Processing ribonucleotides incorporated during eukaryotic DNA replication

Eukaryotic Mismatch Repair in Relation to DNA Replication

(2015) Thomas A. Kunkel et al.   Annual Review of Genetics

Unlocking the steric gate of DNA polymerase η leads to increased genomic instability in Saccharomyces cerevisiae

(2015) Katherine A. Donigan et al.   DNA REPAIR

Alternative solutions and new scenarios for translesion DNA synthesis by human PrimPol

(2015) María I. Martínez-Jiménez et al.   DNA REPAIR

Error-free and mutagenic processing of topoisomerase 1-provoked damage at genomic ribonucleotides

(2015) J. L. Sparks et al.   EMBO JOURNAL

Stimulation of Chromosomal Rearrangements by Ribonucleotides

(2015) H. N. Conover et al.   GENETICS

Elevated Genome-Wide Instability in Yeast Mutants Lacking RNase H Activity

(2015) K. O'Connell et al.   GENETICS

Analysis of Ribonucleotide Removal from DNA by Human Nucleotide Excision Repair

(2015) Laura A. Lindsey-Boltz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Topoisomerase I Alone Is Sufficient to Produce Short DNA Deletions and Can Also Reverse Nicks at Ribonucleotide Sites

(2015) Shar-yin Naomi Huang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Formation and Repair of Mismatches Containing Ribonucleotides and Oxidized Bases at Repeated DNA Sequences

(2015) Piera Cilli et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Major Role of DNA Polymerase δ in Replication of Both the Leading and Lagging DNA Strands

(2015) Robert E. Johnson et al.   MOLECULAR CELL

Lagging-strand replication shapes the mutational landscape of the genome

(2015) Martin A. M. Reijns et al.   NATURE

Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA

(2015) Kyung Duk Koh et al.   NATURE METHODS

Genome-wide mapping of embedded ribonucleotides and other noncanonical nucleotides using emRiboSeq and EndoSeq

(2015) James Ding et al.   Nature Protocols

R loops: new modulators of genome dynamics and function

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

Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation

(2015) Anders R Clausen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A global profile of replicative polymerase usage

(2015) Yasukazu Daigaku et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Evidence that processing of ribonucleotides in DNA by topoisomerase 1 is leading-strand specific

(2015) Jessica S Williams et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Ribonucleotides in DNA: hidden in plain sight

(2015) Sue Jinks-Robertson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Topoisomerase 1-dependent deletions initiated by incision at ribonucleotides are biased to the non-transcribed strand of a highly activated reporter

(2015) Jang-Eun Cho et al.   NUCLEIC ACIDS RESEARCH

TheSaccharomyces cerevisiaeDna2 can function as a sole nuclease in the processing of Okazaki fragments in DNA replication

(2015) Maryna Levikova et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analysis of the specificity and mechanisms of replication infidelity driven by imbalanced dNTP pools

(2015) Danielle L. Watt et al.   NUCLEIC ACIDS RESEARCH

Colon cancer-associated mutator DNA polymerase δ variant causes expansion of dNTP pools increasing its own infidelity

(2015) Tony M. Mertz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

dNTP pool levels modulate mutator phenotypes of error-prone DNA polymerase ε variants

(2015) Lindsey N. Williams et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular underpinnings of Aprataxin RNA/DNA deadenylase function and dysfunction in neurological disease

(2015) Matthew J. Schellenberg et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Breaking bad: R-loops and genome integrity

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

Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation

(2015) Anders R Clausen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A global profile of replicative polymerase usage

(2015) Yasukazu Daigaku et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Evidence that processing of ribonucleotides in DNA by topoisomerase 1 is leading-strand specific

(2015) Jessica S Williams et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Ribonucleotides in DNA: hidden in plain sight

(2015) Sue Jinks-Robertson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Slow mitochondrial repair of 5′-AMP renders mtDNA susceptible to damage in APTX deficient cells

(2015) Mansour Akbari et al.   Scientific Reports

Replicative DNA Polymerase δ but Not ε Proofreads Errors in Cis and in Trans

(2015) Carrie L. Flood et al.   PLoS Genetics

Ribonucleotide triggered DNA damage and RNA-DNA damage responses

(2015) Bret D Wallace et al.   RNA Biology

Transcription-Associated Mutagenesis

(2014) Sue Jinks-Robertson et al.   Annual Review of Genetics

Ribonuclease H2 in health and disease

(2014) Martin A.M. Reijns et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Ribonucleotides in DNA: Origins, repair and consequences

(2014) Jessica S. Williams et al.   DNA REPAIR

Ribonucleotide incorporation by yeast DNA polymerase ζ

(2014) Alena V. Makarova et al.   DNA REPAIR

Recognition and repair of chemically heterogeneous structures at DNA ends

(2014) Sara N. Andres et al.   ENVIRONMENTAL AND MOLECULAR MUTAGENESIS

Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication

(2014) Eve Shinbrot et al.   GENOME RESEARCH

Reduction of hRNase H2 activity in Aicardi–Goutières syndrome cells leads to replication stress and genome instability

(2014) Sara Pizzi et al.   HUMAN MOLECULAR GENETICS

Altered spatio-temporal dynamics of RNase H2 complex assembly at replication and repair sites in Aicardi–Goutières syndrome

(2014) Barbara Kind et al.   HUMAN MOLECULAR GENETICS

The Steric Gate of DNA Polymerase ι Regulates Ribonucleotide Incorporation and Deoxyribonucleotide Fidelity

(2014) Katherine A. Donigan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Proteolytic Degradation of Topoisomerase II (Top2) Enables the Processing of Top2·DNA and Top2·RNA Covalent Complexes by Tyrosyl-DNA-Phosphodiesterase 2 (TDP2)

(2014) Rui Gao et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Defective removal of ribonucleotides from DNA promotes systemic autoimmunity

(2014) Claudia Günther et al.   JOURNAL OF CLINICAL INVESTIGATION

A Saccharomyces cerevisiae RNase H2 Interaction Network Functions To Suppress Genome Instability

(2014) S. Allen-Soltero et al.   MOLECULAR AND CELLULAR BIOLOGY

RNA intrusions change DNA elastic properties and structure

(2014) Hsiang-Chih Chiu et al.   Nanoscale

Avoidance of ribonucleotide-induced mutations by RNase H2 and Srs2-Exo1 mechanisms

(2014) Catherine J. Potenski et al.   NATURE

ATP insertion opposite 8-oxo-deoxyguanosine by Pol4 mediates error-free tolerance in Schizosaccharomyces pombe

(2014) Guillermo Sastre-Moreno et al.   NUCLEIC ACIDS RESEARCH

How the misincorporation of ribonucleotides into genomic DNA can be both harmful and helpful to cells

(2014) Catherine J. Potenski et al.   NUCLEIC ACIDS RESEARCH

Ribose--An Internal Threat to DNA

(2014) K. W. Caldecott   SCIENCE

Replication-induced supercoiling: a neglected DNA transaction regulator?

(2014) Haojie Yu et al.   TRENDS IN BIOCHEMICAL SCIENCES

Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics

(2014) Heidi S. Alvey et al.   Nature Communications

Increased and Imbalanced dNTP Pools Symmetrically Promote Both Leading and Lagging Strand Replication Infidelity

(2014) Robert J. Buckland et al.   PLoS Genetics

Two distinct mechanisms of Topoisomerase 1-dependent mutagenesis in yeast

(2013) Jang-Eun Cho et al.   DNA REPAIR

Ribonucleotides as nucleotide excision repair substrates

(2013) Yuqin Cai et al.   DNA REPAIR

hPrimpol1/CCDC111 is a human DNA primase-polymerase required for the maintenance of genome integrity

(2013) Li Wan et al.   EMBO REPORTS

DNA Repair Mechanisms and the Bypass of DNA Damage in Saccharomyces cerevisiae

(2013) S. Boiteux et al.   GENETICS

DNA polymerase ɛ and δ exonuclease domain mutations in endometrial cancer

(2013) David N. Church et al.   HUMAN MOLECULAR GENETICS

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

Topoisomerase 1-Mediated Removal of Ribonucleotides from Nascent Leading-Strand DNA

(2013) Jessica S. Williams et al.   MOLECULAR CELL

Ribonucleotides Misincorporated into DNA Act as Strand-Discrimination Signals in Eukaryotic Mismatch Repair

(2013) Medini Manohar Ghodgaonkar et al.   MOLECULAR CELL

Ribonucleotides Are Signals for Mismatch Repair of Leading-Strand Replication Errors

(2013) Scott A. Lujan et al.   MOLECULAR CELL

Integrated genomic characterization of endometrial carcinoma

(2013) Gad Getz et al.   NATURE

Aprataxin resolves adenylated RNA–DNA junctions to maintain genome integrity

(2013) Percy Tumbale et al.   NATURE

Repriming of DNA synthesis at stalled replication forks by human PrimPol

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

RNase H2 roles in genome integrity revealed by unlinking its activities

(2013) Hyongi Chon et al.   NUCLEIC ACIDS RESEARCH

Structure-function analysis of ribonucleotide bypass by B family DNA replicases

(2013) A. R. Clausen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Break-Induced DNA Replication

(2013) R. P. Anand et al.   Cold Spring Harbor Perspectives in Biology

Rescuing Stalled or Damaged Replication Forks

(2013) J. T. P. Yeeles et al.   Cold Spring Harbor Perspectives in Biology

Okazaki Fragment Metabolism

(2013) L. Balakrishnan et al.   Cold Spring Harbor Perspectives in Biology

Translesion DNA Polymerases

(2013) M. F. Goodman et al.   Cold Spring Harbor Perspectives in Biology

Removal of Misincorporated Ribonucleotides from Prokaryotic Genomes: An Unexpected Role for Nucleotide Excision Repair

(2013) Alexandra Vaisman et al.   PLoS Genetics

Solution Structure of the Dickerson DNA Dodecamer Containing a Single Ribonucleotide

(2012) Eugene F. DeRose et al.   BIOCHEMISTRY

Enzymatic Removal of Ribonucleotides from DNA Is Essential for Mammalian Genome Integrity and Development

(2012) Martin A.M. Reijns et al.   CELL

Proofreading of ribonucleotides inserted into DNA by yeast DNA polymerase ɛ

(2012) Jessica S. Williams et al.   DNA REPAIR

Transcriptional responses to loss of RNase H2 in Saccharomyces cerevisiae

(2012) Mercedes E. Arana et al.   DNA REPAIR

Ribonucleotide incorporation, proofreading and bypass by human DNA polymerase δ

(2012) Anders R. Clausen et al.   DNA REPAIR

Endogenous DNA replication stress results in expansion of dNTP pools and a mutator phenotype

(2012) Marta B Davidson et al.   EMBO JOURNAL

Structural Factors That Determine Selectivity of a High Fidelity DNA Polymerase for Deoxy-, Dideoxy-, and Ribonucleotides

(2012) Weina Wang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Human DNA Polymerase ϵ Is Able to Efficiently Extend from Multiple Consecutive Ribonucleotides

(2012) A. Yasemin Göksenin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Frequent Incorporation of Ribonucleotides during HIV-1 Reverse Transcription and Their Attenuated Repair in Macrophages

(2012) Edward M. Kennedy et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mammalian RNase H2 removes ribonucleotides from DNA to maintain genome integrity

(2012) Bjoern Hiller et al.   JOURNAL OF EXPERIMENTAL MEDICINE

RNase H2-Initiated Ribonucleotide Excision Repair

(2012) Justin L. Sparks et al.   MOLECULAR CELL

RNase H and Postreplication Repair Protect Cells from Ribonucleotides Incorporated in DNA

(2012) Federico Lazzaro et al.   MOLECULAR CELL

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas

(2012) Claire Palles et al.   NATURE GENETICS

The catalytic cycle for ribonucleotide incorporation by human DNA Pol λ

(2012) Rajendrakumar A. Gosavi et al.   NUCLEIC ACIDS RESEARCH

Causes and consequences of ribonucleotide incorporation into nuclear DNA

(2012) Jacob Z. Dalgaard   TRENDS IN GENETICS

Mismatch Repair Balances Leading and Lagging Strand DNA Replication Fidelity

(2012) Scott A. Lujan et al.   PLoS Genetics

Unlocking the Sugar “Steric Gate” of DNA Polymerases

(2011) Jessica A. Brown et al.   BIOCHEMISTRY

Replication of ribonucleotide-containing DNA templates by yeast replicative polymerases

(2011) Danielle L. Watt et al.   DNA REPAIR

Mismatch repair-independent tandem repeat sequence instability resulting from ribonucleotide incorporation by DNA polymerase ɛ

(2011) Alan B. Clark et al.   DNA REPAIR

Timing and spacing of ubiquitin-dependent DNA damage bypass

(2011) Helle D. Ulrich   FEBS LETTERS

Molecular Insights into DNA Polymerase Deterrents for Ribonucleotide Insertion

(2011) Nisha A. Cavanaugh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Ribonucleotide Discrimination and Reverse Transcription by the Human Mitochondrial DNA Polymerase

(2011) Rajesh Kasiviswanathan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

RNase H and Multiple RNA Biogenesis Factors Cooperate to Prevent RNA:DNA Hybrids from Generating Genome Instability

(2011) Lamia Wahba et al.   MOLECULAR CELL

Epistasis analysis between homologous recombination genes in Saccharomyces cerevisiae identifies multiple repair pathways for Sgs1, Mus81-Mms4 and RNase H2

(2011) Miki Ii et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Mispaired rNMPs in DNA are mutagenic and are targets of mismatch repair and RNases H

(2011) Ying Shen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PCNA directs type 2 RNase H activity on DNA replication and repair substrates

(2011) Doryen Bubeck et al.   NUCLEIC ACIDS RESEARCH

Mutagenic Processing of Ribonucleotides in DNA by Yeast Topoisomerase I

(2011) N. Kim et al.   SCIENCE

Okazaki fragment maturation: nucleases take centre stage

(2011) L. Zheng et al.   Journal of Molecular Cell Biology

Identification of a Novel Type of Spacer Element Required for Imprinting in Fission Yeast

(2011) Suha Sayrac et al.   PLoS Genetics

The Major Roles of DNA Polymerases Epsilon and Delta at the Eukaryotic Replication Fork Are Evolutionarily Conserved

(2011) Izumi Miyabe et al.   PLoS Genetics

The phosphoCTD-interacting domain of Topoisomerase I

(2010) Jianhong Wu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Dna2 on the road to Okazaki fragment processing and genome stability in eukaryotes

(2010) Young-Hoon Kang et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Concurrent genetic alterations in DNA polymerase proofreading and mismatch repair in human colorectal cancer

(2010) Rintaro Yoshida et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

The Structural and Biochemical Characterization of Human RNase H2 Complex Reveals the Molecular Basis for Substrate Recognition and Aicardi-Goutières Syndrome Defects

(2010) Małgorzata Figiel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Structure of the Human RNase H2 Complex Defines Key Interaction Interfaces Relevant to Enzyme Function and Human Disease

(2010) Martin A. M. Reijns et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Crystal Structures of RNase H2 in Complex with Nucleic Acid Reveal the Mechanism of RNA-DNA Junction Recognition and Cleavage

(2010) Monika P. Rychlik et al.   MOLECULAR CELL

Genome instability due to ribonucleotide incorporation into DNA

(2010) Stephanie A Nick McElhinny et al.   Nature Chemical Biology

Highly mutagenic and severely imbalanced dNTP pools can escape detection by the S-phase checkpoint

(2010) Dinesh Kumar et al.   NUCLEIC ACIDS RESEARCH

Mechanisms of mutagenesis in vivo due to imbalanced dNTP pools

(2010) D. Kumar et al.   NUCLEIC ACIDS RESEARCH

Role for topoisomerase 1 in transcription-associated mutagenesis in yeast

(2010) M. J. Lippert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Topoisomerase 1 provokes the formation of short deletions in repeated sequences upon high transcription in Saccharomyces cerevisiae

(2010) T. Takahashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases

(2010) S. A. Nick McElhinny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanism and evolution of DNA primases

(2009) Robert D. Kuchta et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Ribonuclease H: the enzymes in eukaryotes

(2009) Susana M. Cerritelli et al.   FEBS Journal

Quantitation of cellular deoxynucleoside triphosphates

(2009) Paola Ferraro et al.   NUCLEIC ACIDS RESEARCH

Polymerase Dynamics at the Eukaryotic DNA Replication Fork

(2008) Peter M. J. Burgers   JOURNAL OF BIOLOGICAL CHEMISTRY

Contributions of the two accessory subunits, RNASEH2B and RNASEH2C, to the activity and properties of the human RNase H2 complex

(2008) Hyongi Chon et al.   NUCLEIC ACIDS RESEARCH

Dividing the workload at a eukaryotic replication fork

(2008) Thomas A. Kunkel et al.   TRENDS IN CELL BIOLOGY