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Comment on "A commensal strain of Staphylococcus epidermidis protects against skin neoplasia" by Nakatsuji et al.

Kozmin SG, Rogozin IB, Moore EA, Abney M, Schaaper RM, Pavlov YI.

Sci Adv. 2019 Sep 11;5(9):eaaw3915. doi: 10.1126/sciadv.aaw3915. eCollection 2019 Sep.


Nucleotide Weight Matrices Reveal Ubiquitous Mutational Footprints of AID/APOBEC Deaminases in Human Cancer Genomes.

Rogozin IB, Roche-Lima A, Lada AG, Belinky F, Sidorenko IA, Glazko GV, Babenko VN, Cooper DN, Pavlov YI.

Cancers (Basel). 2019 Feb 12;11(2). pii: E211. doi: 10.3390/cancers11020211.


Deletion of the DEF1 gene does not confer UV-immutability but frequently leads to self-diploidization in yeast Saccharomyces cerevisiae.

Stepchenkova EI, Shiriaeva AA, Pavlov YI.

DNA Repair (Amst). 2018 Oct;70:49-54. doi: 10.1016/j.dnarep.2018.08.026. Epub 2018 Aug 23.


Iron-Sulfur Clusters in DNA Polymerases and Primases of Eukaryotes.

Baranovskiy AG, Siebler HM, Pavlov YI, Tahirov TH.

Methods Enzymol. 2018;599:1-20. doi: 10.1016/bs.mie.2017.09.003. Epub 2017 Dec 6.


Activity and fidelity of human DNA polymerase α depend on primer structure.

Baranovskiy AG, Duong VN, Babayeva ND, Zhang Y, Pavlov YI, Anderson KS, Tahirov TH.

J Biol Chem. 2018 May 4;293(18):6824-6843. doi: 10.1074/jbc.RA117.001074. Epub 2018 Mar 19.


Recombination Is Responsible for the Increased Recovery of Drug-Resistant Mutants with Hypermutated Genomes in Resting Yeast Diploids Expressing APOBEC Deaminases.

Lada AG, Stepchenkova EI, Zhuk AS, Kliver SF, Rogozin IB, Polev DE, Dhar A, Pavlov YI.

Front Genet. 2017 Dec 12;8:202. doi: 10.3389/fgene.2017.00202. eCollection 2017.


DNA polymerase η mutational signatures are found in a variety of different types of cancer.

Rogozin IB, Goncearenco A, Lada AG, De S, Yurchenko V, Nudelman G, Panchenko AR, Cooper DN, Pavlov YI.

Cell Cycle. 2018;17(3):348-355. doi: 10.1080/15384101.2017.1404208. Epub 2018 Feb 15.


Measuring deaminated nucleotide surveillance enzyme ITPA activity with an ATP-releasing nucleotide chimera.

Ji D, Stepchenkova EI, Cui J, Menezes MR, Pavlov YI, Kool ET.

Nucleic Acids Res. 2017 Nov 16;45(20):11515-11524. doi: 10.1093/nar/gkx774.


Crystal structure of the human Polϵ B-subunit in complex with the C-terminal domain of the catalytic subunit.

Baranovskiy AG, Gu J, Babayeva ND, Kurinov I, Pavlov YI, Tahirov TH.

J Biol Chem. 2017 Sep 22;292(38):15717-15730. doi: 10.1074/jbc.M117.792705. Epub 2017 Jul 26.


Comment on "The [4Fe4S] cluster of human DNA primase functions as a redox switch using DNA charge transport".

Baranovskiy AG, Babayeva ND, Zhang Y, Blanco L, Pavlov YI, Tahirov TH.

Science. 2017 Jul 21;357(6348). pii: eaan2396. doi: 10.1126/science.aan2396.


Mutational signatures and mutable motifs in cancer genomes.

Rogozin IB, Pavlov YI, Goncearenco A, De S, Lada AG, Poliakov E, Panchenko AR, Cooper DN.

Brief Bioinform. 2018 Nov 27;19(6):1085-1101. doi: 10.1093/bib/bbx049. Review.


Defect of Fe-S cluster binding by DNA polymerase δ in yeast suppresses UV-induced mutagenesis, but enhances DNA polymerase ζ - dependent spontaneous mutagenesis.

Stepchenkova EI, Tarakhovskaya ER, Siebler HM, Pavlov YI.

DNA Repair (Amst). 2017 Jan;49:60-69. doi: 10.1016/j.dnarep.2016.11.004. Epub 2016 Dec 9.


Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers.

Rogozin IB, Lada AG, Goncearenco A, Green MR, De S, Nudelman G, Panchenko AR, Koonin EV, Pavlov YI.

Sci Rep. 2016 Dec 7;6:38133. doi: 10.1038/srep38133.


Divalent ions attenuate DNA synthesis by human DNA polymerase α by changing the structure of the template/primer or by perturbing the polymerase reaction.

Zhang Y, Baranovskiy AG, Tahirov ET, Tahirov TH, Pavlov YI.

DNA Repair (Amst). 2016 Jul;43:24-33. doi: 10.1016/j.dnarep.2016.05.017. Epub 2016 May 12.


Mechanism of Concerted RNA-DNA Primer Synthesis by the Human Primosome.

Baranovskiy AG, Babayeva ND, Zhang Y, Gu J, Suwa Y, Pavlov YI, Tahirov TH.

J Biol Chem. 2016 May 6;291(19):10006-20. doi: 10.1074/jbc.M116.717405. Epub 2016 Mar 14.



Zhuk AS, Stepchenkova EI, Pavlov YI, Inge-Vechtomov SG.

Tsitologiia. 2016;58(12):936-46. English, Russian.


Insight into the Human DNA Primase Interaction with Template-Primer.

Baranovskiy AG, Zhang Y, Suwa Y, Gu J, Babayeva ND, Pavlov YI, Tahirov TH.

J Biol Chem. 2016 Feb 26;291(9):4793-802. doi: 10.1074/jbc.M115.704064. Epub 2015 Dec 28.


Disruption of Transcriptional Coactivator Sub1 Leads to Genome-Wide Re-distribution of Clustered Mutations Induced by APOBEC in Active Yeast Genes.

Lada AG, Kliver SF, Dhar A, Polev DE, Masharsky AE, Rogozin IB, Pavlov YI.

PLoS Genet. 2015 May 5;11(5):e1005217. doi: 10.1371/journal.pgen.1005217. eCollection 2015 May.


Crystal Structure of the Human Pol α B Subunit in Complex with the C-terminal Domain of the Catalytic Subunit.

Suwa Y, Gu J, Baranovskiy AG, Babayeva ND, Pavlov YI, Tahirov TH.

J Biol Chem. 2015 Jun 5;290(23):14328-37. doi: 10.1074/jbc.M115.649954. Epub 2015 Apr 6.


Crystal structure of the human primase.

Baranovskiy AG, Zhang Y, Suwa Y, Babayeva ND, Gu J, Pavlov YI, Tahirov TH.

J Biol Chem. 2015 Feb 27;290(9):5635-46. doi: 10.1074/jbc.M114.624742. Epub 2014 Dec 30.


Structural basis for inhibition of DNA replication by aphidicolin.

Baranovskiy AG, Babayeva ND, Suwa Y, Gu J, Pavlov YI, Tahirov TH.

Nucleic Acids Res. 2014 Dec 16;42(22):14013-21. doi: 10.1093/nar/gku1209. Epub 2014 Nov 27.


The C-terminal domain of the DNA polymerase catalytic subunit regulates the primase and polymerase activities of the human DNA polymerase α-primase complex.

Zhang Y, Baranovskiy AG, Tahirov TH, Pavlov YI.

J Biol Chem. 2014 Aug 8;289(32):22021-34. doi: 10.1074/jbc.M114.570333. Epub 2014 Jun 24.


A novel variant of DNA polymerase ζ, Rev3ΔC, highlights differential regulation of Pol32 as a subunit of polymerase δ versus ζ in Saccharomyces cerevisiae.

Siebler HM, Lada AG, Baranovskiy AG, Tahirov TH, Pavlov YI.

DNA Repair (Amst). 2014 Dec;24:138-149. doi: 10.1016/j.dnarep.2014.04.013. Epub 2014 May 10.


Genome-wide mutation avalanches induced in diploid yeast cells by a base analog or an APOBEC deaminase.

Lada AG, Stepchenkova EI, Waisertreiger IS, Noskov VN, Dhar A, Eudy JD, Boissy RJ, Hirano M, Rogozin IB, Pavlov YI.

PLoS Genet. 2013;9(9):e1003736. doi: 10.1371/journal.pgen.1003736. Epub 2013 Sep 5.


ITPA (inosine triphosphate pyrophosphatase): from surveillance of nucleotide pools to human disease and pharmacogenetics.

Simone PD, Pavlov YI, Borgstahl GE.

Mutat Res. 2013 Oct-Dec;753(2):131-46. doi: 10.1016/j.mrrev.2013.08.001. Epub 2013 Aug 19. Review.


The human ITPA polymorphic variant P32T is destabilized by the unpacking of the hydrophobic core.

Simone PD, Struble LR, Kellezi A, Brown CA, Grabow CE, Khutsishvili I, Marky LA, Pavlov YI, Borgstahl GE.

J Struct Biol. 2013 Jun;182(3):197-208. doi: 10.1016/j.jsb.2013.03.007. Epub 2013 Mar 23.


AID/APOBEC cytosine deaminase induces genome-wide kataegis.

Lada AG, Dhar A, Boissy RJ, Hirano M, Rubel AA, Rogozin IB, Pavlov YI.

Biol Direct. 2012 Dec 18;7:47; discussion 47. doi: 10.1186/1745-6150-7-47.


Role of DNA polymerases in repeat-mediated genome instability.

Shah KA, Shishkin AA, Voineagu I, Pavlov YI, Shcherbakova PV, Mirkin SM.

Cell Rep. 2012 Nov 29;2(5):1088-95. doi: 10.1016/j.celrep.2012.10.006. Epub 2012 Nov 8.


Modulation of mutagenesis in eukaryotes by DNA replication fork dynamics and quality of nucleotide pools.

Waisertreiger IS, Liston VG, Menezes MR, Kim HM, Lobachev KS, Stepchenkova EI, Tahirov TH, Rogozin IB, Pavlov YI.

Environ Mol Mutagen. 2012 Dec;53(9):699-724. doi: 10.1002/em.21735. Epub 2012 Oct 10. Review.


DNA polymerase δ and ζ switch by sharing accessory subunits of DNA polymerase δ.

Baranovskiy AG, Lada AG, Siebler HM, Zhang Y, Pavlov YI, Tahirov TH.

J Biol Chem. 2012 May 18;287(21):17281-7. doi: 10.1074/jbc.M112.351122. Epub 2012 Mar 30.


Pivotal role of inosine triphosphate pyrophosphatase in maintaining genome stability and the prevention of apoptosis in human cells.

Menezes MR, Waisertreiger IS, Lopez-Bertoni H, Luo X, Pavlov YI.

PLoS One. 2012;7(2):e32313. doi: 10.1371/journal.pone.0032313. Epub 2012 Feb 27.


Isolation and characterization of high affinity aptamers against DNA polymerase iota.

Lakhin AV, Kazakov AA, Makarova AV, Pavlov YI, Efremova AS, Shram SI, Tarantul VZ, Gening LV.

Nucleic Acid Ther. 2012 Feb;22(1):49-57. doi: 10.1089/nat.2011.0324. Epub 2012 Jan 5.


Replication protein A (RPA) hampers the processive action of APOBEC3G cytosine deaminase on single-stranded DNA.

Lada AG, Waisertreiger IS, Grabow CE, Prakash A, Borgstahl GE, Rogozin IB, Pavlov YI.

PLoS One. 2011;6(9):e24848. doi: 10.1371/journal.pone.0024848. Epub 2011 Sep 15.


Mutator effects and mutation signatures of editing deaminases produced in bacteria and yeast.

Lada AG, Krick CF, Kozmin SG, Mayorov VI, Karpova TS, Rogozin IB, Pavlov YI.

Biochemistry (Mosc). 2011 Jan;76(1):131-46.


Inaccurate DNA synthesis in cell extracts of yeast producing active human DNA polymerase iota.

Makarova AV, Grabow C, Gening LV, Tarantul VZ, Tahirov TH, Bessho T, Pavlov YI.

PLoS One. 2011 Jan 31;6(1):e16612. doi: 10.1371/journal.pone.0016612.


The role of DNA polymerase alpha in the control of mutagenesis in Saccharomyces cerevisiae cells starved for nutrients.

Babudri N, Achilli A, Martinelli C, Moore E, Lancioni H, Pavlov YI.

Ekol Genet. 2011;9(1):53-61.


Mismatch repair-independent increase in spontaneous mutagenesis in yeast lacking non-essential subunits of DNA polymerase ε.

Aksenova A, Volkov K, Maceluch J, Pursell ZF, Rogozin IB, Kunkel TA, Pavlov YI, Johansson E.

PLoS Genet. 2010 Nov 18;6(11):e1001209. doi: 10.1371/journal.pgen.1001209.


Elevated Levels of DNA Strand Breaks Induced by a Base Analog in the Human Cell Line with the P32T ITPA Variant.

Waisertreiger IS, Menezes MR, Randazzo J, Pavlov YI.

J Nucleic Acids. 2010 Sep 26;2010. pii: 872180. doi: 10.4061/2010/872180.


DNA polymerases at the eukaryotic fork-20 years later.

Pavlov YI, Shcherbakova PV.

Mutat Res. 2010 Mar 1;685(1-2):45-53. doi: 10.1016/j.mrfmmm.2009.08.002. Epub 2009 Aug 12. Review.


Functional study of the P32T ITPA variant associated with drug sensitivity in humans.

Stepchenkova EI, Tarakhovskaya ER, Spitler K, Frahm C, Menezes MR, Simone PD, Kolar C, Marky LA, Borgstahl GE, Pavlov YI.

J Mol Biol. 2009 Sep 25;392(3):602-13. doi: 10.1016/j.jmb.2009.07.051. Epub 2009 Jul 23.


X-ray structure of the complex of regulatory subunits of human DNA polymerase delta.

Baranovskiy AG, Babayeva ND, Liston VG, Rogozin IB, Koonin EV, Pavlov YI, Vassylyev DG, Tahirov TH.

Cell Cycle. 2008 Oct;7(19):3026-36. Epub 2008 Oct 4.


Crystallization and preliminary crystallographic analysis of the complex of the second and third regulatory subunits of human Pol delta.

Baranovskiy AG, Babayeva ND, Pavlov YI, Tahirov TH.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Sep 1;64(Pt 9):822-4. doi: 10.1107/S1744309108025086. Epub 2008 Aug 20.


A highly conserved family of inactivated archaeal B family DNA polymerases.

Rogozin IB, Makarova KS, Pavlov YI, Koonin EV.

Biol Direct. 2008 Aug 6;3:32. doi: 10.1186/1745-6150-3-32.


YcbX and yiiM, two novel determinants for resistance of Escherichia coli to N-hydroxylated base analogues.

Kozmin SG, Leroy P, Pavlov YI, Schaaper RM.

Mol Microbiol. 2008 Apr;68(1):51-65. doi: 10.1111/j.1365-2958.2008.06128.x. Epub 2008 Feb 26.


High rate of starvation-associated mutagenesis in Ung(-) yeast caused by the overproduction of human activation-induced deaminase.

Lucaccioni A, Pavlov YI, Achilli A, Babudri N.

Curr Genet. 2007 Nov;52(5-6):239-45. Epub 2007 Oct 13.


Mutator alleles of yeast DNA polymerase zeta.

Sakamoto AN, Stone JE, Kissling GE, McCulloch SD, Pavlov YI, Kunkel TA.

DNA Repair (Amst). 2007 Dec 1;6(12):1829-38. Epub 2007 Aug 21.


Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase.

Rogozin IB, Iyer LM, Liang L, Glazko GV, Liston VG, Pavlov YI, Aravind L, Pancer Z.

Nat Immunol. 2007 Jun;8(6):647-56. Epub 2007 Apr 29.


Roles of DNA polymerases in replication, repair, and recombination in eukaryotes.

Pavlov YI, Shcherbakova PV, Rogozin IB.

Int Rev Cytol. 2006;255:41-132. Review.


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