Cooperative assembly of p97 complexes involved in replication termination
Olga V. Kochenova, Sirisha Mukkavalli, Malavika Raman Walter JC
Nat Communications 2022 Nov 3 doi: 10.1038/s41467-022-34210-y Online ahead of print.

CDC7-independent G1/S transition revealed by targeted protein degradation.
Suski JM, Ratnayeke N, Braun M, Zhang T, Strmiska V, Michowski W, Can G, Simoneau A, Snioch K, Cup M, Sullivan CM, Wu X, Nowacka J, Branigan TB, Pack LR, DeCaprio JA, Geng Y, Zou L, Gygi SP, Walter JC, Meyer T, Sicinski P.
Nature. 2022 May 4. doi: 10.1038/s41586-022-04698-x. Online ahead of print.


Structure of CRL2Lrr1, the E3 ubiquitin ligase that promotes DNA replication termination in vertebrates.
Zhou H, Zaher MS, Walter JC, Brown A.
Nucleic Acids Res.2021 Dec 1:gkab1174.

ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation.
van der Weegen Y, de Lint K, van den Heuvel D, Nakazawa Y, Mevissen TET, van Schie JJM, San Martin Alonso M, Boer DEC, González-Prieto R, Narayanan IV, Klaassen NHM, Wondergem AP, Roohollahi K, Dorsman JC, Hara Y, Vertegaal ACO, de Lange J, Walter JC, Noordermeer SM, Ljungman M, Ogi T, Wolthuis RMF, Luijsterburg MS.
Nat Cell Biol. 2021 Jun;23(6):595-607.

Mechanisms of Vertebrate DNA Interstrand Cross-Link Repair.
Semlow DR, Walter JC.
Annu Rev Biochem. 2021 Jun 20;90:107-135.

The Ubiquitin Ligase TRAIP: Double-Edged Sword at the Replisome.
Wu RA, Pellman DS, Walter JC.
Trends Cell Biol. 2021 Feb;31(2):75-85.

Single-strand DNA breaks cause replisome disassembly.
Vrtis KB, Dewar JM, Chistol G, Wu RA, Graham TGW, Walter JC.
Mol Cell. 2021 Mar 18;81(6):1309-1318.e6.


The DNA replication fork suppresses CMG unloading from chromatin before termination.
Low E, Chistol G, Zaher MS, Kochenova OV, Walter JC.
Genes Dev. 2020 Nov 1;34(21-22):1534-1545.

The Histone Chaperone FACT Induces Cas9 Multi-turnover Behavior and Modifies Genome Manipulation in Human Cells.
Wang AS, Chen LC, Wu RA, Hao Y, McSwiggen DT, Heckert AB, Richardson CD, Gowen BG, Kazane KR, Vu JT, Wyman SK, Shin JJ, Darzacq X, Walter JC, Corn JE.
Mol Cell. 2020 Jul 16;79(2):221-233.e5.

A new varietal of DNA interstrand crosslink repair.
Amunugama R, Walter JC.
Cell Res. 2020 Jun;30(6):459-460.

The cooperative action of CSB, CSA, and UVSSA target TFIIH to DNA damage-stalled RNA polymerase II.
van der Weegen Y, Golan-Berman H, Mevissen TET, Apelt K, González-Prieto R, Goedhart J, Heilbrun EE, Vertegaal ACO, van den Heuvel D, Walter JC, Adar S, Luijsterburg MS.
Nat Commun. 2020 Apr 30;11(1):2104.

A Mechanism to Minimize Errors during Non-homologous End Joining.
Stinson BM, Moreno AT, Walter JC, Loparo JJ.
Mol Cell. 2020 Mar 5;77(5):1080-1091.e8. 


Mitotic CDK Promotes Replisome Disassembly, Fork Breakage, and Complex DNA Rearrangements.
Deng L, Wu RA, Sonneville R, Kochenova OV, Labib K, Pellman D, Walter JC.
Mol Cell. 2019 Mar 7;73(5):915-929.e6.

Cold Spring Harb Protoc. 2019 Mar 1;2019(3).


A single XLF dimer bridges DNA ends during nonhomologous end joining.
Graham TGW, Carney SM, Walter JC, Loparo JJ.
Nat Struct Mol Biol. 2018 Sep;25(9):877-884.

Replication Fork Reversal during DNA Interstrand Crosslink Repair Requires CMG Unloading.
Amunugama R, Willcox S, Wu RA, Abdullah UB, El-Sagheer AH, Brown T, McHugh PJ, Griffith JD, Walter JC.
Cell Rep. 2018 Jun 19;23(12):3419-3428.


Ensemble and Single-Molecule Analysis of Non-Homologous End Joining in Frog Egg Extracts.
Graham TGW, Walter JC, Loparo JJ.
Methods Enzymol. 2017;591:233-270.

Mechanisms of DNA replication termination.
Dewar JM, Walter JC.
Nat Rev Mol Cell Biol. 2017 Aug;18(8):507-516

CRL2Lrr1 promotes unloading of the vertebrate replisome from chromatin during replication termination.
Dewar JM, Low E, Mann M, Räschle M, Walter JC.
Genes Dev. 2017 Feb 1;31(3):275-290.


Replication-Dependent Unhooking of DNA Interstrand Cross-Links by the NEIL3 Glycosylase.
Semlow DR, Zhang J, Budzowska M, Drohat AC, Walter JC.
Cell. 2016 Oct 6;167(2):498-511.e14

Assays to Study Mitotic Centrosome and Spindle Pole Assembly and Regulation.
Joukov V, Walter JC, De Nicolo A.
Methods Mol Biol. 2016;1413:207-35.

Two-Stage Synapsis of DNA Ends during Non-homologous End Joining.
Graham TG, Walter JC, Loparo JJ.
Mol Cell. 2016 Mar 17;61(6):850-8.


What is the DNA repair defect underlying Fanconi anemia?
Duxin JP, Walter JC.
Curr Opin Cell Biol. 2015 Dec;37:49-60.

The mechanism of DNA replication termination in vertebrates.
Dewar JM, Budzowska M, Walter JC.
Nature. 2015 Sep 17;525(7569):345-50.

Regulation of the Rev1-pol ζ complex during bypass of a DNA interstrand cross-link.
Budzowska M, Graham TG, Sobeck A, Waga S, Walter JC.
EMBO J. 2015 Jul 14;34(14):1971-85.

DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links.
Räschle M, Smeenk G, Hansen RK, Temu T, Oka Y, Hein MY, Nagaraj N, Long DT, Walter JC, Hofmann K, Storchova Z, Cox J, Bekker-Jensen S, Mailand N, Mann M.
Science. 2015 May 1;348(6234):1253671.

Single-Molecule Visualization of MCM2-7 DNA Loading: Seeing Is Believing.
Chistol G, Walter JC.
Cell. 2015 Apr 23;161(3):429-430.

DNA interstrand cross-link repair requires replication-fork convergence.
Zhang J, Dewar JM, Budzowska M, Motnenko A, Cohn MA, Walter JC.
Nat Struct Mol Biol. 2015 Mar;22(3):242-7.


Repair of a DNA-protein crosslink by replication-coupled proteolysis.
Duxin JP, Dewar JM, Yardimci H, Walter JC.
Cell. 2014 Oct 9;159(2):346-57.

BRCA1 promotes unloading of the CMG helicase from a stalled DNA replication fork.
Long DT, Joukov V, Budzowska M, Walter JC.
Mol Cell. 2014 Oct 2;56(1):174-85.

The Cep192-organized aurora A-Plk1 cascade is essential for centrosome cycle and bipolar spindle assembly.
Joukov V, Walter JC, De Nicolo A.
Mol Cell. 2014 Aug 21;55(4):578-91.

Thymine DNA glycosylase is a CRL4Cdt2 substrate.
Slenn TJ, Morris B, Havens CG, Freeman RM Jr, Takahashi TS, Walter JC.
J Biol Chem. 2014 Aug 15;289(33):23043-23055.

Mechanism and regulation of incisions during DNA interstrand cross-link repair.
Zhang J, Walter JC.
DNA Repair (Amst). 2014 Jul;19:135-42.

XPF-ERCC1 acts in Unhooking DNA interstrand crosslinks in cooperation with FANCD2 and FANCP/SLX4.
Klein Douwel D, Boonen RA, Long DT, Szypowska AA, Räschle M, Walter JC, Knipscheer P.
Mol Cell. 2014 May 8;54(3):460-71.

Prereplication-complex formation: a molecular double take?
Yardimci H, Walter JC.
Nat Struct Mol Biol. 2014 Jan;21(1):20-5.


The MCM8-MCM9 complex promotes RAD51 recruitment at DNA damage sites to facilitate homologous recombination.
Park J, Long DT, Lee KY, Abbas T, Shibata E, Negishi M, Luo Y, Schimenti JC, Gambus A, Walter JC, Dutta A.
Mol Cell Biol. 2013 Apr;33(8):1632-44.

Chromosome biology: conflict management for replication and transcription.
Dewar JM, Walter JC.
Curr Biol. 2013 Mar 4;23(5):R200-2.


Bypass of a protein barrier by a replicative DNA helicase.
Yardimci H, Wang X, Loveland AB, Tappin I, Rudner DZ, Hurwitz J, van Oijen AM, Walter JC.
Nature. 2012 Dec 13;492(7428):205-9.

A general approach to break the concentration barrier in single-molecule imaging.
Loveland AB, Habuchi S, Walter JC, van Oijen AM.
Nat Methods. 2012 Oct;9(10):987-92.

Replication-coupled DNA interstrand cross-link repair in Xenopus egg extracts.
Knipscheer P, Räschle M, Schärer OD, Walter JC.
Methods Mol Biol. 2012;920:221-43.

Construction of plasmids containing site-specific DNA interstrand cross-links for biochemical and cell biological studies.
Enoiu M, Ho TV, Long DT, Walter JC, Schärer OD.
Methods Mol Biol. 2012;920:203-19.

Single-molecule analysis of DNA replication in Xenopus egg extracts.
Yardimci H, Loveland AB, van Oijen AM, Walter JC.
Methods. 2012 Jun;57(2):179-86.

Ribonucleotide reductase activity is coupled to DNA synthesis via proliferating cell nuclear antigen.
Salguero I, Guarino E, Shepherd ME, Deegan TD, Havens CG, MacNeill SA, Walter JC, Kearsey SE.
Curr Biol. 2012 Apr 24;22(8):720-6.

A novel function for BRCA1 in crosslink repair.
Long DT, Walter JC.
Mol Cell. 2012 Apr 27;46(2):111-2.

Direct role for proliferating cell nuclear antigen in substrate recognition by the E3 ubiquitin ligase CRL4Cdt2.
Havens CG, Shobnam N, Guarino E, Centore RC, Zou L, Kearsey SE, Walter JC.
J Biol Chem. 2012 Mar 30;287(14):11410-21.


A genome-wide screen identifies p97 as an essential regulator of DNA damage-dependent CDT1 destruction.
Raman M, Havens CG, Walter JC, Harper JW.
Mol Cell. 2011 Oct 7;44(1):72-84.

Selective bypass of a lagging strand roadblock by the eukaryotic replicative DNA helicase.
Fu YV, Yardimci H, Long DT, Ho TV, Guainazzi A, Bermudez VP, Hurwitz J, van Oijen A, Schärer OD, Walter JC.
Cell. 2011 Sep 16;146(6):931-41.

Mechanism of CRL4(Cdt2), a PCNA-dependent E3 ubiquitin ligase.
Havens CG, Walter JC.
Genes Dev. 2011 Aug 1;25(15):1568-82.

Mechanism of RAD51-dependent DNA interstrand cross-link repair.
Long DT, Räschle M, Joukov V, Walter JC.
Science. 2011 Jul 1;333(6038):84-7.

DNA is a co-factor for its own replication in Xenopus egg extracts.
Lebofsky R, van Oijen AM, Walter JC.
Nucleic Acids Res. 2011 Jan;39(2):545-55.


Uncoupling of sister replisomes during eukaryotic DNA replication.
Yardimci H, Loveland AB, Habuchi S, van Oijen AM, Walter JC.
Mol Cell. 2010 Dec 10;40(5):834-40.

Centrosomal protein of 192 kDa (Cep192) promotes centrosome-driven spindle assembly by engaging in organelle-specific Aurora A activation.
Joukov V, De Nicolo A, Rodriguez A, Walter JC, Livingston DM.
Proc Natl Acad Sci U S A. 2010 Dec 7;107(49):21022-7.

CRL4(Cdt2)-mediated destruction of the histone methyltransferase Set8 prevents premature chromatin compaction in S phase.
Centore RC, Havens CG, Manning AL, Li JM, Flynn RL, Tse A, Jin J, Dyson NJ, Walter JC, Zou L.
Mol Cell. 2010 Oct 8;40(1):22-33.

DNA replication: metazoan Sld3 steps forward.
Fu YV, Walter JC.
Curr Biol. 2010 Jun 22;20(12):R515-7.


The Fanconi anemia pathway promotes replication-dependent DNA interstrand cross-link repair.
Knipscheer P, Räschle M, Smogorzewska A, Enoiu M, Ho TV, Schärer OD, Elledge SJ, Walter JC.
Science. 2009 Dec 18;326(5960):1698-701.

DNA replication in nucleus-free Xenopus egg extracts.
Lebofsky R, Takahashi T, Walter JC.
Methods Mol Biol. 2009;521:229-52.

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.
J Biol Chem. 2009 Jun 26;284(26):17700-10.


Mechanism of replication-coupled DNA interstrand crosslink repair.
Räschle M, Knipscheer P, Enoiu M, Angelov T, Sun J, Griffith JD, Ellenberger TE, Schärer OD, Walter JC.
Cell. 2008 Sep 19;134(6):969-80.

Cdc7-Drf1 kinase links chromosome cohesion to the initiation of DNA replication in Xenopus egg extracts.
Takahashi TS, Basu A, Bermudez V, Hurwitz J, Walter JC.
Genes Dev. 2008 Jul 15;22(14):1894-905.

Domain architecture and biochemical characterization of vertebrate Mcm10.
Robertson PD, Warren EM, Zhang H, Friedman DB, Lary JW, Cole JL, Tutter AV, Walter JC, Fanning E, Eichman BF.
J Biol Chem. 2008 Feb 8;283(6):3338-3348.


New Myc-anisms for DNA replication and tumorigenesis?
Lebofsky R, Walter JC.
Cancer Cell. 2007 Aug;12(2):102-3.


The BRCA1/BARD1 heterodimer modulates ran-dependent mitotic spindle assembly.
Joukov V, Groen AC, Prokhorova T, Gerson R, White E, Rodriguez A, Walter JC, Livingston DM.
Cell. 2006 Nov 3;127(3):539-52.

Chromosomal DNA replication in a soluble cell-free system derived from Xenopus eggs.
Tutter AV, Walter JC.
Methods Mol Biol. 2006;322:121-37.

PCNA is a cofactor for Cdt1 degradation by CUL4/DDB1-mediated N-terminal ubiquitination.
Senga T, Sivaprasad U, Zhu W, Park JH, Arias EE, Walter JC, Dutta A.
J Biol Chem. 2006 Mar 10;281(10):6246-52.

Protein phosphatase 2A antagonizes ATM and ATR in a Cdk2- and Cdc7-independent DNA damage checkpoint.
Petersen P, Chou DM, You Z, Hunter T, Walter JC, Walter G.
Mol Cell Biol. 2006 Mar;26(5):1997-2011.

The nucleosomal surface as a docking station for Kaposi’s sarcoma herpesvirus LANA.
Barbera AJ, Chodaparambil JV, Kelley-Clarke B, Joukov V, Walter JC, Luger K, Kaye KM.
Science. 2006 Feb 10;311(5762):856-61.

Localization of MCM2-7, Cdc45, and GINS to the site of DNA unwinding during eukaryotic DNA replication.
Pacek M, Tutter AV, Kubota Y, Takisawa H, Walter JC.
Mol Cell. 2006 Feb 17;21(4):581-7.


Pumps, paradoxes and ploughshares: mechanism of the MCM2-7 DNA helicase.
Takahashi TS, Wigley DB, Walter JC.
Trends Biochem Sci. 2005 Aug;30(8):437-44.

Eukaryotic origins of DNA replication: could you please be more specific?
Cvetic C, Walter JC.
Semin Cell Dev Biol. 2005 Jun;16(3):343-53.

Functional uncoupling of MCM helicase and DNA polymerase activities activates the ATR-dependent checkpoint.
Byun TS, Pacek M, Yee MC, Walter JC, Cimprich KA.
Genes Dev. 2005 May 1;19(9):1040-52.


Recruitment of Xenopus Scc2 and cohesin to chromatin requires the pre-replication complex.
Takahashi TS, Yiu P, Chou MF, Gygi S, Walter JC.
Nat Cell Biol. 2004 Oct;6(10):991-6.

Initiation of DNA replication in Xenopus egg extracts.
Arias EE, Walter JC.
Front Biosci. 2004 Sep 1;9:3029-45.

Self-assembling protein microarrays.
Ramachandran N, Hainsworth E, Bhullar B, Eisenstein S, Rosen B, Lau AY, Walter JC, LaBaer J.
Science. 2004 Jul 2;305(5680):86-90.

Cdk1: unsung hero of S phase?
Pacek M, Prokhorova TA, Walter JC.
Cell Cycle. 2004 Apr;3(4):401-3.


DNA replication of mitotic chromatin in Xenopus egg extracts.
Prokhorova TA, Mowrer K, Gilbert CH, Walter JC.
Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13241-6.

Sequence-independent DNA binding and replication initiation by the human origin recognition complex.
Vashee S, Cvetic C, Lu W, Simancek P, Kelly TJ, Walter JC.
Genes Dev. 2003 Aug 1;17(15):1894-908.


The Xenopus Xmus101 protein is required for the recruitment of Cdc45 to origins of DNA replication.
Van Hatten RA, Tutter AV, Holway AH, Khederian AM, Walter JC, Michael WM.
J Cell Biol. 2002 Nov 25;159(4):541-7.

Protein phosphatase 2A regulates binding of Cdc45 to the prereplication complex.
Chou DM, Petersen P, Walter JC, Walter G.
J Biol Chem. 2002 Oct 25;277(43):40520-7.

MCM2-7 complexes bind chromatin in a distributed pattern surrounding the origin recognition complex in Xenopus egg extracts.
Edwards MC, Tutter AV, Cvetic C, Gilbert CH, Prokhorova TA, Walter JC.
J Biol Chem. 2002 Sep

Xenopus Mcm10 binds to origins of DNA replication after Mcm2-7 and stimulates origin binding of Cdc45.
Wohlschlegel JA, Dhar SK, Prokhorova TA, Dutta A, Walter JC.
Mol Cell. 2002 Feb;9(2):233-40.


Inhibition of eukaryotic DNA replication by geminin binding to Cdt1.
Wohlschlegel JA, Dwyer BT, Dhar SK, Cvetic C, Walter JC, Dutta A.
Science. 2000 Dec 22;290(5500):2309-12.


Protein phosphatase 2A is required for the initiation of chromosomal DNA replication.
Lin XH, Walter J, Scheidtmann K, Ohst K, Newport J, Walter G.
Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14693-8.

Regulated chromosomal DNA replication in the absence of a nucleus.
Walter J, Sun L, Newport J.
Mol Cell. 1998 Mar;1(4):519-29.


Regulation of replicon size in Xenopus egg extracts.
Walter J, Newport JW.
Science. 1997 Feb 14;275(5302):993-5.


DNA binding specificity of two homeodomain proteins in vitro and in Drosophila embryos.
Walter J, Biggin MD.
Proc Natl Acad Sci U S A. 1996 Apr 2;93(7):2680-5.