Cimprich Lab



Direct visualization of transcription-replication conflicts reveals post-replicative DNA:RNA hybrids

Stoy H, Zwicky K, Kuster D, Lang KS, Krietsch J, Crossley MP, Schmid JA, Cimprich KA, Merrikh H, Lopes M.(2023) Nat Struct Mol Biol.. Mar;30(3):348-359.doi: 10.1038/s41594-023-00928-6 PubMed PMID: 36864174. [PubMed]

R-loop-derived cytoplasmic RNA-DNA hybrids activate an immune response

Crossley MP, Song C, Bocek MJ, Choi JH, Kousorous J, Sathirachinda A, Lin C, Brickner JR, Bai G, Lans H, Vermeulen W, Abu-Remaileh M, Cimprich KA.(2023) Nature. Jan;613(7942):187-194. doi: 10.1038/s41586-022-05545-9. PubMed PMID: 36544021 . [PubMed]



Walking a tightrope: The complex balancing act of R-loops in genome stability

Brickner JR, Garzon JL, Cimprich KA.(2022) Mol Cell. Jun 16;82(12):2267-2297.doi: 10.1016/j.molcel.2022.04.014. PubMed PMID: 35508167. [PubMed]

ATR activity controls stem cell quiescence via the cyclin F-SCF complex.

Salvi JS, Kang J, Kim S, Colville AJ, de Morrée A, Billeskov TB, Larsen MC, Kanugovi A, van Velthoven CTJ, Cimprich KA, Rando TA.(2022) Proc Natl Acad Sci USA. May 3;119(18):e2115638119.doi: 10.1073/pnas.2115638119. PubMed PMID: 35476521. [PubMed]

Quantitative DNA-RNA Immunoprecipitation Sequencing with Spike-Ins.

Crossley MP, Cimprich KA. (2022) Methods in molecular biology (Clifton, N.J.). 2528: 381-410. doi:  10.1007/978-1-0716-2477-7_26. PubMed PMID: 35704206. [PubMed]



Catalytically inactive, purified RNase H1: A specific and sensitive probe for RNA-DNA hybrid imaging

Crossley MP, Brickner JR, Song C, Zar SMT, Maw SS, Chédin F, Tsai MS,  Cimprich KA. (2021) J Cell Biol2021 Sep 6;220(9)doi:  10.1083/jcb.202101092. Epub 2021 Jul 7. PubMed PMID: 34232287. [PubMed]



qDRIP: a method to quantitatively assess RNA-DNA hybrid formation genome-wide.

Crossley, MP., Bocek, MJ., Hamperl, S., Swigut, T., Cimprich, KA. (2020) Nucleic Acids Res2020 Aug 20;48(14):e84doi: 10.1093/nar/gkaa500. PubMed PMID: 32544226; PubMed Central PMCID: PMC7641308 [PubMed]

HLTF Promotes Fork Reversal, Limiting Replication Stress Resistance and Preventing Multiple Mechanisms of Unrestrained DNA Synthesis.

Bai, G., Kermi, C., Stoy, H., Schiltz, C., Bacal, J., Zaino, A., Hadden, K.M., Eichman, B., Lopes, M., Cimprich KA. (2020) Mol Cell2020 Jun 18;78(6):1237-1251doi: 10.1016/j.molcel.2020.04.031. Review. PubMed PMID: 32442397. [PubMed]


R-Loops as Cellular Regulators and Genomic Threats.

Crossley MP, Bocek M, Cimprich KA. (2019) Mol Cell2019 Feb 7;73(3):398-411doi: 10.1016/j.molcel.2019.01.024. Review. PubMed PMID: 30735654; PubMed Central PMCID: PMC6402819. [PubMed]

PPARγ Interaction with UBR5/ATMIN Promotes DNA Repair to Maintain Endothelial Homeostasis.

Li CG, Mahon C, Sweeney NM, Verschueren E, Kantamani V, Li D, Hennigs JK, Marciano DP, Diebold I, Abu-Halawa O, Elliott M, Sa S, Guo F, Wang L, Cao A, Guignabert C, Sollier J, Nickel NP, Kaschwich M, Cimprich KA, Rabinovitch M. (2019) Cell Rep2019 Jan 29;26(5):1333-1343.e7doi: 10.1016/j.celrep.2019.01.013. PubMed PMID: 30699358; PubMed Central PMCID: PMC6436616. [PubMed]


An intrinsic S/G2 checkpoint enforced by ATR.

Saldivar JC, Hamperl S, Bocek MJ, Chung M, Bass TE, Cisneros-Soberanis F, Samejima K, Xie L, Paulson JR, Earnshaw WC, Cortez D, Meyer T, Cimprich KA. (2018) Science2018 Aug 24;361(6404):806-810doi: 10.1126/science.aap9346. PubMed PMID: 30139873; PubMed Central PMCID: PMC6365305. [PubMed]

Stochastic Endogenous Replication Stress Causes ATR-Triggered Fluctuations in CDK2 Activity that Dynamically Adjust Global DNA Synthesis Rates.

Daigh LH, Liu C, Chung M, Cimprich KA, Meyer T. (2018) Cell Syst2018 Jul 25;7(1):17-27.e3doi: 10.1016/j.cels.2018.05.011. Epub 2018 Jun 13. PubMed PMID: 29909278; PubMed Central PMCID: PMC6436092. [PubMed]

Faulty Replication Can Sting.

Crossley MP, Cimprich KA. (2018) Nature. 2018 May;557(7703):34-35. doi: 10.1038/d41586-018-02804-6.[PubMed]

A New Mitotic Activity Comes Into Focus.

Saldivar JC, Cimprich KA. (2018) Science. 2018 Jan 5;359(6371):30-31. doi: 10.1126/science.aar4799. [PubMed]


The Essential Kinase ATR: Ensuring Faithful Duplication Of A Challenging Genome.

Saldivar JC, Cortez D, Cimprich KA. (2017) Nat Rev Mol Cell Biol. 2017 Aug 16. doi: 10.1038/nrm.2017.67. [PubMed]

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

Hamperl S, Bocek MJ, Saldivar JC, Swigut T, Cimprich KA. (2017) Cell. 2017 Aug 10;170(4):774-786.e19. doi: 10.1016/j.cell.2017.07.043. [PubMed]


Conflict Resolution In The Genome: How Transcription And Replication Make It Work.

Hamperl S, Cimprich KA. (2016) Cell. 2016 Dec 1;167(6):1455-1467. doi: 10.1016/j.cell.2016.09.053. [PubMed]

Directed Evolution Using DCas9-Targeted Somatic Hypermutation In Mammalian Cells.

Hess GT, Frésard L, Han K, Lee CH, Li A, Cimprich KA, Montgomery SB, Bassik MC. (2016) Nat Methods. 2016 Oct 31. doi: 10.1038/nmeth.4038. [PubMed]

Co-Transcriptional R-Loops Are The Main Cause Of Estrogen-Induced Dna Damage.

Stork CT, Bocek M, Crossley MP, Sollier J, Sanz LA, Chédin F, Swigut T, Cimprich KA. (2016) Elife. 2016 Aug 23;5. pii: e17548. doi: 10.7554/eLife.17548. [PubMed]

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Breaking Bad: R-Loops And Genome Integrity.

Sollier J, Cimprich KA. (2015) Trends Cell Biol. 2015 Sep;25(9):514-22. [PubMed]

HLTF’s Ancient Hiran Domain Binds 3′ DNA Ends To Drive Replication Fork Reversal.

Kile AC, Chavez DA, Bacal J, Eldirany S, Korzhnev DM, Bezsonova I, Eichman BF, Cimprich KA. (2015) Mol Cell. 2015 Jun 18;58(6):1090-100. [PubMed]


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

Sollier J, Stork CT, García-Rubio ML, Paulsen RD, Aguilera A, Cimprich KA. (2014) Mol Cell. 2014 Dec 18;56(6):777-85. [PubMed]

DNA Damage-Specific Deubiquitination Regulates Rad18 Functions To Suppress Mutagenesis.

Zeman MK, Lin JR, Freire R, Cimprich KA. (2014) J Cell Biol. 2014 Jul 21;206(2):231-43. [PubMed]

The Contribution Of Co-Transcriptional RNA:DNA Hybrid Structures To DNA Damage And Genome Instability.

Hamperl S, Cimprich KA. (2014) DNA Repair (Amst). 2014 Jul;19:84-94. [PubMed]

Whole Exome Sequencing Reveals Topbp1 As A Novel Gene In Idiopathic Pulmonary Arterial Hypertension.

de Jesus Perez VA, Yuan K, Lyuksyutova MA, Dewey F, Orcholski ME, Shuffle EM, Mathur M, Yancy L Jr, Rojas V, Li CG, Cao A, Alastalo TP, Khazeni N, Cimprich KA, Butte AJ, Ashley E, Zamanian RT. (2014) Am J Respir Crit Care Med. 2014 May 15;189(10):1260-72. [PubMed]

Causes And Consequences Of Replication Stress.

Zeman MK, Cimprich KA. (2014) Nat Cell Biol. 2014 Jan;16(1):2-9. [PubMed]


NEK8 Links The ATR-Regulated Replication Stress Response And S Phase CDK Activity To Renal Ciliopathies.

Choi HJ, Lin JR, Vannier JB, Slaats GG, Kile AC, Paulsen RD, Manning DK, Beier DR, Giles RH, Boulton SJ, Cimprich KA. (2013) Mol Cell. 51(4):423-39. [PubMed]

A Role For The MRN Complex In ATR Activation Via TOPBP1 Recruitment.

Duursma AM, Driscoll R, Elias JE, Cimprich KA. (2013) Mol. Cell. 50(1):116-22 [PubMed]


A Two-Dimensional ERK-AKT Signaling Code For An NGF-Triggered Cell-Fate Decision.

Chen JY, Lin JR, Cimprich KA, Meyer T. (2012) Mol. Cell 45(2):196-209 [PubMed]


SHPRH And HLTF Act In A Damage-Specific Manner To Coordinate Different Forms Of Postreplication Repair And Prevent Mutagenesis.

Lin JR, Zeman MK, Chen JY, Yee MC, Cimprich KA. (2011) Mol. Cell 42(2):237-49 [PubMed]

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Checkpoint Recovery After DNA Damage: A Rolling Stop For CDKs.

Duursma AM, Cimprich KA. (2010) EMBO Rep. 11(6):411-2 [PubMed]


HARPing On About The DNA Damage Response During Replication.

Driscoll R, Cimprich KA. (2009) Genes Dev. 23(20):2359-65 [PubMed]

A Genome-Wide SiRNA Screen Reveals Diverse Cellular Processes And Pathways That Mediate Genome Stability.

Paulsen RD, Soni DV, Wollman R, Hahn AT, Yee MC, Guan A, Hesley JA, Miller SC, Cromwell EF, Solow-Cordero DE, Meyer T, Cimprich KA. (2009) Mol. Cell 35(2):228-39 [PubMed]

Proliferating Cell Nuclear Antigen Uses Two Distinct Modes To Move Along DNA.

Kochaniak AB, Habuchi S, Loparo JJ, Chang DJ, Cimprich KA, Walter JC, van Oijen AM. (2009) J. Biol. Chem. 284(26):17700-10 [PubMed]

DNA Damage Tolerance: When It’s OK To Make Mistakes.

Chang DJ, Cimprich KA. (2009) Nat. Chem. Biol. 5(2):82-90 [PubMed]


ATR: An Essential Regulator Of Genome Integrity.

Cimprich KA, Cortez D. (2008) Nat. Rev. Mol. Cell Biol. 9(8):616-27 [PubMed]

Probing ATR Activation With Model DNA Templates.

Cimprich KA. (2007) Cell Cycle 6(19):2348-54 [PubMed]

The ATR Pathway: Fine-Tuning The Fork.

Paulsen RD, Cimprich KA. (2007) DNA Repair (Amst.) 6(7):953-66 [PubMed]


Analyzing The ATR-Mediated Checkpoint Using Xenopus Egg Extracts.

Lupardus PJ, Van C, Cimprich KA. (2007) Methods 41(2):222-31 [PubMed]


Monoubiquitination Of Proliferating Cell Nuclear Antigen Induced By Stalled Replication Requires Uncoupling Of DNA Polymerase And Mini-Chromosome Maintenance Helicase Activities.

Chang DJ, Lupardus PJ, Cimprich KA. (2006) J. Biol. Chem. 281(43):32081-8 [PubMed]

Opposing Effects Of The UV Lesion Repair Protein XPA And UV Bypass Polymerase Eta On ATR Checkpoint Signaling

Bomgarden RD, Lupardus PJ, Soni DV, Yee MC, Ford JM, Cimprich KA. (2006) EMBO J. 25(11):2605-14 [PubMed]

Phosphorylation Of Xenopus Rad1 And Hus1 Defines A Readout For ATR Activation That Is Independent Of Claspin And The Rad9 Carboxy Terminus.

Lupardus PJ, Cimprich KA. (2006) Mol. Biol. Cell 17(4):1559-69 [PubMed]

Fanconi Anemia Proteins Are Required To Prevent Accumulation Of Replication-Associated DNA Double-Strand Breaks.

Sobeck A, Stone S, Costanzo V, de Graaf B, Reuter T, de Winter J, Wallisch M, Akkari Y, Olson S, Wang W, Joenje H, Christian JL, Lupardus PJ, Cimprich KA, Gautier J, Hoatlin ME. (2006) Mol. Cell. Biol. 26(2):425-37 [PubMed]

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A Cell-Permeable, Activity-Based Probe For Protein And Lipid Kinases.

Yee MC, Fas SC, Stohlmeyer MM, Wandless TJ, Cimprich KA. (2005) J. Biol. Chem. 280(32):29053-9 [PubMed]

Functional Uncoupling Of MCM Helicase And DNA Polymerase Activities Activates The ATR-Dependent Checkpoint.

Byun TS, Pacek M, Yee MC, Walter JC, Cimprich KA. (2005) Genes Dev. 19(9):1040-52 [PubMed]

G2 Damage Checkpoints: What Is The Turn-On?

O’Connell MJ, Cimprich KA. (2005) J. Cell. Sci. 118(Pt 1):1-6 [PubMed]


Checkpoint Adaptation; Molecular Mechanisms Uncovered.

Lupardus PJ, Cimprich KA. (2004) Cell 117(5):555-6 [PubMed]

A Novel Protein Activity Mediates DNA Binding Of An ATR-ATRIP Complex.

Bomgarden RD, Yean D, Yee MC, Cimprich KA. (2004) J. Biol. Chem. 279(14):13346-53 [PubMed]


ATR Kinase Activity Regulates The Intranuclear Translocation Of ATR And RPA Following Ionizing Radiation.

Barr SM, Leung CG, Chang EE, Cimprich KA. (2003) Curr. Biol. 13(12):1047-51 [PubMed]

Fragile Sites: Breaking Up Over A Slowdown.

Cimprich KA. (2003) Curr. Biol. 13(6):R231-3 [PubMed]

Enforced Proximity In The Function Of A Famous Scaffold.

Ferrell JE, Cimprich KA. (2003) Mol. Cell 11(2):289-91 [PubMed]

An ATR- And Cdc7-Dependent DNA Damage Checkpoint That Inhibits Initiation Of DNA Replication.

Costanzo V, Shechter D, Lupardus PJ, Cimprich KA, Gottesman M, Gautier J. (2003) Mol. Cell 11(1):203-13 [PubMed]


A Requirement For Replication In Activation Of The ATR-Dependent DNA Damage Checkpoint.

Lupardus PJ, Byun T, Yee MC, Hekmat-Nejad M, Cimprich KA. (2002) Genes Dev. 16(18):2327-32 [PubMed]


Phosphorylation Of Serines 635 And 645 Of Human Rad17 Is Cell Cycle Regulated And Is Required For G(1)/S Checkpoint Activation In Response To DNA Damage.

Post S, Weng YC, Cimprich K, Chen LB, Xu Y, Lee EY. (2001) Proc. Natl. Acad. Sci. U.S.A. 98(23):13102-7 [PubMed]

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Xenopus ATR Is A Replication-Dependent Chromatin-Binding Protein Required For The DNA Replication Checkpoint.

Hekmat-Nejad M, You Z, Yee MC, Newport JW, Cimprich KA. (2000) Curr. Biol. 10(24):1565-73 [PubMed]


Activation Of The ATM Kinase By Ionizing Radiation And Phosphorylation Of P53.

Canman CE, Lim DS, Cimprich KA, Taya Y, Tamai K, Sakaguchi K, Appella E, Kastan MB, Siliciano JD. (1998) Science 281(5383):1677-9 [PubMed]

Overexpression Of A Kinase-Inactive ATR Protein Causes Sensitivity To DNA-Damaging Agents And Defects In Cell Cycle Checkpoints.

Cliby WA, Roberts CJ, Cimprich KA, Stringer CM, Lamb JR, Schreiber SL, Friend SH. (1998) EMBO J. 17(1):159-69 [PubMed]


CDNA Cloning And Gene Mapping Of A Candidate Human Cell Cycle Checkpoint Protein.

Cimprich KA, Shin TB, Keith CT, Schreiber SL. (1996) Proc. Natl. Acad. Sci. U.S.A. 93(7):2850-5 [PubMed]

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