ArticleCell2019
Bacteria-to-Human Protein Networks Reveal Origins of Endogenous DNA Damage.
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In one paragraph
Article in Cell, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
63citing papers in PubMed, 1 pooled it
5.1field-weighted citation impact, top 4% of its field
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
63 citing papers in PubMed, 1 synthesis or guideline pooled it, 93 citations in OpenAlex.
- Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer.Nature genetics · 2022Pooled it
- LIG1 Loss in TP53-mutant Triple Negative Breast Cancer Rewires DNA Repair and Confers Sensitivity to PARP-ATR Inhibitor Combinations.Molecular cancer therapeutics · 2026Article
- A novel ψ-χ fusion protein for unravelling the contributions of χ to DNA replication and repair.Nucleic acids research · 2026Article
- A NovelbioRxiv : the preprint server for biology · 2026Article
- Single-cell full-length transcriptome of human lung reveals genetic effects on isoform regulation beyond gene-level expression.bioRxiv : the preprint server for biology · 2026Article
- The Stem Cell Transcription Factor OCT4 Silences Target DNA Methyltransferase 1 to Strengthen DNA Damage Response in Cisplatin-Treated Gastric Cancer Cells.Biotechnology and applied biochemistry · 2025Article
- Transcription-replication collisions trigger high-fidelity replication reset.Nucleic acids research · 2025Article
- Article
- Clues to transcription/replication collision-induced DNA damage: it was RNAP, in the chromosome, with the fork.FEBS letters · 2025Review
- A bacterial expression cloning screen reveals single-stranded DNA-binding proteins as potent desicco-protectants.Cell reports · 2024Article
- Transcriptomic changes and gene fusions during the progression from Barrett's esophagus to esophageal adenocarcinoma.Biomarker research · 2024Article
- RNA polymerase stalling-derived genome instability underlies ribosomal antibiotic efficacy and resistance evolution.Nature communications · 2024Article
- The F plasmid conjutome: the repertoire ofmSphere · 2024Article
- Lung Cancer in Ever- and Never-Smokers: Findings from Multi-Population GWAS Studies.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2024Article
- Life, the genome and everything.Journal of bacteriology · 2023Article
- Generation and Repair of Postreplication Gaps in Escherichia coli.Microbiology and molecular biology reviews : MMBR · 2023Review
- RecF protein targeting to post-replication (daughter strand) gaps II: RecF interaction with replisomes.Nucleic acids research · 2023Article
- Drugging evolution of antibiotic resistance at a regulatory network hub.Science advances · 2023Article
- RecF protein targeting to postreplication (daughter strand) gaps I: DNA binding by RecF and RecFR.Nucleic acids research · 2023Article
- RecA and SSB genome-wide distribution in ssDNA gaps and ends in Escherichia coli.Nucleic acids research · 2023Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
34 authors at 7 institutions in 1 country.
Jun XiaDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA.
Li-Ya ChiuDepartment of Molecular Biosciences, LIVESTRONG Cancer Institute of the Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA.
Ralf B NehringDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
María Angélica Bravo NúñezDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Qian MeiDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Systems, Synthetic and Physical Biology Program, Rice University, Houston, TX 77030, USA.
Mercedes PerezDepartment of Molecular Biosciences, LIVESTRONG Cancer Institute of the Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA.
Yin ZhaiDepartment of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Devon M FitzgeraldDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
John P PribisDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA.
Yumeng WangGraduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Chenyue W HuDepartment of Bioengineering, Rice University, Houston, TX 77030, USA.
Reid T PowellInstitute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA.
Sandra A LaBonteDepartment of Biochemistry and Biophysics, Texas A&M University and Texas AgriLife Research, College Station, TX 77843, USA.
Ali JalaliDan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA.
Meztli L Matadamas GuzmánDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Alfred M LentzschDepartment of Molecular Biosciences, LIVESTRONG Cancer Institute of the Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA.
Adam T SzafranDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
Mohan C JoshiDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Megan RichtersDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Janet L GibsonDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Ryan L FrischDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
P J HastingsDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
David BatesDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Christine QueitschDepartment of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Susan G HilsenbeckDan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Cristian CoarfaDan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
James C HuDepartment of Biochemistry and Biophysics, Texas A&M University and Texas AgriLife Research, College Station, TX 77843, USA.
Deborah A SiegeleDepartment of Biology, Texas A&M University, College Station, TX 77843, USA.
Kenneth L ScottDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA.
Han LiangGraduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Michael A ManciniDan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
Christophe HermanDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address: herman@bcm.edu.
Kyle M MillerDan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Biosciences, LIVESTRONG Cancer Institute of the Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA. Electronic address: kyle.miller@austin.utexas.edu.
Susan M RosenbergDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA; Systems, Synthetic and Physical Biology Program, Rice University, Houston, TX 77030, USA. Electronic address: smr@bcm.edu.
Baylor College of Medicine · USTexas A&M University · USLivestrong Foundation · USRice University · USBaylor Genetics · USThe University of Texas MD Anderson Cancer Center · USUniversity of Washington · US
Funding
Tumor Evolution and Metastasis ProgramP30CA016672 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Fabien Delerue · 1985 to 2026
$290.8MTumor BiologyP30CA125123 · NCI · BAYLOR COLLEGE OF MEDICINE · PI Michael M Ittmann · 2007 to 2026
$73.9MTissue Analysis & Molecular Imaging CoreP30DK056338 · NIDDK · BAYLOR COLLEGE OF MEDICINE · PI James Versalovic · 2001 to 2026
$28.3MVirology CoreP30AI036211 · NIAID · BAYLOR COLLEGE OF MEDICINE · PI KLINE, MARK W. · 1994 to 2015
$21.7MTRANSGENIC MOUSE MODELS TO STUDY OVARIAN FUNCTIONU54HD007495 · NICHD · BAYLOR COLLEGE OF MEDICINE · PI MATZUK, MARTIN M. · 1998 to 2013
$19.9MTRAINING PROGRAM IN CELL AND MOLECULAR BIOLOGYT32GM008231 · NIGMS · BAYLOR COLLEGE OF MEDICINE · PI NELSON, DAVID LOREN · 1990 to 2019
$7.2MBiological annotation of TCGA dataU01CA168394 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI MILLS, GORDON B. · 2012 to 2016
$4.7MTCPA: an Integrated Bioinformatics Resource for Functional Cancer Proteomic DataU24CA209851 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI LIANG, HAN, MILLS, GORDON B. · 2016 to 2020
$4.0MIntegrative bioinformatics and functional characterization of oncogenic driver aberrations in cancerU01CA217842 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI DENEEN, BENJAMIN, MILLS, GORDON B. · 2017 to 2021
$3.6MShaping DNA Damage Response Networks Via Histone H2A VariantsR01CA198279 · NCI · UNIVERSITY OF TEXAS AT AUSTIN · PI Kyle M Miller · 2016 to 2026
$3.3MMolecular Noise, Transcription Errors and Heritable Phenotypic ChangeR01GM088653 · NIGMS · BAYLOR COLLEGE OF MEDICINE · PI HERMAN, CHRISTOPHE · 2010 to 2019
$3.1MMUTATIONAL SIGNATURE(S) OF HUMAN GENOMIC REARRANGEMENT MECHANISMSR01GM106373 · NIGMS · BAYLOR COLLEGE OF MEDICINE · PI HASTINGS, PHILIP JOHN, LUPSKI, JAMES R. · 2014 to 2022
$3.1MHSRD VA IIR 18-035NCI NIH HHS DP1 CA174424NCI NIH HHS P30 CA016672NCI NIH HHS P30 CA125123NCI NIH HHS R01 CA175486NCI NIH HHS R01 CA198279NCI NIH HHS R01 CA201268NCI NIH HHS U01 CA168394NCI NIH HHS U01 CA217842NCI NIH HHS U24 CA209851NCRR NIH HHS S10 RR024574NIAID NIH HHS P30 AI036211NICHD NIH HHS P30 HD007495NICHD NIH HHS T32 HD007495NICHD NIH HHS U54 HD007495NIDDK NIH HHS P30 DK056338NIGMS NIH HHS R01 GM088653NIGMS NIH HHS R01 GM089636NIGMS NIH HHS R01 GM102679NIGMS NIH HHS R01 GM106373NIGMS NIH HHS R35 GM122598NIGMS NIH HHS T32 GM008231NIH HHS DP2 OD008371
Abstract
DNA damage provokes mutations and cancer and results from external carcinogens or endogenous cellular processes. However, the intrinsic instigators of endogenous DNA damage are poorly understood. Here, we identify proteins that promote endogenous DNA damage when overproduced: the DNA "damage-up" proteins (DDPs). We discover a large network of DDPs in Escherichia coli and deconvolute them into six function clusters, demonstrating DDP mechanisms in three: reactive oxygen increase by transmembrane transporters, chromosome loss by replisome binding, and replication stalling by transcription factors. Their 284 human homologs are over-represented among known cancer drivers, and their RNAs in tumors predict heavy mutagenesis and a poor prognosis. Half of the tested human homologs promote DNA damage and mutation when overproduced in human cells, with DNA damage-elevating mechanisms like those in E. coli. Our work identifies networks of DDPs that provoke endogenous DNA damage and may reveal DNA damage-associated functions of many human known and newly implicated cancer-promoting proteins.
Indexed as
Bacterial ProteinsChromosomal InstabilityDNA-Binding ProteinsDNA DamageDNA RepairDNA ReplicationEscherichia coliGenomic InstabilityHumansMembrane Transport ProteinsMutagenesisMutationTranscription FactorsBacterial ProteinsDNA-Binding ProteinsMembrane Transport ProteinsTranscription FactorscancerDNA damage responseDNA double-strand breaksDNMT1Escherichia colievolutiongenome instabilityhuman cellsmicrobial cancer modelsreplication fork reversal
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