RNA polymerase pausing, stalling and bypass during transcription of damaged DNA: from molecular basis to functional consequences

RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder

(2022) Juntaek Oh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Peek Inside the Machines of Bacterial Nucleotide Excision Repair

(2021) Thanyalak Kraithong et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Structural basis for transcription complex disruption by the Mfd translocase

(2021) Jin Young Kang et al.   eLife

NusG, an Ancient Yet Rapidly Evolving Transcription Factor

(2021) Bing Wang et al.   Frontiers in Microbiology

Transcription-Coupled DNA Repair: From Mechanism to Human Disorder

(2021) Diana van den Heuvel et al.   TRENDS IN CELL BIOLOGY

Antivirals with common targets against highly pathogenic viruses

(2021) Lu Lu et al.   CELL

Opposite roles of transcription elongation factors Spt4/5 and Elf1 in RNA polymerase II transcription through B-form versus non-B DNA structures

(2021) Jun Xu et al.   NUCLEIC ACIDS RESEARCH

Cotranscriptional R-loop formation by Mfd involves topological partitioning of DNA

(2021) James R. Portman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacillus subtilis PcrA Helicase Removes Trafficking Barriers

(2021) María Moreno-del Álamo et al.   Cells

The Transcription-Repair Coupling Factor Mfd Prevents and Promotes Mutagenesis in a Context-Dependent Manner

(2021) Laura A. Lindsey-Boltz et al.   Frontiers in Molecular Biosciences

Transcription-coupled nucleotide excision repair: New insights revealed by genomic approaches

(2021) Mingrui Duan et al.   DNA REPAIR

Structural basis of human transcription–DNA repair coupling

(2021) Goran Kokic et al.   NATURE

Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability

(2021) Marit E. Geijer et al.   NATURE CELL BIOLOGY

Two distinct pathways of RNA polymerase backtracking determine the requirement for the Trigger Loop during RNA hydrolysis

(2021) Hamed Mosaei et al.   NUCLEIC ACIDS RESEARCH

β-CASP proteins removing RNA polymerase from DNA: when a torpedo is needed to shoot a sitting duck

(2021) Jana Wiedermannová et al.   NUCLEIC ACIDS RESEARCH

Bypass of complex co-directional replication-transcription collisions by replisome skipping

(2021) Jan-Gert Brüning et al.   NUCLEIC ACIDS RESEARCH

Three human RNA polymerases interact with TFIIH via a common RPB6 subunit

(2021) Masahiko Okuda et al.   NUCLEIC ACIDS RESEARCH

Promoter-proximal elongation regulates transcription in archaea

(2021) Fabian Blombach et al.   Nature Communications

Analysis of the PcrA-RNA polymerase complex reveals a helicase interaction motif and a role for PcrA/UvrD helicase in the suppression of R-loops

(2021) Inigo Urrutia-Irazabal et al.   eLife

Transcription-coupled repair and the transcriptional response to UV-Irradiation

(2021) Liam Gaul et al.   DNA REPAIR

Transcription coupled base excision repair in mammalian cells: So little is known and so much to uncover

(2021) Anirban Chakraborty et al.   DNA REPAIR

Dealing with transcription-blocking DNA damage: Repair mechanisms, RNA polymerase II processing and human disorders

(2021) Nan Jia et al.   DNA REPAIR

Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA

(2021) Kun Huang et al.   SCIENCE

Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair

(2021) Chunli Yan et al.   Nature Communications

Translesion DNA Synthesis and Carcinogenesis

(2020) E. S. Shilkin et al.   BIOCHEMISTRY-MOSCOW

Ubiquitination of DNA Damage-Stalled RNAPII Promotes Transcription-Coupled Repair

(2020) Yuka Nakazawa et al.   CELL

Role of the trigger loop in translesion RNA synthesis by bacterial RNA polymerase

(2020) Aleksei Agapov et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Chemical roadblocking of DNA transcription for nascent RNA display

(2020) Eric J. Strobel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Ribosome reactivates transcription by physically pushing RNA polymerase out of transcription arrest

(2020) Flint Stevenson-Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair–π and CH–π interactions

(2020) Juntaek Oh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The cooperative action of CSB, CSA, and UVSSA target TFIIH to DNA damage-stalled RNA polymerase II

(2020) Yana van der Weegen et al.   Nature Communications

A Genetic Map of the Response to DNA Damage in Human Cells

(2020) Michele Olivieri et al.   CELL

Bacillus subtilis PcrA Couples DNA Replication, Transcription, Recombination and Segregation

(2020) María Moreno-del Alamo et al.   Frontiers in Molecular Biosciences

Structural basis of Mfd-dependent transcription termination

(2020) Jing Shi et al.   NUCLEIC ACIDS RESEARCH

Molecular basis of transcriptional pausing, stalling, and transcription-coupled repair initiation

(2020) Juntaek Oh et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Genome-wide surveillance of transcription errors in response to genotoxic stress

(2020) C. Fritsch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mfd regulates RNA polymerase association with hard-to-transcribe regions in vivo, especially those with structured RNAs

(2020) Mark N. Ragheb et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular basis for RNA polymerase-dependent transcription complex recycling by the helicase-like motor protein HelD

(2020) Timothy P. Newing et al.   Nature Communications

Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase

(2020) Tomáš Kouba et al.   Nature Communications

The δ subunit and NTPase HelD institute a two-pronged mechanism for RNA polymerase recycling

(2020) Hao-Hong Pei et al.   Nature Communications

Distinct effects of DNA lesions on RNA synthesis by Escherichia coli RNA polymerase

(2019) Danil Pupov et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

DNA Methylation Reprogramming during Mammalian Development

(2019) Yang Zeng et al.   Genes

Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at DNA lesions

(2019) Sriyans Jain et al.   Nature Communications

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

(2019) Haruhiko Ehara et al.   SCIENCE

8-Oxo-guanine DNA damage induces transcription errors by escaping two distinct fidelity control checkpoints of RNA polymerase II

(2019) Kirill A. Konovalov et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Quantitation of Apurinic/Apyrimidinic Sites in Isolated DNA and in Mammalian Tissue with a Reduced Level of Artifacts

(2019) Haoqing Chen et al.   ANALYTICAL CHEMISTRY

The Extended ‘Two-Barrel’ Polymerases Superfamily: Structure, Function and Evolution

(2019) Ludovic Sauguet   JOURNAL OF MOLECULAR BIOLOGY

The enigmatic role of Mfd in replication-transcription conflicts in bacteria

(2019) Mark Ragheb et al.   DNA REPAIR

The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase

(2019) Georgiy A. Belogurov et al.   JOURNAL OF MOLECULAR BIOLOGY

Mechanisms of Transcriptional Pausing in Bacteria

(2019) Jin Young Kang et al.   JOURNAL OF MOLECULAR BIOLOGY

3.1 Å structure of yeast RNA polymerase II elongation complex stalled at a cyclobutane pyrimidine dimer lesion solved using streptavidin affinity grids

(2019) Indrajit Lahiri et al.   JOURNAL OF STRUCTURAL BIOLOGY

De Novo Heterozygous POLR2A Variants Cause a Neurodevelopmental Syndrome with Profound Infantile-Onset Hypotonia

(2019) Hanneke A. Haijes et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The DNA damage response to transcription stress

(2019) Hannes Lans et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Gre-family factors modulate DNA damage sensing by Deinococcus radiodurans RNA polymerase

(2019) Aleksei Agapov et al.   RNA Biology

Structure and function relationships in mammalian DNA polymerases

(2019) Nicole M. Hoitsma et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

5-Formylcytosine-induced DNA–peptide cross-links reduce transcription efficiency, but do not cause transcription errors in human cells

(2019) Shaofei Ji et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The pause-initiation limit restricts transcription activation in human cells

(2019) Saskia Gressel et al.   Nature Communications

Translesion and Repair DNA Polymerases: Diverse Structure and Mechanism

(2018) Wei Yang et al.   Annual Review of Biochemistry

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

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

Structural Basis for Transcript Elongation Control by NusG Family Universal Regulators

(2018) Jin Young Kang et al.   CELL

Specialised DNA polymerases in Escherichia coli: roles within multiple pathways

(2018) Sarah S. Henrikus et al.   CURRENT GENETICS

Transcription fidelity and its roles in the cell

(2018) Pamela Gamba et al.   CURRENT OPINION IN MICROBIOLOGY

Eukaryotic DNA polymerases

(2018) Rinku Jain et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Transcription-Coupled Repair and Complex Biology

(2018) James R. Portman et al.   JOURNAL OF MOLECULAR BIOLOGY

RNA Polymerase Accommodates a Pause RNA Hairpin by Global Conformational Rearrangements that Prolong Pausing

(2018) Jin Young Kang et al.   MOLECULAR CELL

Structural Basis for NusA Stabilized Transcriptional Pausing

(2018) Xieyang Guo et al.   MOLECULAR CELL

O6-methylguanine–induced transcriptional mutagenesis reduces p53 tumor-suppressor function

(2018) Monika Ezerskyte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Cellular Response to Transcription-Blocking DNA Damage

(2018) Lea H. Gregersen et al.   TRENDS IN BIOCHEMICAL SCIENCES

What happens at the lesion does not stay at the lesion: Transcription-coupled nucleotide excision repair and the effects of DNA damage on transcription in cis and trans

(2018) Marit E. Geijer et al.   DNA REPAIR

Structural basis of DNA lesion recognition for eukaryotic transcription-coupled nucleotide excision repair

(2018) Wei Wang et al.   DNA REPAIR

Structural basis of RNA polymerase I stalling at UV light-induced DNA damage

(2018) Marta Sanz-Murillo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-nucleotide resolution analysis of nucleotide excision repair of ribosomal DNA in humans and mice

(2018) Yanyan Yang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Inhibiting the Evolution of Antibiotic Resistance

(2018) Mark N. Ragheb et al.   MOLECULAR CELL

TFS and Spt4/5 accelerate transcription through archaeal histone-based chromatin

(2018) Travis J. Sanders et al.   MOLECULAR MICROBIOLOGY

Structure of transcribing RNA polymerase II-nucleosome complex

(2018) Lucas Farnung et al.   Nature Communications

Mechanisms of DNA damage, repair, and mutagenesis

(2017) Nimrat Chatterjee et al.   ENVIRONMENTAL AND MOLECULAR MUTAGENESIS

Conserved functions of the trigger loop and Gre factors in RNA cleavage by bacterial RNA polymerases

(2017) Nataliya Miropolskaya et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

RNA polymerase II is released from the DNA template during transcription-coupled repair in mammalian cells

(2017) Yi-Ying Chiou et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing

(2017) Wei Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural basis for the initiation of eukaryotic transcription-coupled DNA repair

(2017) Jun Xu et al.   NATURE

Widespread adenine N6-methylation of active genes in fungi

(2017) Stephen J Mondo et al.   NATURE GENETICS

Plant organellar DNA polymerases are replicative and translesion DNA synthesis polymerases

(2017) Noe Baruch-Torres et al.   NUCLEIC ACIDS RESEARCH

Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation and rNTP/dNTP discrimination

(2017) Michelle Marasco et al.   NUCLEIC ACIDS RESEARCH

Mfd Protein and Transcription-Repair Coupling inEscherichia coli

(2017) Christopher P. Selby   PHOTOCHEMISTRY AND PHOTOBIOLOGY

Mechanism of RNA polymerase II stalling by DNA alkylation

(2017) Stefano Malvezzi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide transcription-coupled repair inEscherichia coliis mediated by the Mfd translocase

(2017) Ogun Adebali et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Trigger loop of RNA polymerase is a positional, not acid–base, catalyst for both transcription and proofreading

(2017) Tatiana V. Mishanina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanism of DNA alkylation-induced transcriptional stalling, lesion bypass, and mutagenesis

(2017) Liang Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Factor-dependent archaeal transcription termination

(2017) Julie E. Walker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of the complete elongation complex of RNA polymerase II with basal factors

(2017) Haruhiko Ehara et al.   SCIENCE

A Magic Spot in Genome Maintenance

(2017) Aviram Rasouly et al.   TRENDS IN GENETICS

Mechanism of transcription-coupled DNA modification recognition

(2017) Ji Hyun Shin et al.   Cell and Bioscience

Transcription-coupled repair: an update

(2016) Graciela Spivak   ARCHIVES OF TOXICOLOGY

Real-Time Observation of Backtracking by Bacterial RNA Polymerase

(2016) Agnieszka Lass-Napiorkowska et al.   BIOCHEMISTRY

When DNA repair goes wrong: BER-generated DNA-protein crosslinks to oxidative lesions

(2016) Jason Luis Quiñones et al.   DNA REPAIR

Transcription-coupled repair of UV damage in the halophilic archaea

(2016) Nicole Stantial et al.   DNA REPAIR

Conservation and Divergence in Nucleotide Excision Repair Lesion Recognition

(2016) Nicolas Wirth et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Molecular Structures of Transcribing RNA Polymerase I

(2016) Lucas Tafur et al.   MOLECULAR CELL

DNA methylation on N6-adenine in mammalian embryonic stem cells

(2016) Tao P. Wu et al.   NATURE

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

(2016) Tatiana García-Muse et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Influence of major-groove chemical modifications of DNA on transcription by bacterial RNA polymerases

(2016) Veronika Raindlová et al.   NUCLEIC ACIDS RESEARCH

Regulation of transcriptional pausing through the secondary channel of RNA polymerase

(2016) Daria Esyunina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ppGpp couples transcription to DNA repair in E. coli

(2016) V. Kamarthapu et al.   SCIENCE

XRN2 Links Transcription Termination to DNA Damage and Replication Stress

(2016) Julio C. Morales et al.   PLoS Genetics

NusG inhibits RNA polymerase backtracking by stabilizing the minimal transcription bubble

(2016) Matti Turtola et al.   eLife

DNA Methylation on N6-Adenine in C. elegans

(2015) Eric Lieberman Greer et al.   CELL

N6-Methyladenine DNA Modification in Drosophila

(2015) Guoqiang Zhang et al.   CELL

Repair of UV induced DNA lesions in ribosomal gene chromatin and the role of “Odd” RNA polymerases (I and III)

(2015) Romain Charton et al.   DNA REPAIR

Nucleotide Excision Repair and Transcription-coupled DNA Repair Abrogate the Impact of DNA Damage on Transcription

(2015) Aditi Nadkarni et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Ratcheted and Ratchetable Structural States of RNA Polymerase Underlie Multiple Transcriptional Functions

(2015) Shun-ichi Sekine et al.   MOLECULAR CELL

Molecular structures of unbound and transcribing RNA polymerase III

(2015) Niklas A. Hoffmann et al.   NATURE

Molecular basis for 5-carboxycytosine recognition by RNA polymerase II elongation complex

(2015) Lanfeng Wang et al.   NATURE

Transcriptional inhibition and mutagenesis induced by N-nitroso compound-derived carboxymethylated thymidine adducts in DNA

(2015) Changjun You et al.   NUCLEIC ACIDS RESEARCH

Transcription blockage by stable H-DNA analogs in vitro

(2015) Shristi Pandey et al.   NUCLEIC ACIDS RESEARCH

Impact of template backbone heterogeneity on RNA polymerase II transcription

(2015) L. Xu et al.   NUCLEIC ACIDS RESEARCH

Structural basis for transcription reactivation by RapA

(2015) Bin Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An underlying mechanism for the increased mutagenesis of lagging-strand genes inBacillus subtilis

(2015) Samuel Million-Weaver et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanism of RNA polymerase II bypass of oxidative cyclopurine DNA lesions

(2015) Celine Walmacq et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular basis of transcriptional fidelity and DNA lesion-induced transcriptional mutagenesis

(2014) Liang Xu et al.   DNA REPAIR

UvrD facilitates DNA repair by pulling RNA polymerase backwards

(2014) Vitaly Epshtein et al.   NATURE

Transcriptional bypass of regioisomeric ethylated thymidine lesions by T7 RNA polymerase and human RNA polymerase II

(2014) Changjun You et al.   NUCLEIC ACIDS RESEARCH

Millisecond dynamics of RNA polymerase II translocation at atomic resolution

(2014) D.-A. Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stalled transcription complexes promote DNA repair at a distance

(2014) N. M. Haines et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of Tet-mediated Oxidation Products of 5-Methylcytosine on DNA Transcription in vitro and in Mammalian Cells

(2014) Changjun You et al.   Scientific Reports

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

Control of Transcriptional Fidelity by Active Center Tuning as Derived from RNA Polymerase Endonuclease Reaction

(2013) Ekaterina Sosunova et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Effect of a Monofunctional Phenanthriplatin-DNA Adduct on RNA Polymerase II Transcriptional Fidelity and Translesion Synthesis

(2013) Matthew W. Kellinger et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription

(2013) William A. Pastor et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Transcription-replication encounters, consequences and genomic instability

(2013) Anne Helmrich et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Interplay between the trigger loop and the F loop during RNA polymerase catalysis

(2013) Nataliya Miropolskaya et al.   NUCLEIC ACIDS RESEARCH

UV light-induced DNA lesions cause dissociation of yeast RNA polymerases-I and establishment of a specialized chromatin structure at rRNA genes

(2013) Maxime Tremblay et al.   NUCLEIC ACIDS RESEARCH

Antitumor activity of a pyrrole-imidazole polyamide

(2013) F. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection and simultaneous quantification of three smoking-related ethylthymidine adducts in human salivary DNA by liquid chromatography tandem mass spectrometry

(2013) Hauh-Jyun Candy Chen et al.   TOXICOLOGY LETTERS

DNA Base Damage by Reactive Oxygen Species, Oxidizing Agents, and UV Radiation

(2013) J. Cadet et al.   Cold Spring Harbor Perspectives in Biology

Base Excision Repair

(2013) H. E. Krokan et al.   Cold Spring Harbor Perspectives in Biology

Transcription Blockage by Bulky End Termini at Single-Strand Breaks in the DNA Template: Differential Effects of 5′ and 3′ Adducts

(2012) Alexander J. Neil et al.   BIOCHEMISTRY

Structural basis of transcription elongation

(2012) Fuensanta W. Martinez-Rucobo et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Ubiquitylation and degradation of elongating RNA polymerase II: The last resort

(2012) Marcus D. Wilson et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

RNA Polymerase Backtracking in Gene Regulation and Genome Instability

(2012) Evgeny Nudler   CELL

A Movie of RNA Polymerase II Transcription

(2012) Alan C.M. Cheung et al.   CELL

Mechanism of Translesion Transcription by RNA Polymerase II and Its Role in Cellular Resistance to DNA Damage

(2012) Celine Walmacq et al.   MOLECULAR CELL

Effects of DNA lesions on the transcription reaction of mitochondrial RNA polymerase: implications for bypass RNA synthesis on oxidative DNA lesions

(2012) Nozomi Nakanishi et al.   MUTAGENESIS

Initiation of transcription-coupled repair characterized at single-molecule resolution

(2012) Kévin Howan et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

A quantitative assay for assessing the effects of DNA lesions on transcription

(2012) Changjun You et al.   Nature Chemical Biology

5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription

(2012) Matthew W Kellinger et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Active site opening and closure control translocation of multisubunit RNA polymerase

(2012) Anssi M. Malinen et al.   NUCLEIC ACIDS RESEARCH

Phenanthriplatin, a monofunctional DNA-binding platinum anticancer drug candidate with unusual potency and cellular activity profile

(2012) Ga Young Park et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Monofunctional Platinum-DNA Adducts Are Strong Inhibitors of Transcription and Substrates for Nucleotide Excision Repair in Live Mammalian Cells

(2011) G. Zhu et al.   CANCER RESEARCH

Linking RNA Polymerase Backtracking to Genome Instability in E. coli

(2011) Dipak Dutta et al.   CELL

Structural basis of RNA polymerase II backtracking, arrest and reactivation

(2011) Alan C. M. Cheung et al.   NATURE

8-Oxo-7,8-dihydroguanine in DNA does not constitute a barrier to transcription, but is converted into transcription-blocking damage by OGG1

(2011) Nataliya Kitsera et al.   NUCLEIC ACIDS RESEARCH

Controlled interplay between trigger loop and Gre factor in the RNA polymerase active centre

(2011) M. Roghanian et al.   NUCLEIC ACIDS RESEARCH

Stepwise mechanism for transcription fidelity

(2010) Yulia Yuzenkova et al.   BMC BIOLOGY

Chemical investigation of light induced DNA bipyrimidine damage and repair

(2010) Korbinian Heil et al.   CHEMICAL SOCIETY REVIEWS

Regulation and Rate Enhancement during Transcription-Coupled DNA Repair

(2010) Laura Manelyte et al.   MOLECULAR CELL

Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein

(2010) Shunsuke Tagami et al.   NATURE

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

O 6-Methylguanine induces altered proteins at the level of transcription in human cells

(2010) John A. Burns et al.   NUCLEIC ACIDS RESEARCH

Spt4/5 stimulates transcription elongation through the RNA polymerase clamp coiled-coil motif

(2010) Angela Hirtreiter et al.   NUCLEIC ACIDS RESEARCH

Multiple roles of the RNA polymerase β′ SW2 region in transcription initiation, promoter escape, and RNA elongation

(2010) Danil Pupov et al.   NUCLEIC ACIDS RESEARCH

X-ray structure and mechanism of RNA polymerase II stalled at an antineoplastic monofunctional platinum-DNA adduct

(2010) D. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Roles for the transcription elongation factor NusA in both DNA repair and damage tolerance pathways in Escherichia coli

(2010) S. E. Cohen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Abasic sites and strand breaks in DNA cause transcriptional mutagenesis in Escherichia coli

(2010) Cheryl L. Clauson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Central role of the RNA polymerase trigger loop in intrinsic RNA hydrolysis

(2010) Y. Yuzenkova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Cooperation Between Translating Ribosomes and RNA Polymerase in Transcription Elongation

(2010) S. Proshkin et al.   SCIENCE

Molecular Basis of Transcriptional Mutagenesis at 8-Oxoguanine

(2009) Gerke E. Damsma et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural Basis of Transcription: Mismatch-Specific Fidelity Mechanisms and Paused RNA Polymerase II with Frayed RNA

(2009) Jasmin F. Sydow et al.   MOLECULAR CELL

Role of the RNA polymerase trigger loop in catalysis and pausing

(2009) Jinwei Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcriptional Mutagenesis Induced by 8-Oxoguanine in Mammalian Cells

(2009) Damien Brégeon et al.   PLoS Genetics

Transcription of DNA containing the 5-guanidino-4-nitroimidazole lesion by human RNA polymerase II and bacteriophage T7 RNA polymerase

(2008) Alexandra Dimitri et al.   DNA REPAIR

8,5′-Cyclopurine-2′-deoxynucleosides in DNA: Mechanisms of formation, measurement, repair and biological effects

(2008) Pawel Jaruga et al.   DNA REPAIR

Effects of the bacterial transcription-repair coupling factor during transcription of DNA containing non-bulky lesions

(2008) A SMITH et al.   DNA REPAIR

Differential Blocking Effects of the Acetaldehyde-derived DNA LesionN2-Ethyl-2′-deoxyguanosine on Transcription by Multisubunit and Single Subunit RNA Polymerases

(2008) Tsu-Fan Cheng et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

G4-forming Sequences in the Non-transcribed DNA Strand Pose Blocks to T7 RNA Polymerase and Mammalian RNA Polymerase II

(2008) Silvia Tornaletti et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Transient Reversal of RNA Polymerase II Active Site Closing Controls Fidelity of Transcription Elongation

(2008) Maria L. Kireeva et al.   MOLECULAR CELL

The RNA Polymerase II Trigger Loop Functions in Substrate Selection and Is Directly Targeted by α-Amanitin

(2008) Craig D. Kaplan et al.   MOLECULAR CELL

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

(2008) Richard T. Pomerantz et al.   NATURE

Structural basis of transcription inhibition by α-amanitin and implications for RNA polymerase II translocation

(2008) Florian Brueckner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription elongation past O6-methylguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase

(2008) Alexandra Dimitri et al.   NUCLEIC ACIDS RESEARCH

8-Oxoguanine-mediated transcriptional mutagenesis causes Ras activation in mammalian cells

(2008) T. T. Saxowsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription Processing at 1,N2-Ethenoguanine by Human RNA Polymerase II and Bacteriophage T7 RNA Polymerase

(2007) Alexandra Dimitri et al.   JOURNAL OF MOLECULAR BIOLOGY