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Volumn 11, Issue 5, 2015, Pages

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

Author keywords

[No Author keywords available]

Indexed keywords

APOLIPOPROTEIN B MESSENGER RNA EDITING ENZYME CATALYTIC POLYPEPTIDE 1; APOLIPOPROTEIN B MESSENGER RNA EDITING ENZYME CATALYTIC POLYPEPTIDE 3G; CYTOSINE DEAMINASE; DNA BINDING PROTEIN; PROTEIN PMCDA1; PROTEIN SUB1; SINGLE STRANDED DNA; UNCLASSIFIED DRUG; AMINO ACID TRANSPORTER; ASPARTATE CARBAMOYLTRANSFERASE; CAN1 PROTEIN, S CEREVISIAE; CARBAMOYL PHOSPHATE SYNTHASE (GLUTAMINE HYDROLYSING); CATION TRANSPORT PROTEIN; CYTIDINE DEAMINASE; SACCHAROMYCES CEREVISIAE PROTEIN; SUB1 PROTEIN, S CEREVISIAE; TRANSCRIPTION FACTOR; TRK1 PROTEIN, S CEREVISIAE; URA2 PROTEIN, S CEREVISIAE;

EID: 84930795728     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1005217     Document Type: Article
Times cited : (47)

References (82)
  • 1
    • 33845496081 scopus 로고    scopus 로고
    • Roles of DNA polymerases in replication, repair, and recombination in eukaryotes
    • Pavlov YI, Shcherbakova PV, Rogozin IB, Roles of DNA polymerases in replication, repair, and recombination in eukaryotes. Int Rev Cytol. 2006;255:41–132. 17178465
    • (2006) Int Rev Cytol , vol.255 , pp. 41-132
    • Pavlov, Y.I.1    Shcherbakova, P.V.2    Rogozin, I.B.3
  • 2
    • 78649460241 scopus 로고    scopus 로고
    • Mutator phenotypes due to DNA replication infidelity
    • Arana ME, Kunkel TA, Mutator phenotypes due to DNA replication infidelity. Semin Cancer Biol. 2010;20:304–11. doi: 10.1016/j.semcancer.2010.10.003 20934516
    • (2010) Semin Cancer Biol , vol.20 , pp. 304-311
    • Arana, M.E.1    Kunkel, T.A.2
  • 4
    • 34249807921 scopus 로고    scopus 로고
    • DNA deamination in immunity: AID in the context of its APOBEC relatives
    • Conticello SG, Langlois MA, Yang Z, Neuberger MS, DNA deamination in immunity: AID in the context of its APOBEC relatives. Adv Immunol. 2007;94:37–73. 17560271
    • (2007) Adv Immunol , vol.94 , pp. 37-73
    • Conticello, S.G.1    Langlois, M.A.2    Yang, Z.3    Neuberger, M.S.4
  • 5
    • 38449114171 scopus 로고    scopus 로고
    • Vertebrate immunity: mutator proteins and their evolution
    • Lada AG, Iyer LM, Rogozin IB, Aravind L, Pavlov Iu I, Vertebrate immunity: mutator proteins and their evolution]. Genetika. 2007;43:1311–27. 18069336
    • (2007) Genetika , vol.43 , pp. 1311-1327
    • Lada, A.G.1    Iyer, L.M.2    Rogozin, I.B.3    Aravind, L.4    Pavlov, I.I.5
  • 6
    • 84908153041 scopus 로고    scopus 로고
    • AID and APOBEC deaminases: balancing DNA damage in epigenetics and immunity
    • Franchini DM, Petersen-Mahrt SK, AID and APOBEC deaminases: balancing DNA damage in epigenetics and immunity. Epigenomics. 2014;6:427–43. doi: 10.2217/epi.14.35 25333851
    • (2014) Epigenomics , vol.6 , pp. 427-443
    • Franchini, D.M.1    Petersen-Mahrt, S.K.2
  • 7
    • 0348140581 scopus 로고    scopus 로고
    • DNA-cytosine deaminases: from antibody maturation to antiviral defense
    • Bhagwat AS, DNA-cytosine deaminases: from antibody maturation to antiviral defense. DNA Repair (Amst). 2004;3:85–9. 14697763
    • (2004) DNA Repair (Amst) , vol.3 , pp. 85-89
    • Bhagwat, A.S.1
  • 8
    • 84861541343 scopus 로고    scopus 로고
    • Mutational processes molding the genomes of 21 breast cancers
    • Nik-Zainal S, Alexandrov LB, Wedge DC, Van Loo P, Greenman CD, Raine K, et al. Mutational processes molding the genomes of 21 breast cancers. Cell. 2012;149:979–93. doi: 10.1016/j.cell.2012.04.024 22608084
    • (2012) Cell , vol.149 , pp. 979-993
    • Nik-Zainal, S.1    Alexandrov, L.B.2    Wedge, D.C.3    Van Loo, P.4    Greenman, C.D.5    Raine, K.6
  • 10
    • 84883432724 scopus 로고    scopus 로고
    • An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers
    • Roberts SA, Lawrence MS, Klimczak LJ, Grimm SA, Fargo D, Stojanov P, et al. An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers. Nat Genet. 2013;45:970–6. doi: 10.1038/ng.2702 23852170
    • (2013) Nat Genet , vol.45 , pp. 970-976
    • Roberts, S.A.1    Lawrence, M.S.2    Klimczak, L.J.3    Grimm, S.A.4    Fargo, D.5    Stojanov, P.6
  • 11
    • 84895784747 scopus 로고    scopus 로고
    • Mechanisms of base substitution mutagenesis in cancer genomes
    • Bacolla A, Cooper DN, Vasquez KM, Mechanisms of base substitution mutagenesis in cancer genomes. Genes (Basel). 2014;5:108–46. doi: 10.3390/genes5010108 24705290
    • (2014) Genes (Basel) , vol.5 , pp. 108-146
    • Bacolla, A.1    Cooper, D.N.2    Vasquez, K.M.3
  • 12
    • 1542328859 scopus 로고    scopus 로고
    • Comparison of the differential context-dependence of DNA deamination by APOBEC enzymes: correlation with mutation spectra in vivo
    • Beale RC, Petersen-Mahrt SK, Watt IN, Harris RS, Rada C, Neuberger MS, Comparison of the differential context-dependence of DNA deamination by APOBEC enzymes: correlation with mutation spectra in vivo. Journal of Molecular Biology. 2004;337:585–96. 15019779
    • (2004) Journal of Molecular Biology , vol.337 , pp. 585-596
    • Beale, R.C.1    Petersen-Mahrt, S.K.2    Watt, I.N.3    Harris, R.S.4    Rada, C.5    Neuberger, M.S.6
  • 13
    • 84883356320 scopus 로고    scopus 로고
    • Evidence for APOBEC3B mutagenesis in multiple human cancers
    • Burns MB, Temiz NA, Harris RS, Evidence for APOBEC3B mutagenesis in multiple human cancers. Nat Genet. 2013;45:977–83. doi: 10.1038/ng.2701 23852168
    • (2013) Nat Genet , vol.45 , pp. 977-983
    • Burns, M.B.1    Temiz, N.A.2    Harris, R.S.3
  • 14
    • 84874188583 scopus 로고    scopus 로고
    • APOBEC3B is an enzymatic source of mutation in breast cancer
    • Burns MB, Lackey L, Carpenter MA, Rathore A, Land AM, Leonard B, et al. APOBEC3B is an enzymatic source of mutation in breast cancer. Nature. 2013;494:366–70. doi: 10.1038/nature11881 23389445
    • (2013) Nature , vol.494 , pp. 366-370
    • Burns, M.B.1    Lackey, L.2    Carpenter, M.A.3    Rathore, A.4    Land, A.M.5    Leonard, B.6
  • 15
    • 84869159477 scopus 로고    scopus 로고
    • APOBEC3B can impair genomic stability by inducing base substitutions in genomic DNA in human cells
    • Shinohara M, Io K, Shindo K, Matsui M, Sakamoto T, Tada K, et al. APOBEC3B can impair genomic stability by inducing base substitutions in genomic DNA in human cells. Scientific Reports. 2012;2:806. doi: 10.1038/srep00806 23150777
    • (2012) Scientific Reports , vol.2 , pp. 806
    • Shinohara, M.1    Io, K.2    Shindo, K.3    Matsui, M.4    Sakamoto, T.5    Tada, K.6
  • 16
    • 84924341659 scopus 로고    scopus 로고
    • The RNA editing enzyme APOBEC1 induces somatic mutations and a compatible mutational signature is present in esophageal adenocarcinomas
    • Saraconi G, Severi F, Sala C, Mattiuz G, Conticello SG, The RNA editing enzyme APOBEC1 induces somatic mutations and a compatible mutational signature is present in esophageal adenocarcinomas. Genome Biology. 2014;15:417. doi: 10.1186/s13059-014-0417-z 25085003
    • (2014) Genome Biology , vol.15 , pp. 417
    • Saraconi, G.1    Severi, F.2    Sala, C.3    Mattiuz, G.4    Conticello, S.G.5
  • 17
    • 0037926476 scopus 로고    scopus 로고
    • Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation
    • Pham P, Bransteitter R, Petruska J, Goodman MF, Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation. Nature. 2003;424:103–7. 12819663
    • (2003) Nature , vol.424 , pp. 103-107
    • Pham, P.1    Bransteitter, R.2    Petruska, J.3    Goodman, M.F.4
  • 19
    • 84879061509 scopus 로고    scopus 로고
    • DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis
    • Taylor BJ, Nik-Zainal S, Wu YL, Stebbings LA, Raine K, Campbell PJ, et al. DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis. Elife. 2013;2:e00534. doi: 10.7554/eLife.00534 23599896
    • (2013) Elife , vol.2 , pp. e00534
    • Taylor, B.J.1    Nik-Zainal, S.2    Wu, Y.L.3    Stebbings, L.A.4    Raine, K.5    Campbell, P.J.6
  • 20
    • 84902318918 scopus 로고    scopus 로고
    • Break-induced replication is a source of mutation clusters underlying kataegis
    • Sakofsky CJ, Roberts SA, Malc E, Mieczkowski PA, Resnick MA, Gordenin DA, et al. Break-induced replication is a source of mutation clusters underlying kataegis. Cell Rep. 2014;7:1640–8. doi: 10.1016/j.celrep.2014.04.053 24882007
    • (2014) Cell Rep , vol.7 , pp. 1640-1648
    • Sakofsky, C.J.1    Roberts, S.A.2    Malc, E.3    Mieczkowski, P.A.4    Resnick, M.A.5    Gordenin, D.A.6
  • 21
    • 60049097628 scopus 로고    scopus 로고
    • Stochastic properties of processive cytidine DNA deaminases AID and APOBEC3G
    • Chelico L, Pham P, Goodman MF, Stochastic properties of processive cytidine DNA deaminases AID and APOBEC3G. Philos Trans R Soc Lond B Biol Sci. 2009;364:583–93. doi: 10.1098/rstb.2008.0195 19022738
    • (2009) Philos Trans R Soc Lond B Biol Sci , vol.364 , pp. 583-593
    • Chelico, L.1    Pham, P.2    Goodman, M.F.3
  • 22
    • 47749085064 scopus 로고    scopus 로고
    • Impact of phosphorylation and phosphorylation-null mutants on the activity and deamination specificity of activation-induced cytidine deaminase
    • Pham P, Smolka MB, Calabrese P, Landolph A, Zhang K, Zhou H, et al. Impact of phosphorylation and phosphorylation-null mutants on the activity and deamination specificity of activation-induced cytidine deaminase. J Biol Chem. 2008;283:17428–39. doi: 10.1074/jbc.M802121200 18417471
    • (2008) J Biol Chem , vol.283 , pp. 17428-17439
    • Pham, P.1    Smolka, M.B.2    Calabrese, P.3    Landolph, A.4    Zhang, K.5    Zhou, H.6
  • 23
    • 80052842909 scopus 로고    scopus 로고
    • 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, et al. Replication protein A (RPA) hampers the processive action of APOBEC3G cytosine deaminase on single-stranded DNA. PLoS One. 2011;6:e24848. doi: 10.1371/journal.pone.0024848 21935481
    • (2011) PLoS One , vol.6 , pp. e24848
    • Lada, A.G.1    Waisertreiger, I.S.2    Grabow, C.E.3    Prakash, A.4    Borgstahl, G.E.5    Rogozin, I.B.6
  • 24
    • 0037019315 scopus 로고    scopus 로고
    • AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification
    • Petersen-Mahrt SK, Harris RS, Neuberger MS, AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification. Nature. 2002;418:99–103. 12097915
    • (2002) Nature , vol.418 , pp. 99-103
    • Petersen-Mahrt, S.K.1    Harris, R.S.2    Neuberger, M.S.3
  • 25
    • 0036863733 scopus 로고    scopus 로고
    • RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators
    • Harris RS, Petersen-Mahrt SK, Neuberger MS, RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators. Mol Cell. 2002;10:1247–53. 12453430
    • (2002) Mol Cell , vol.10 , pp. 1247-1253
    • Harris, R.S.1    Petersen-Mahrt, S.K.2    Neuberger, M.S.3
  • 26
    • 26444443118 scopus 로고    scopus 로고
    • Expression of human AID in yeast induces mutations in context similar to the context of somatic hypermutation at G-C pairs in immunoglobulin genes
    • Mayorov VI, Rogozin IB, Adkison LR, Frahm C, Kunkel TA, Pavlov YI, Expression of human AID in yeast induces mutations in context similar to the context of somatic hypermutation at G-C pairs in immunoglobulin genes. BMC Immunol. 2005;6:10. 15949042
    • (2005) BMC Immunol , vol.6 , pp. 10
    • Mayorov, V.I.1    Rogozin, I.B.2    Adkison, L.R.3    Frahm, C.4    Kunkel, T.A.5    Pavlov, Y.I.6
  • 28
    • 84884686754 scopus 로고    scopus 로고
    • 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, et al. Genome-wide mutation avalanches induced in diploid yeast cells by a base analog or an APOBEC deaminase. PLoS Genet. 2013;9:e1003736. doi: 10.1371/journal.pgen.1003736 24039593
    • (2013) PLoS Genet , vol.9 , pp. e1003736
    • Lada, A.G.1    Stepchenkova, E.I.2    Waisertreiger, I.S.3    Noskov, V.N.4    Dhar, A.5    Eudy, J.D.6
  • 29
    • 34249065874 scopus 로고    scopus 로고
    • 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, et al. Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase. Nat Immunol. 2007;8:647–56. 17468760
    • (2007) Nat Immunol , vol.8 , pp. 647-656
    • Rogozin, I.B.1    Iyer, L.M.2    Liang, L.3    Glazko, G.V.4    Liston, V.G.5    Pavlov, Y.I.6
  • 30
    • 67649415203 scopus 로고    scopus 로고
    • Genetic control of metabolism of mutagenic purine base analogs 6-hydroxylaminopurine and 2-amino-6-hydroxylaminopurine in yeast Saccharomyces cerevisiae
    • Stepchenkova EI, Koz'min SG, Alenin VV, Pavlov Iu I, Genetic control of metabolism of mutagenic purine base analogs 6-hydroxylaminopurine and 2-amino-6-hydroxylaminopurine in yeast Saccharomyces cerevisiae]. Genetika. 2009;45:471–7. 19514135
    • (2009) Genetika , vol.45 , pp. 471-477
    • Stepchenkova, E.I.1    Koz'min, S.G.2    Alenin, V.V.3    Pavlov Iu, I.4
  • 31
  • 32
    • 79551683756 scopus 로고    scopus 로고
    • The multiple personalities of Watson and Crick strands
    • Cartwright RA, Graur D, The multiple personalities of Watson and Crick strands. Biol Direct. 2011;6:7. doi: 10.1186/1745-6150-6-7 21303550
    • (2011) Biol Direct , vol.6 , pp. 7
    • Cartwright, R.A.1    Graur, D.2
  • 33
    • 34249790004 scopus 로고    scopus 로고
    • Molecular mechanisms of antibody somatic hypermutation
    • Di Noia JM, Neuberger MS, Molecular mechanisms of antibody somatic hypermutation. Annu Rev Biochem. 2007;76:1–22. 17328676
    • (2007) Annu Rev Biochem , vol.76 , pp. 1-22
    • Di Noia, J.M.1    Neuberger, M.S.2
  • 34
    • 45549088326 scopus 로고    scopus 로고
    • The transcriptional landscape of the yeast genome defined by RNA sequencing
    • Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008;320:1344–9. doi: 10.1126/science.1158441 18451266
    • (2008) Science , vol.320 , pp. 1344-1349
    • Nagalakshmi, U.1    Wang, Z.2    Waern, K.3    Shou, C.4    Raha, D.5    Gerstein, M.6
  • 35
    • 80555156087 scopus 로고    scopus 로고
    • Sub1 and RPA associate with RNA polymerase II at different stages of transcription
    • Sikorski TW, Ficarro SB, Holik J, Kim T, Rando OJ, Marto JA, et al. Sub1 and RPA associate with RNA polymerase II at different stages of transcription. Mol Cell. 2011;44:397–409. doi: 10.1016/j.molcel.2011.09.013 22055186
    • (2011) Mol Cell , vol.44 , pp. 397-409
    • Sikorski, T.W.1    Ficarro, S.B.2    Holik, J.3    Kim, T.4    Rando, O.J.5    Marto, J.A.6
  • 37
    • 34547740652 scopus 로고    scopus 로고
    • Too many mutants with multiple mutations
    • Drake JW, Too many mutants with multiple mutations. Crit Rev Biochem Mol Biol. 2007;42:247–58. 17687667
    • (2007) Crit Rev Biochem Mol Biol , vol.42 , pp. 247-258
    • Drake, J.W.1
  • 38
    • 74249092035 scopus 로고    scopus 로고
    • Participation of DNA polymerase zeta in replication of undamaged DNA in Saccharomyces cerevisiae
    • Northam MR, Robinson HA, Kochenova OV, Shcherbakova PV, Participation of DNA polymerase zeta in replication of undamaged DNA in Saccharomyces cerevisiae. Genetics. 2010;184:27–42. doi: 10.1534/genetics.109.107482 19841096
    • (2010) Genetics , vol.184 , pp. 27-42
    • Northam, M.R.1    Robinson, H.A.2    Kochenova, O.V.3    Shcherbakova, P.V.4
  • 40
    • 84925497848 scopus 로고    scopus 로고
    • Hypermutation in human cancer genomes: footprints and mechanisms
    • Roberts SA, Gordenin DA, Hypermutation in human cancer genomes: footprints and mechanisms. Nat Rev Cancer. 2014;14:786–800. 25568919
    • (2014) Nat Rev Cancer , vol.14 , pp. 786-800
    • Roberts, S.A.1    Gordenin, D.A.2
  • 41
    • 84896728239 scopus 로고    scopus 로고
    • Clustered and genome-wide transient mutagenesis in human cancers: Hypermutation without permanent mutators or loss of fitness
    • Roberts SA, Gordenin DA, Clustered and genome-wide transient mutagenesis in human cancers: Hypermutation without permanent mutators or loss of fitness. Bioessays. 2014;36:382–93.
    • (2014) Bioessays , vol.36 , pp. 382-393
    • Roberts, S.A.1    Gordenin, D.A.2
  • 42
    • 84861460657 scopus 로고    scopus 로고
    • Clustered mutations in yeast and in human cancers can arise from damaged long single-strand DNA regions
    • Roberts SA, Sterling J, Thompson C, Harris S, Mav D, Shah R, et al. Clustered mutations in yeast and in human cancers can arise from damaged long single-strand DNA regions. Mol Cell. 2012;46:424–35. doi: 10.1016/j.molcel.2012.03.030 22607975
    • (2012) Mol Cell , vol.46 , pp. 424-435
    • Roberts, S.A.1    Sterling, J.2    Thompson, C.3    Harris, S.4    Mav, D.5    Shah, R.6
  • 43
    • 0032855533 scopus 로고    scopus 로고
    • Locating regions of differential variability in DNA and protein sequences
    • Tang H, Lewontin RC, Locating regions of differential variability in DNA and protein sequences. Genetics. 1999;153:485–95. 10471728
    • (1999) Genetics , vol.153 , pp. 485-495
    • Tang, H.1    Lewontin, R.C.2
  • 44
    • 0042847380 scopus 로고    scopus 로고
    • Theoretical analysis of mutation hotspots and their DNA sequence context specificity
    • Rogozin IB, Pavlov YI, Theoretical analysis of mutation hotspots and their DNA sequence context specificity. Mutat Res. 2003;544:65–85. 12888108
    • (2003) Mutat Res , vol.544 , pp. 65-85
    • Rogozin, I.B.1    Pavlov, Y.I.2
  • 45
    • 84908894973 scopus 로고    scopus 로고
    • Genome-wide analysis of noncoding regulatory mutations in cancer
    • Weinhold N, Jacobsen A, Schultz N, Sander C, Lee W, Genome-wide analysis of noncoding regulatory mutations in cancer. Nat Genet. 2014;46:1160–5. doi: 10.1038/ng.3101 25261935
    • (2014) Nat Genet , vol.46 , pp. 1160-1165
    • Weinhold, N.1    Jacobsen, A.2    Schultz, N.3    Sander, C.4    Lee, W.5
  • 46
    • 48949094603 scopus 로고    scopus 로고
    • Transcription induces strand-specific mutations at the 5' end of human genes
    • Polak P, Arndt PF, Transcription induces strand-specific mutations at the 5' end of human genes. Genome Res. 2008;18:1216–23. doi: 10.1101/gr.076570.108 18463301
    • (2008) Genome Res , vol.18 , pp. 1216-1223
    • Polak, P.1    Arndt, P.F.2
  • 47
    • 84880507665 scopus 로고    scopus 로고
    • Mutational heterogeneity in cancer and the search for new cancer-associated genes
    • Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 2013;499:214–8. doi: 10.1038/nature12213 23770567
    • (2013) Nature , vol.499 , pp. 214-218
    • Lawrence, M.S.1    Stojanov, P.2    Polak, P.3    Kryukov, G.V.4    Cibulskis, K.5    Sivachenko, A.6
  • 48
    • 70349333227 scopus 로고    scopus 로고
    • The evolutionary consequences of erroneous protein synthesis
    • Drummond DA, Wilke CO, The evolutionary consequences of erroneous protein synthesis. Nat Rev Genet. 2009;10:715–24. doi: 10.1038/nrg2662 19763154
    • (2009) Nat Rev Genet , vol.10 , pp. 715-724
    • Drummond, D.A.1    Wilke, C.O.2
  • 49
    • 63449132404 scopus 로고    scopus 로고
    • Origin and evolution of the genetic code: the universal enigma
    • Koonin EV, Novozhilov AS, Origin and evolution of the genetic code: the universal enigma. IUBMB life. 2009;61:99–111. doi: 10.1002/iub.146 19117371
    • (2009) IUBMB life , vol.61 , pp. 99-111
    • Koonin, E.V.1    Novozhilov, A.S.2
  • 50
    • 84857191660 scopus 로고    scopus 로고
    • Transcription as a source of genome instability
    • Kim N, Jinks-Robertson S, Transcription as a source of genome instability. Nat Rev Genet. 2012;13:204–14. doi: 10.1038/nrg3152 22330764
    • (2012) Nat Rev Genet , vol.13 , pp. 204-214
    • Kim, N.1    Jinks-Robertson, S.2
  • 51
    • 84913596602 scopus 로고    scopus 로고
    • Transcription-associated mutagenesis
    • Jinks-Robertson S, Bhagwat AS, Transcription-associated mutagenesis. Annu Rev Genet. 2014;48:341–59. doi: 10.1146/annurev-genet-120213-092015 25251854
    • (2014) Annu Rev Genet , vol.48 , pp. 341-359
    • Jinks-Robertson, S.1    Bhagwat, A.S.2
  • 52
    • 56749157389 scopus 로고    scopus 로고
    • Transcription-coupled DNA repair: two decades of progress and surprises
    • Hanawalt PC, Spivak G, Transcription-coupled DNA repair: two decades of progress and surprises. Nat Rev Mol Cell Biol. 2008;9:958–70. doi: 10.1038/nrm2549 19023283
    • (2008) Nat Rev Mol Cell Biol , vol.9 , pp. 958-970
    • Hanawalt, P.C.1    Spivak, G.2
  • 53
    • 0032127810 scopus 로고    scopus 로고
    • Somatic hypermutation in the heavy chain locus correlates with transcription
    • Fukita Y, Jacobs H, Rajewsky K, Somatic hypermutation in the heavy chain locus correlates with transcription. Immunity. 1998;9:105–14. 9697840
    • (1998) Immunity , vol.9 , pp. 105-114
    • Fukita, Y.1    Jacobs, H.2    Rajewsky, K.3
  • 54
    • 80051823466 scopus 로고    scopus 로고
    • Guanine repeat-containing sequences confer transcription-dependent instability in an orientation-specific manner in yeast
    • Kim N, Jinks-Robertson S, Guanine repeat-containing sequences confer transcription-dependent instability in an orientation-specific manner in yeast. DNA Repair (Amst). 2011;10:953–60. doi: 10.1016/j.dnarep.2011.07.002 21813340
    • (2011) DNA Repair (Amst) , vol.10 , pp. 953-960
    • Kim, N.1    Jinks-Robertson, S.2
  • 55
    • 58249095957 scopus 로고    scopus 로고
    • Transcriptional pausing and stalling causes multiple clustered mutations by human activation-induced deaminase
    • Canugovi C, Samaranayake M, Bhagwat AS, Transcriptional pausing and stalling causes multiple clustered mutations by human activation-induced deaminase. FASEB J. 2009;23:34–44. doi: 10.1096/fj.08-115352 18772346
    • (2009) FASEB J , vol.23 , pp. 34-44
    • Canugovi, C.1    Samaranayake, M.2    Bhagwat, A.S.3
  • 57
    • 0035871625 scopus 로고    scopus 로고
    • Increased transcription levels induce higher mutation rates in a hypermutating cell line
    • Bachl J, Carlson C, Gray-Schopfer V, Dessing M, Olsson C, Increased transcription levels induce higher mutation rates in a hypermutating cell line. J Immunol. 2001;166:5051–7. 11290786
    • (2001) J Immunol , vol.166 , pp. 5051-5057
    • Bachl, J.1    Carlson, C.2    Gray-Schopfer, V.3    Dessing, M.4    Olsson, C.5
  • 58
    • 0030462462 scopus 로고    scopus 로고
    • Transcription-induced mutations: increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli
    • Beletskii A, Bhagwat AS, Transcription-induced mutations: increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli. Proc Natl Acad Sci U S A. 1996;93:13919–24. 8943036
    • (1996) Proc Natl Acad Sci U S A , vol.93 , pp. 13919-13924
    • Beletskii, A.1    Bhagwat, A.S.2
  • 59
    • 84870204989 scopus 로고    scopus 로고
    • A role for the RNA pol II-associated PAF complex in AID-induced immune diversification
    • Willmann KL, Milosevic S, Pauklin S, Schmitz KM, Rangam G, Simon MT, et al. A role for the RNA pol II-associated PAF complex in AID-induced immune diversification. J Exp Med. 2012;209:2099–111. doi: 10.1084/jem.20112145 23008333
    • (2012) J Exp Med , vol.209 , pp. 2099-2111
    • Willmann, K.L.1    Milosevic, S.2    Pauklin, S.3    Schmitz, K.M.4    Rangam, G.5    Simon, M.T.6
  • 60
    • 84919941546 scopus 로고    scopus 로고
    • B Cell Super-Enhancers and Regulatory Clusters Recruit AID Tumorigenic Activity
    • Qian J, Wang Q, Dose M, Pruett N, Kieffer-Kwon KR, Resch W, et al. B Cell Super-Enhancers and Regulatory Clusters Recruit AID Tumorigenic Activity. Cell. 2014;159:1524–37. doi: 10.1016/j.cell.2014.11.013 25483777
    • (2014) Cell , vol.159 , pp. 1524-1537
    • Qian, J.1    Wang, Q.2    Dose, M.3    Pruett, N.4    Kieffer-Kwon, K.R.5    Resch, W.6
  • 62
    • 84922298785 scopus 로고    scopus 로고
    • Active RNAP pre-initiation sites are highly mutated by cytidine deaminases in yeast, with AID targeting small RNA genes
    • Taylor BJ, Wu YL, Rada C, Active RNAP pre-initiation sites are highly mutated by cytidine deaminases in yeast, with AID targeting small RNA genes. Elife. 2014;3:e03553. doi: 10.7554/eLife.03553 25237741
    • (2014) Elife , vol.3 , pp. e03553
    • Taylor, B.J.1    Wu, Y.L.2    Rada, C.3
  • 63
    • 74249102477 scopus 로고    scopus 로고
    • Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism
    • Liu X, Bushnell DA, Wang D, Calero G, Kornberg RD, Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism. Science. 2010;327:206–9. doi: 10.1126/science.1182015 19965383
    • (2010) Science , vol.327 , pp. 206-209
    • Liu, X.1    Bushnell, D.A.2    Wang, D.3    Calero, G.4    Kornberg, R.D.5
  • 64
    • 70450171352 scopus 로고    scopus 로고
    • RNA polymerase II-TFIIB structure and mechanism of transcription initiation
    • Kostrewa D, Zeller ME, Armache KJ, Seizl M, Leike K, Thomm M, et al. RNA polymerase II-TFIIB structure and mechanism of transcription initiation. Nature. 2009;462:323–30. doi: 10.1038/nature08548 19820686
    • (2009) Nature , vol.462 , pp. 323-330
    • Kostrewa, D.1    Zeller, M.E.2    Armache, K.J.3    Seizl, M.4    Leike, K.5    Thomm, M.6
  • 65
    • 73049092277 scopus 로고    scopus 로고
    • Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex
    • Andrecka J, Treutlein B, Arcusa MA, Muschielok A, Lewis R, Cheung AC, et al. Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex. Nucleic Acids Res. 2009;37:5803–9. doi: 10.1093/nar/gkp601 19620213
    • (2009) Nucleic Acids Res , vol.37 , pp. 5803-5809
    • Andrecka, J.1    Treutlein, B.2    Arcusa, M.A.3    Muschielok, A.4    Lewis, R.5    Cheung, A.C.6
  • 66
    • 77956628136 scopus 로고    scopus 로고
    • Replication protein A: directing traffic at the intersection of replication and repair
    • Oakley GG, Patrick SM, Replication protein A: directing traffic at the intersection of replication and repair. Front Biosci (Landmark Ed). 2010;15:883–900. 20515732
    • (2010) Front Biosci (Landmark Ed) , vol.15 , pp. 883-900
    • Oakley, G.G.1    Patrick, S.M.2
  • 67
    • 0030908093 scopus 로고    scopus 로고
    • Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism
    • Wold MS, Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism. Annu Rev Biochem. 1997;66:61–92. 9242902
    • (1997) Annu Rev Biochem , vol.66 , pp. 61-92
    • Wold, M.S.1
  • 69
    • 0031030449 scopus 로고    scopus 로고
    • Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA
    • Bochkarev A, Pfuetzner RA, Edwards AM, Frappier L, Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA. Nature. 1997;385:176–81. 8990123
    • (1997) Nature , vol.385 , pp. 176-181
    • Bochkarev, A.1    Pfuetzner, R.A.2    Edwards, A.M.3    Frappier, L.4
  • 70
    • 85011942159 scopus 로고    scopus 로고
    • Sub1/PC4 a chromatin associated protein with multiple functions in transcription
    • Conesa C, Acker J, Sub1/PC4 a chromatin associated protein with multiple functions in transcription. RNA Biol. 2010;7:287–90. 20305379
    • (2010) RNA Biol , vol.7 , pp. 287-290
    • Conesa, C.1    Acker, J.2
  • 71
    • 2942720576 scopus 로고    scopus 로고
    • The single-strand DNA binding activity of human PC4 prevents mutagenesis and killing by oxidative DNA damage
    • Wang JY, Sarker AH, Cooper PK, Volkert MR, The single-strand DNA binding activity of human PC4 prevents mutagenesis and killing by oxidative DNA damage. Mol Cell Biol. 2004;24:6084–93. 15199162
    • (2004) Mol Cell Biol , vol.24 , pp. 6084-6093
    • Wang, J.Y.1    Sarker, A.H.2    Cooper, P.K.3    Volkert, M.R.4
  • 72
    • 4444239054 scopus 로고    scopus 로고
    • Activation-induced cytidine deaminase (AID) can target both DNA strands when the DNA is supercoiled
    • Shen HM, Storb U, Activation-induced cytidine deaminase (AID) can target both DNA strands when the DNA is supercoiled. Proc Natl Acad Sci U S A. 2004;101:12997–3002. 15328407
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 12997-13002
    • Shen, H.M.1    Storb, U.2
  • 73
    • 84889004332 scopus 로고    scopus 로고
    • DNA sequences that interfere with transcription: implications for genome function and stability
    • Belotserkovskii BP, Mirkin SM, Hanawalt PC, DNA sequences that interfere with transcription: implications for genome function and stability. Chem Rev. 2013;113:8620–37. doi: 10.1021/cr400078y 23972098
    • (2013) Chem Rev , vol.113 , pp. 8620-8637
    • Belotserkovskii, B.P.1    Mirkin, S.M.2    Hanawalt, P.C.3
  • 74
    • 84860338675 scopus 로고    scopus 로고
    • R loops: from transcription byproducts to threats to genome stability
    • Aguilera A, Garcia-Muse T, R loops: from transcription byproducts to threats to genome stability. Mol Cell. 2012;46:115–24. doi: 10.1016/j.molcel.2012.04.009 22541554
    • (2012) Mol Cell , vol.46 , pp. 115-124
    • Aguilera, A.1    Garcia-Muse, T.2
  • 75
    • 34347218988 scopus 로고    scopus 로고
    • Activation-induced cytidine deaminase action is strongly stimulated by mutations of the THO complex
    • Gomez-Gonzalez B, Aguilera A, Activation-induced cytidine deaminase action is strongly stimulated by mutations of the THO complex. Proc Natl Acad Sci U S A. 2007;104:8409–14. 17488823
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 8409-8414
    • Gomez-Gonzalez, B.1    Aguilera, A.2
  • 76
    • 84861660740 scopus 로고    scopus 로고
    • How cancer shapes evolution, and how evolution shapes cancer
    • Casas-Selves M, Degregori J, How cancer shapes evolution, and how evolution shapes cancer. Evolution. 2011;4:624–34. 23705033
    • (2011) Evolution , vol.4 , pp. 624-634
    • Casas-Selves, M.1    Degregori, J.2
  • 78
    • 84881309354 scopus 로고    scopus 로고
    • BayesHammer: Bayesian clustering for error correction in single-cell sequencing
    • Nikolenko SI, Korobeynikov AI, Alekseyev MA, BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics. 2013;14 Suppl 1:S7. doi: 10.1186/1471-2164-14-S1-S7 23368723
    • (2013) BMC Genomics , vol.14 , pp. S7
    • Nikolenko, S.I.1    Korobeynikov, A.I.2    Alekseyev, M.A.3
  • 79
  • 80
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: a program to analyze DNA sequences
    • Benson G, Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573–80. 9862982
    • (1999) Nucleic Acids Res , vol.27 , pp. 573-580
    • Benson, G.1
  • 81
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL, Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9. doi: 10.1038/nmeth.1923 22388286
    • (2012) Nat Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 82
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7:562–78. doi: 10.1038/nprot.2012.016 22383036
    • (2012) Nat Protoc , vol.7 , pp. 562-578
    • Trapnell, C.1    Roberts, A.2    Goff, L.3    Pertea, G.4    Kim, D.5    Kelley, D.R.6


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