On the public citation graph

R-loop homeostasis and cancer mutagenesis promoted by the DNA cytosine deaminase APOBEC3B

https://doi.org/10.1101/2021.08.30.458235

0 signed · 131 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.

Claim with ORCID

Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.

See reference health

What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/jmr.2284openalex-snapshot

The sub‐nanomolar binding of DNA–RNA hybrids by the single‐chain Fv fragment of antibody S9.6

inferredcites →https://doi.org/10.1002/wrna.1593openalex-snapshot

Transcription and splicing: A two‐way street

inferredcites →https://doi.org/10.1016/0022-1759(86)90040-2openalex-snapshot

Characterization of monoclonal antibody to DNA · RNA and its application to immunodetection of hybrids

inferredcites →https://doi.org/10.1016/j.cbpa.2018.01.016openalex-snapshot

Harnessing natural DNA modifying activities for editing of the genome and epigenome

inferredcites →https://doi.org/10.1016/j.cell.2005.06.008openalex-snapshot

Inactivation of the SR Protein Splicing Factor ASF/SF2 Results in Genomic Instability

inferredcites →https://doi.org/10.1016/j.cell.2012.04.024openalex-snapshot

Mutational Processes Molding the Genomes of 21 Breast Cancers

inferredcites →https://doi.org/10.1016/j.cell.2015.12.050openalex-snapshot

Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair

inferredcites →https://doi.org/10.1016/j.cell.2017.07.043openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.cell.2019.08.055openalex-snapshot

R Loops: From Physiological to Pathological Roles

inferredcites →https://doi.org/10.1016/j.cellsig.2008.03.001openalex-snapshot

Phorbol ester-stimulated NF-κB-dependent transcription: Roles for isoforms of novel protein kinase C

inferredcites →https://doi.org/10.1016/j.celrep.2016.01.021openalex-snapshot

APOBEC3A and APOBEC3B Preferentially Deaminate the Lagging Strand Template during DNA Replication

inferredcites →https://doi.org/10.1016/j.celrep.2017.12.086openalex-snapshot

BRCA2 Regulates Transcription Elongation by RNA Polymerase II to Prevent R-Loop Accumulation

inferredcites →https://doi.org/10.1016/j.celrep.2018.04.025openalex-snapshot

RNA/DNA Hybrid Interactome Identifies DXH9 as a Molecular Player in Transcriptional Termination and R-Loop-Associated DNA Damage

inferredcites →https://doi.org/10.1016/j.celrep.2018.12.084openalex-snapshot

Binding of FANCI-FANCD2 Complex to RNA and R-Loops Stimulates Robust FANCD2 Monoubiquitination

inferredcites →https://doi.org/10.1016/j.celrep.2020.108166openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.chembiol.2017.10.007openalex-snapshot

APOBEC Enzymes as Targets for Virus and Cancer Therapy

inferredcites →https://doi.org/10.1016/j.dnarep.2010.02.010openalex-snapshot

Determinants of sequence-specificity within human AID and APOBEC3G

inferredcites →https://doi.org/10.1016/j.dnarep.2014.03.023openalex-snapshot

The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability

inferredcites →https://doi.org/10.1016/j.dnarep.2015.11.011openalex-snapshot

Antibody diversification caused by disrupted mismatch repair and promiscuous DNA polymerases

inferredcites →https://doi.org/10.1016/j.dnarep.2018.08.009openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.dnarep.2019.102700openalex-snapshot

The spectrum of APOBEC3 activity: From anti-viral agents to anti-cancer opportunities

inferredcites →https://doi.org/10.1016/j.ggedit.2021.100005openalex-snapshot

Base editors: Expanding the types of DNA damage products harnessed for genome editing

inferredcites →https://doi.org/10.1016/j.jmb.2013.07.040openalex-snapshot

The Local Dinucleotide Preference of APOBEC3G Can Be Altered from 5′-CC to 5′-TC by a Single Amino Acid Substitution

inferredcites →https://doi.org/10.1016/j.jmb.2013.12.014openalex-snapshot

APOBEC3 Multimerization Correlates with HIV-1 Packaging and Restriction Activity in Living Cells

inferredcites →https://doi.org/10.1016/j.jmb.2016.08.031openalex-snapshot

R Loops and Links to Human Disease

inferredcites →https://doi.org/10.1016/j.jmb.2017.04.021openalex-snapshot

Family-Wide Comparative Analysis of Cytidine and Methylcytidine Deamination by Eleven Human APOBEC Proteins

inferredcites →https://doi.org/10.1016/j.jmb.2018.04.044openalex-snapshot

APOBEC3B Nuclear Localization Requires Two Distinct N-Terminal Domain Surfaces

inferredcites →https://doi.org/10.1016/j.molcel.2011.04.026openalex-snapshot

Human Senataxin Resolves RNA/DNA Hybrids Formed at Transcriptional Pause Sites to Promote Xrn2-Dependent Termination

inferredcites →https://doi.org/10.1016/j.molcel.2012.04.009openalex-snapshot

R Loops: From Transcription Byproducts to Threats to Genome Stability

inferredcites →https://doi.org/10.1016/j.molcel.2014.10.020openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.molcel.2015.01.011openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.molcel.2015.09.012openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.molcel.2016.05.032openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.molcel.2017.10.008openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.molcel.2017.12.029openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.molcel.2018.10.011openalex-snapshot

Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence

inferredcites →https://doi.org/10.1016/j.molcel.2019.01.024openalex-snapshot

R-Loops as Cellular Regulators and Genomic Threats

inferredcites →https://doi.org/10.1016/j.molcel.2019.07.017openalex-snapshot

Disease-Causing Mutations in SF3B1 Alter Splicing by Disrupting Interaction with SUGP1

inferredcites →https://doi.org/10.1016/j.tcb.2015.05.003openalex-snapshot

Breaking bad: R-loops and genome integrity

inferredcites →https://doi.org/10.1016/j.trecan.2019.08.006openalex-snapshot

R Loops and Their Composite Cancer Connections

inferredcites →https://doi.org/10.1016/j.virol.2015.03.012openalex-snapshot

APOBECs and virus restriction

inferredcites →https://doi.org/10.1016/s0092-8674(03)00423-9openalex-snapshot

DNA Deamination Mediates Innate Immunity to Retroviral Infection

inferredcites →https://doi.org/10.1021/acs.chemrev.6b00296openalex-snapshot

Functions and Malfunctions of Mammalian DNA-Cytosine Deaminases

inferredcites →https://doi.org/10.1021/acs.jctc.8b00545openalex-snapshot

Structural Analysis of the Active Site and DNA Binding of Human Cytidine Deaminase APOBEC3B

inferredcites →https://doi.org/10.1038/bjc.2017.133openalex-snapshot

Elevated APOBEC3B expression drives a kataegic-like mutation signature and replication stress-related therapeutic vulnerabilities in p53-defective cells

inferredcites →https://doi.org/10.1038/nature00939openalex-snapshot

Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein

inferredcites →https://doi.org/10.1038/nature01707openalex-snapshot

The cytidine deaminase CEM15 induces hypermutation in newly synthesized HIV-1 DNA

inferredcites →https://doi.org/10.1038/nature01709openalex-snapshot

Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts

inferredcites →https://doi.org/10.1038/nature06547openalex-snapshot

Two levels of protection for the B cell genome during somatic hypermutation

inferredcites →https://doi.org/10.1038/nature11881openalex-snapshot

APOBEC3B is an enzymatic source of mutation in breast cancer

inferredcites →https://doi.org/10.1038/nature12477openalex-snapshot

Signatures of mutational processes in human cancer

inferredcites →https://doi.org/10.1038/nature13374openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nature17676openalex-snapshot

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

inferredcites →https://doi.org/10.1038/ncb1984openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nchem.1795openalex-snapshot

Oligomerization transforms human APOBEC3G from an efficient enzyme to a slowly dissociating nucleic acid-binding protein

inferredcites →https://doi.org/10.1038/ncomms11383openalex-snapshot

The topography of mutational processes in breast cancer genomes

inferredcites →https://doi.org/10.1038/ncomms13087openalex-snapshot

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

inferredcites →https://doi.org/10.1038/ng.2701openalex-snapshot

Evidence for APOBEC3B mutagenesis in multiple human cancers

inferredcites →https://doi.org/10.1038/ng.2702openalex-snapshot

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

inferredcites →https://doi.org/10.1038/ng.2955openalex-snapshot

Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer

inferredcites →https://doi.org/10.1038/ng.3378openalex-snapshot

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers

inferredcites →https://doi.org/10.1038/nn1014-1297openalex-snapshot

A two-way street

inferredcites →https://doi.org/10.1038/nrc3816openalex-snapshot

Hypermutation in human cancer genomes: footprints and mechanisms

inferredcites →https://doi.org/10.1038/nrg3729openalex-snapshot

Mechanisms underlying mutational signatures in human cancers

inferredcites →https://doi.org/10.1038/nri.2016.2openalex-snapshot

Mutations, kataegis and translocations in B cells: understanding AID promiscuous activity

inferredcites →https://doi.org/10.1038/nri3814openalex-snapshot

Germinal centres and B cell lymphomagenesis

inferredcites →https://doi.org/10.1038/nsmb.3344openalex-snapshot

Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B

inferredcites →https://doi.org/10.1038/s41388-020-01583-7openalex-snapshot

Induction of APOBEC3B expression by chemotherapy drugs is mediated by DNA-PK-directed activation of NF-κB

inferredcites →https://doi.org/10.1038/s41467-018-02894-wopenalex-snapshot

Senataxin resolves RNA:DNA hybrids forming at DNA double-strand breaks to prevent translocations

inferredcites →https://doi.org/10.1038/s41467-020-17503-yopenalex-snapshot

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

inferredcites →https://doi.org/10.1038/s41564-018-0284-6openalex-snapshot

Epstein–Barr virus BORF2 inhibits cellular APOBEC3B to preserve viral genome integrity

inferredcites →https://doi.org/10.1038/s41586-020-1943-3openalex-snapshot

The repertoire of mutational signatures in human cancer

inferredcites →https://doi.org/10.1038/s41586-020-1969-6openalex-snapshot

Pan-cancer analysis of whole genomes

inferredcites →https://doi.org/10.1038/s41588-020-0674-6openalex-snapshot

DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers

inferredcites →https://doi.org/10.1038/s41588-021-00867-2openalex-snapshot

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

inferredcites →https://doi.org/10.1073/pnas.1522325113openalex-snapshot

Strand-biased cytosine deamination at the replication fork causes cytosine to thymine mutations in Escherichia coli

inferredcites →https://doi.org/10.1073/pnas.1904024116openalex-snapshot

The deaminase APOBEC3B triggers the death of cells lacking uracil DNA glycosylase

inferredcites →https://doi.org/10.1073/pnas.1922472117openalex-snapshot

Analysis of APOBEC-induced mutations in yeast strains with low levels of replicative DNA polymerases

inferredcites →https://doi.org/10.1074/jbc.m110.107987openalex-snapshot

Structural Model for Deoxycytidine Deamination Mechanisms of the HIV-1 Inactivation Enzyme APOBEC3G

inferredcites →https://doi.org/10.1074/jbc.m110.177402openalex-snapshot

Local Sequence Targeting in the AID/APOBEC Family Differentially Impacts Retroviral Restriction and Antibody Diversification

inferredcites →https://doi.org/10.1074/jbc.m803726200openalex-snapshot

APOBEC3G Subunits Self-associate via the C-terminal Deaminase Domain

inferredcites →https://doi.org/10.1074/jbc.ra119.008443openalex-snapshot

The DNA deaminase APOBEC3B interacts with the cell-cycle protein CDK4 and disrupts CDK4-mediated nuclear import of Cyclin D1

inferredcites →https://doi.org/10.1080/22221751.2020.1725398openalex-snapshot

DHX9 interacts with APOBEC3B and attenuates the anti-HBV effect of APOBEC3B

inferredcites →https://doi.org/10.1083/jcb.201409073openalex-snapshot

Splicing function of mitotic regulators links R-loop–mediated DNA damage to tumor cell killing

inferredcites →https://doi.org/10.1083/jcb.202004079openalex-snapshot

Recognition of RNA by the S9.6 antibody creates pervasive artifacts when imaging RNA:DNA hybrids

inferredcites →https://doi.org/10.1084/jem.20092238openalex-snapshot

Altering the spectrum of immunoglobulin V gene somatic hypermutation by modifying the active site of AID

inferredcites →https://doi.org/10.1084/jem.20200261openalex-snapshot

APOBEC3A catalyzes mutation and drives carcinogenesis in vivo

inferredcites →https://doi.org/10.1093/annonc/mdy003openalex-snapshot

Perspective: APOBEC mutagenesis in drug resistance and immune escape in HIV and cancer evolution

inferredcites →https://doi.org/10.1093/jncics/pky002openalex-snapshot

Mutation Signatures Including APOBEC in Cancer Cell Lines

inferredcites →https://doi.org/10.1093/nar/gkx362openalex-snapshot

Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation

inferredcites →https://doi.org/10.1093/nar/gkx564openalex-snapshot

Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation

inferredcites →https://doi.org/10.1093/nar/gkx832openalex-snapshot

Enzyme cycling contributes to efficient induction of genome mutagenesis by the cytidine deaminase APOBEC3B

inferredcites →https://doi.org/10.1093/narcan/zcab025openalex-snapshot

Analysis of gene expression and mutation data points on contribution of transcription to the mutagenesis by APOBEC enzymes

inferredcites →https://doi.org/10.1096/fba.2019-00068openalex-snapshot

Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3B

inferredcites →https://doi.org/10.1101/gad.242990.114openalex-snapshot

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

inferredcites →https://doi.org/10.1101/gad.331231.119openalex-snapshot

Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity

inferredcites →https://doi.org/10.1101/gad.336024.119openalex-snapshot

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

inferredcites →https://doi.org/10.1101/gad.573310openalex-snapshot

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

inferredcites →https://doi.org/10.1101/gr.197046.115openalex-snapshot

APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication

inferredcites →https://doi.org/10.1126/science.aaw2872openalex-snapshot

Passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features

inferredcites →https://doi.org/10.1158/0008-5472.can-13-1753openalex-snapshot

APOBEC3B Upregulation and Genomic Mutation Patterns in Serous Ovarian Carcinoma

inferredcites →https://doi.org/10.1158/0008-5472.can-15-2171-topenalex-snapshot

The PKC/NF-κB Signaling Pathway Induces APOBEC3B Expression in Multiple Human Cancers

inferredcites →https://doi.org/10.1158/2159-8290.cd-15-0344openalex-snapshot

APOBEC Enzymes: Mutagenic Fuel for Cancer Evolution and Heterogeneity

inferredcites →https://doi.org/10.1186/s13059-018-1478-1openalex-snapshot

DNA Topoisomerase I differentially modulates R-loops across the human genome

inferredcites →https://doi.org/10.1371/journal.pgen.1004630openalex-snapshot

Out of Balance: R-loops in Human Disease

inferredcites →https://doi.org/10.1371/journal.pgen.1005674openalex-snapshot

The Fanconi Anemia Pathway Protects Genome Integrity from R-loops

inferredcites →https://doi.org/10.1371/journal.pgen.1006107openalex-snapshot

XRN2 Links Transcription Termination to DNA Damage and Replication Stress

inferredcites →https://doi.org/10.1371/journal.pgen.1008545openalex-snapshot

APOBEC3A is a prominent cytidine deaminase in breast cancer

inferredcites →https://doi.org/10.1371/journal.pone.0023993openalex-snapshot

Triptolide (TPL) Inhibits Global Transcription by Inducing Proteasome-Dependent Degradation of RNA Polymerase II (Pol II)

inferredcites →https://doi.org/10.1371/journal.ppat.1004024openalex-snapshot

Different Mutagenic Potential of HIV-1 Restriction Factors APOBEC3G and APOBEC3F Is Determined by Distinct Single-Stranded DNA Scanning Mechanisms

inferredcites →https://doi.org/10.15252/embj.2018100986openalex-snapshot

Arginine methylation of the DDX5 helicase RGG/RG motif by PRMT5 regulates resolution of RNA:DNA hybrids

inferredcites →https://doi.org/10.15698/cst2019.02.175openalex-snapshot

R-loops: formation, function, and relevance to cell stress

inferredcites →https://doi.org/10.26508/lsa.201900606openalex-snapshot

MagnEdit—interacting factors that recruit DNA-editing enzymes to single base targets

inferredcites →https://doi.org/10.26508/lsa.202000762openalex-snapshot

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

inferredcites →https://doi.org/10.3389/fimmu.2019.00438openalex-snapshot

Mutating for Good: DNA Damage Responses During Somatic Hypermutation

inferredcites →https://doi.org/10.4161/trns.2.3.16172openalex-snapshot

Inhibiting eukaryotic transcription. Which compound to choose? How to evaluate its activity?

inferredcites →https://doi.org/10.7554/elife.00534openalex-snapshot

DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis

inferredcites →https://doi.org/10.7554/elife.17548openalex-snapshot

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

inferredcites →https://doi.org/10.7554/elife.61287openalex-snapshot

Characterization of the mechanism by which the RB/E2F pathway controls expression of the cancer genomic DNA deaminase APOBEC3B

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/978-1-0716-2477-7_14openalex-snapshot

R-Loop Immunoprecipitation: A Method to Detect R-Loop Interacting Factors

inferred← citeshttps://doi.org/10.1016/j.biochi.2023.07.002openalex-snapshot

Non-B DNA structures as a booster of genome instability

inferred← citeshttps://doi.org/10.1038/s41419-023-05867-0openalex-snapshot

APOBEC3B coordinates R-loop to promote replication stress and sensitize cancer cells to ATR/Chk1 inhibitors

inferred← citeshttps://doi.org/10.1038/s41467-023-36445-9openalex-snapshot

APOBEC3B drives PKR-mediated translation shutdown and protects stress granules in response to viral infection

inferred← citeshttps://doi.org/10.1101/2022.10.21.513235openalex-snapshot

R-Loop Editing by DNA Cytosine Deaminase APOBEC3B Determines the Activity of Estrogen Receptor Enhancers

inferred← citeshttps://doi.org/10.1128/msphere.00451-22openalex-snapshot

Ancestral APOBEC3B Nuclear Localization Is Maintained in Humans and Apes and Altered in Most Other Old World Primate Species

inferred← citeshttps://doi.org/10.1371/journal.pgen.1011043openalex-snapshot

Mutational impact of APOBEC3A and APOBEC3B in a human cell line and comparisons to breast cancer

inferred← citeshttps://doi.org/10.3390/ijms24065966openalex-snapshot

Clinical and Mechanistic Implications of R-Loops in Human Leukemias

inferred← citeshttps://doi.org/10.70675/dce63b34z1573z4c87z9c02z6d5c0807db2aopenalex-snapshot

L'implication des hybrides ADN : ARN et de la modification m6A des ARN dans la réparation des cassures double-brins de l'ADN

inferred← citeshttps://doi.org/10.7554/elife.83893openalex-snapshot

Evidence linking APOBEC3B genesis and evolution of innate immune antagonism by gamma-herpesvirus ribonucleotide reductases

inferred← citeshttps://doi.org/10.7554/elife.97348openalex-snapshot

Human immunodeficiency virus-1 induces host genomic R-loops and preferentially integrates its genome near the R-loop regions

inferred← citeshttps://doi.org/10.7554/elife.97348.1openalex-snapshot

Human immunodeficiency virus-1 induces and targets host genomic R-loops for viral genome integration

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.