by regulating RAD51 and PCNA in response to replication stress

(2019) Su Hyung Park et al.   Nature Communications

Transcription-mediated organization of the replication initiation program across large genes sets common fragile sites genome-wide

(2019) Olivier Brison et al.   Nature Communications

The Clash of Macromolecular Titans: Replication-Transcription Conflicts in Bacteria

(2018) Kevin S. Lang et al.   Annual Review of Microbiology

Yra1-bound RNA–DNA hybrids cause orientation-independent transcription–replication collisions and telomere instability

(2018) María García-Rubio et al.   GENES & DEVELOPMENT

The Augmented R-Loop Is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High-Risk Splicing Factor Mutations

(2018) Liang Chen et al.   MOLECULAR CELL

Chromatin conformation regulates the coordination between DNA replication and transcription

(2018) Ricardo Almeida et al.   Nature Communications

Multiple signaling kinases target Mrc1 to prevent genomic instability triggered by transcription-replication conflicts

(2018) Alba Duch et al.   Nature Communications

Intragenic origins due to short G1 phases underlie oncogene-induced DNA replication stress

(2018) Morgane Macheret et al.   NATURE

The CMG Helicase Bypasses DNA-Protein Cross-Links to Facilitate Their Repair

(2018) Justin L. Sparks et al.   CELL

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

(2018) Saša Šviković et al.   EMBO JOURNAL

FANCD2 protects genome stability by recruiting RNA processing enzymes to resolve R-loops during mild replication stress

(2018) Yusuke Okamoto et al.   FEBS Journal

BRD4 and Cancer: going beyond transcriptional regulation

(2018) Benedetta Donati et al.   Molecular Cancer

Transcription shapes DNA replication initiation and termination in human cells

(2018) Yu-Hung Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription-dependent regulation of replication dynamics modulates genome stability

(2018) Marion Blin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SIRT7 and the DEAD-box helicase DDX21 cooperate to resolve genomic R loops and safeguard genome stability

(2017) Chenlin Song et al.   GENES & DEVELOPMENT

The DEAD-box protein DDX43 (HAGE) is a dual RNA-DNA helicase and has a K-homology domain required for full nucleic acid unwinding activity

(2017) Tanu Talwar et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

RECQ-like helicases Sgs1 and BLM regulate R-loop–associated genome instability

(2017) Emily Yun-Chia Chang et al.   JOURNAL OF CELL BIOLOGY

Senataxin: Genome Guardian at the Interface of Transcription and Neurodegeneration

(2017) Matthias Groh et al.   JOURNAL OF MOLECULAR BIOLOGY

R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters

(2017) Liang Chen et al.   MOLECULAR CELL

Histone Mutants Separate R Loop Formation from Genome Instability Induction

(2017) Desiré García-Pichardo et al.   MOLECULAR CELL

Replication Fork Reversal: Players and Guardians

(2017) Annabel Quinet et al.   MOLECULAR CELL

The elongation factor Spt4/5 regulates RNA polymerase II transcription through the nucleosome

(2017) John B. Crickard et al.   NUCLEIC ACIDS RESEARCH

Dormant origins and fork protection mechanisms rescue sister forks arrested by transcription

(2017) Alessandra Brambati et al.   NUCLEIC ACIDS RESEARCH

FANCD2 binding identifies conserved fragile sites at large transcribed genes in avian cells

(2017) Constanze Pentzold et al.   NUCLEIC ACIDS RESEARCH

Histone Marks in the ‘Driver’s Seat’: Functional Roles in Steering the Transcription Cycle

(2017) Leah A. Gates et al.   TRENDS IN BIOCHEMICAL SCIENCES

PIF1 family DNA helicases suppress R-loop mediated genome instability at tRNA genes

(2017) Phong Lan Thao Tran et al.   Nature Communications

Transcription Dynamics Prevent RNA-Mediated Genomic Instability through SRPK2-Dependent DDX23 Phosphorylation

(2017) Sreerama Chaitanya Sridhara et al.   Cell Reports

Transcription leads to pervasive replisome instability in bacteria

(2017) Sarah M Mangiameli et al.   eLife

Aquarius is required for proper CtIP expression and homologous recombination repair

(2017) Ryo Sakasai et al.   Scientific Reports

Repriming by PrimPol is critical for DNA replication restart downstream of lesions and chain-terminating nucleosides

(2016) Kaori Kobayashi et al.   CELL CYCLE

Transcription-replication conflicts at chromosomal fragile sites—consequences in M phase and beyond

(2016) Vibe H. Oestergaard et al.   CHROMOSOMA

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

Expression of Ribosomal RNA and Protein Genes in Human Embryonic Stem Cells Is Associated With the Activating H3K4me3 Histone Mark

(2016) Sayyed K. Zaidi et al.   JOURNAL OF CELLULAR PHYSIOLOGY

FANCD2 Facilitates Replication through Common Fragile Sites

(2016) Advaitha Madireddy et al.   MOLECULAR CELL

Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals

(2016) Lionel A. Sanz et al.   MOLECULAR CELL

The nature of mutations induced by replication–transcription collisions

(2016) T. Sabari Sankar et al.   NATURE

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

(2016) Joseph S Osmundson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2016) Panagiotis Kotsantis et al.   Nature Communications

Replication landscape of the human genome

(2016) Nataliya Petryk et al.   Nature Communications

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

(2016) Joseph S Osmundson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage

(2016) Caroline Townsend Stork et al.   eLife

DNA Secondary Structure at Chromosomal Fragile Sites in Human Disease

(2015) Ryan G. Thys et al.   CURRENT GENOMICS

Dynamic loading and redistribution of the Mcm2-7 helicase complex through the cell cycle

(2015) S. K. Powell 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

Peaks cloaked in the mist: The landscape of mammalian replication origins

(2015) Olivier Hyrien   JOURNAL OF CELL BIOLOGY

Post-licensing Specification of Eukaryotic Replication Origins by Facilitated Mcm2-7 Sliding along DNA

(2015) Julien Gros et al.   MOLECULAR CELL

DNA replication origin activation in space and time

(2015) Michalis Fragkos et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

R loops regulate promoter-proximal chromatin architecture and cellular differentiation

(2015) Poshen B Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Uncoupling histone turnover from transcription-associated histone H3 modifications

(2015) Paolo Ferrari et al.   NUCLEIC ACIDS RESEARCH

Head-to-head antisense transcription and R-loop formation promotes transcriptional activation

(2015) Raquel Boque-Sastre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Oncogenes create a unique landscape of fragile sites

(2015) Karin Miron et al.   Nature Communications

R loops regulate promoter-proximal chromatin architecture and cellular differentiation

(2015) Poshen B Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Are common fragile sites merely structural domains or highly organized “functional” units susceptible to oncogenic stress?

(2014) Alexandros G. Georgakilas 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

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

(2014) E. Herrera-Moyano 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

Transcription-Coupled Nucleotide Excision Repair Factors Promote R-Loop-Induced Genome Instability

(2014) Julie Sollier et al.   MOLECULAR CELL

R-loops induce repressive chromatin marks over mammalian gene terminators

(2014) Konstantina Skourti-Stathaki et al.   NATURE

Promoter-Bound Trinucleotide Repeat mRNA Drives Epigenetic Silencing in Fragile X Syndrome

(2014) D. Colak et al.   SCIENCE

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

(2014) Matthias Groh et al.   PLoS Genetics

Transcription-Associated R-Loop Formation across the Human FMR1 CGG-Repeat Region

(2014) Erick W. Loomis et al.   PLoS Genetics

Proteasome-Mediated Processing of Def1, a Critical Step in the Cellular Response to Transcription Stress

(2013) Marcus D. Wilson et al.   CELL

Identification of Early Replicating Fragile Sites that Contribute to Genome Instability

(2013) Jacqueline H. Barlow et al.   CELL

Early replication fragile sites: where replication–transcription collisions cause genetic instability

(2013) Oliver Mortusewicz et al.   EMBO JOURNAL

ATAD5 regulates the lifespan of DNA replication factories by modulating PCNA level on the chromatin

(2013) Kyoo-young Lee et al.   JOURNAL OF CELL BIOLOGY

Oncogenes induce genotoxic stress by mitotic processing of unusual replication intermediates

(2013) Kai J. Neelsen et al.   JOURNAL OF CELL BIOLOGY

The DNA Translocase FANCM/MHF Promotes Replication Traverse of DNA Interstrand Crosslinks

(2013) Jing Huang et al.   MOLECULAR CELL

PrimPol Bypasses UV Photoproducts during Eukaryotic Chromosomal DNA Replication

(2013) Julie Bianchi et al.   MOLECULAR CELL

PrimPol, an Archaic Primase/Polymerase Operating in Human Cells

(2013) Sara García-Gómez et al.   MOLECULAR CELL

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

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

Accelerated gene evolution through replication–transcription conflicts

(2013) Sandip Paul et al.   NATURE

Repriming of DNA synthesis at stalled replication forks by human PrimPol

(2013) Silvana Mourón et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PNUTS/PP1 Regulates RNAPII-Mediated Gene Expression and Is Necessary for Developmental Growth

(2013) Anita Ciurciu et al.   PLoS Genetics

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

Transcription coupled repair at the interface between transcription elongation and mRNP biogenesis

(2012) Hélène Gaillard et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

(2012) Amaya Alzu et al.   CELL

RNA Polymerase II Collision Interrupts Convergent Transcription

(2012) David J. Hobson et al.   MOLECULAR CELL

Replication–transcription conflicts in bacteria

(2012) Houra Merrikh et al.   NATURE REVIEWS MICROBIOLOGY

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

(2011) Rodrigo Bermejo et al.   CELL

Human DHX9 helicase preferentially unwinds RNA-containing displacement loops (R-loops) and G-quadruplexes

(2011) Prasun Chakraborty et al.   DNA REPAIR

Genome-wide function of THO/TREX in active genes prevents R-loop-dependent replication obstacles

(2011) Belén Gómez-González et al.   EMBO JOURNAL

Restriction of histone gene transcription to S phase by phosphorylation of a chromatin boundary protein

(2011) C. F. Kurat et al.   GENES & DEVELOPMENT

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

(2011) Anne Helmrich et al.   MOLECULAR CELL

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

(2011) Mikel Zaratiegui et al.   NATURE

What happens when replication and transcription complexes collide?

(2010) Richard T. Pomerantz et al.   CELL CYCLE

Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis

(2010) A. El Hage et al.   GENES & DEVELOPMENT

Human ELG1 Regulates the Level of Ubiquitinated Proliferating Cell Nuclear Antigen (PCNA) through Its Interactions with PCNA and USP1

(2010) Kyoo-young Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification and Characterization of a Novel Human PP1 Phosphatase Complex

(2010) Jeong-Heon Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Co-Orientation of Replication and Transcription Preserves Genome Integrity

(2010) Anjana Srivatsan et al.   PLoS Genetics

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

A Role for DEAD Box 1 at DNA Double-Strand Breaks

(2008) L. Li et al.   MOLECULAR AND CELLULAR BIOLOGY

The replisome uses mRNA as a primer after colliding with RNA polymerase

(2008) Richard T. Pomerantz et al.   NATURE

Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail

(2008) William F. Marzluff et al.   NATURE REVIEWS GENETICS

DNA Combing Reveals Intrinsic Temporal Disorder in the Replication of Yeast Chromosome VI

(2007) Daniel M. Czajkowsky et al.   JOURNAL OF MOLECULAR BIOLOGY