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Volumn 6, Issue APR, 2015, Pages

Replication and transcription on a collision course: Eukaryotic regulation mechanisms and implications for DNA stability

Author keywords

Cancer; Epigenetic instability; Genetic instability; Neurodegeneration; R loops; Replication stress; Replication transcription conflicts

Indexed keywords

CHROMOSOMAL INSTABILITY; CHROMOSOME REPLICATION; DEGENERATIVE DISEASE; DNA DAMAGE CHECKPOINT; DNA TRANSCRIPTION; EPIGENETICS; GENETIC RECOMBINATION; NONHUMAN; SHORT SURVEY; SIGNAL TRANSDUCTION;

EID: 84940025910     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2015.00166     Document Type: Short Survey
Times cited : (42)

References (84)
  • 1
    • 84857430552 scopus 로고    scopus 로고
    • Chromatin replication and epigenome maintenance
    • Alabert, C., and Groth, A. (2012). Chromatin replication and epigenome maintenance. Nat. Rev. Mol. Cell Biol. 13, 153-167. doi: 10.1038/nrm3288.
    • (2012) Nat. Rev. Mol. Cell Biol , vol.13 , pp. 153-167
    • Alabert, C.1    Groth, A.2
  • 2
    • 84869026790 scopus 로고    scopus 로고
    • Senataxin associates with replication forks to protect fork integrity across RNA-polymerase-II-transcribed genes
    • Alzu, A., Bermejo, R., Begnis, M., Lucca, C., Piccini, D., Carotenuto, W., et al. (2012). Senataxin associates with replication forks to protect fork integrity across RNA-polymerase-II-transcribed genes. Cell 151, 835-846. doi: 10.1016/j.cell.2012.09.041.
    • (2012) Cell , vol.151 , pp. 835-846
    • Alzu, A.1    Bermejo, R.2    Begnis, M.3    Lucca, C.4    Piccini, D.5    Carotenuto, W.6
  • 4
    • 47249100637 scopus 로고    scopus 로고
    • A RECQ5-RNA polymerase II association identified by targeted proteomic analysis of human chromatin
    • Aygun, O., Svejstrup, J., and Liu, Y. (2008). A RECQ5-RNA polymerase II association identified by targeted proteomic analysis of human chromatin. Proc. Natl. Acad. Sci. U.S.A. 105, 8580-8584. doi: 10.1073/pnas.0804424105.
    • (2008) Proc. Natl. Acad. Sci. U.S.A , vol.105 , pp. 8580-8584
    • Aygun, O.1    Svejstrup, J.2    Liu, Y.3
  • 5
    • 67449113551 scopus 로고    scopus 로고
    • Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae
    • Azvolinsky, A., Giresi, P. G., Lieb, J. D., and Zakian, V. A. (2009). Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae. Mol. Cell 34, 722-734. doi: 10.1016/j.molcel.2009.05.022.
    • (2009) Mol. Cell , vol.34 , pp. 722-734
    • Azvolinsky, A.1    Giresi, P.G.2    Lieb, J.D.3    Zakian, V.A.4
  • 6
    • 84873310832 scopus 로고    scopus 로고
    • Identification of early replicating fragile sites that contribute to genome instability
    • Barlow, J. H., Faryabi, R. B., Callen, E., Wong, N., Malhowski, A., Chen, H. T., et al. (2013). Identification of early replicating fragile sites that contribute to genome instability. Cell 152, 620-632. doi: 10.1016/j.cell.2013.01.006.
    • (2013) Cell , vol.152 , pp. 620-632
    • Barlow, J.H.1    Faryabi, R.B.2    Callen, E.3    Wong, N.4    Malhowski, A.5    Chen, H.T.6
  • 7
    • 33845235459 scopus 로고    scopus 로고
    • Oncogene-induced senescence is part of the tumorigenesis barrier imposed by DNA damage checkpoints
    • Bartkova, J., Rezaei, N., Liontos, M., Karakaidos, P., Kletsas, D., Issaeva, N., et al. (2006). Oncogene-induced senescence is part of the tumorigenesis barrier imposed by DNA damage checkpoints. Nature 444, 633-637. doi: 10.1038/nature05268.
    • (2006) Nature , vol.444 , pp. 633-637
    • Bartkova, J.1    Rezaei, N.2    Liontos, M.3    Karakaidos, P.4    Kletsas, D.5    Issaeva, N.6
  • 8
    • 79960802984 scopus 로고    scopus 로고
    • The replication checkpoint protects fork stability by releasing transcribed genes from nuclear pores
    • Bermejo, R., Capra, T., Jossen, R., Colosio, A., Frattini, C., Carotenuto, W., et al. (2011). The replication checkpoint protects fork stability by releasing transcribed genes from nuclear pores. Cell 146, 233-246. doi: 10.1016/j.cell.2011.06.033.
    • (2011) Cell , vol.146 , pp. 233-246
    • Bermejo, R.1    Capra, T.2    Jossen, R.3    Colosio, A.4    Frattini, C.5    Carotenuto, W.6
  • 9
    • 84859042868 scopus 로고    scopus 로고
    • Preventing replication stress to maintain genome stability: resolving conflicts between replication and transcription
    • Bermejo, R., Lai, M. S., and Foiani, M. (2012). Preventing replication stress to maintain genome stability: resolving conflicts between replication and transcription. Mol. Cell 45, 710-718. doi: 10.1016/j.molcel.2012.03.001.
    • (2012) Mol. Cell , vol.45 , pp. 710-718
    • Bermejo, R.1    Lai, M.S.2    Foiani, M.3
  • 10
    • 84904459138 scopus 로고    scopus 로고
    • BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2
    • Bhatia, V., Barroso, S. I., Garcia-Rubio, M. L., Tumini, E., Herrera-Moyano, E., and Aguilera, A. (2014). BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2. Nature 511, 362-365. doi: 10.1038/nature13374.
    • (2014) Nature , vol.511 , pp. 362-365
    • Bhatia, V.1    Barroso, S.I.2    Garcia-Rubio, M.L.3    Tumini, E.4    Herrera-Moyano, E.5    Aguilera, A.6
  • 11
    • 0344338368 scopus 로고
    • Gene gating: a hypothesis
    • Blobel, G. (1985). Gene gating: a hypothesis. Proc. Natl. Acad. Sci. U.S.A. 82, 8527-8529. doi: 10.1073/pnas.82.24.8527.
    • (1985) Proc. Natl. Acad. Sci. U.S.A , vol.82 , pp. 8527-8529
    • Blobel, G.1
  • 12
    • 34848908787 scopus 로고    scopus 로고
    • The yeast Pif1p DNA helicase preferentially unwinds RNA DNA substrates
    • Boule, J. B., and Zakian, V. A. (2007). The yeast Pif1p DNA helicase preferentially unwinds RNA DNA substrates. Nucleic Acids Res. 35, 5809-5818. doi: 10.1093/nar/gkm613.
    • (2007) Nucleic Acids Res , vol.35 , pp. 5809-5818
    • Boule, J.B.1    Zakian, V.A.2
  • 13
    • 84874362586 scopus 로고    scopus 로고
    • Replication stress links structural and numerical cancer chromosomal instability
    • Burrell, R. A., McClelland, S. E., Endesfelder, D., Groth, P., Weller, M. C., Shaikh, N., et al. (2013). Replication stress links structural and numerical cancer chromosomal instability. Nature 494, 492-496. doi: 10.1038/nature11935.
    • (2013) Nature , vol.494 , pp. 492-496
    • Burrell, R.A.1    McClelland, S.E.2    Endesfelder, D.3    Groth, P.4    Weller, M.C.5    Shaikh, N.6
  • 14
    • 0037074013 scopus 로고    scopus 로고
    • ATR regulates fragile site stability
    • Casper, A. M., Nghiem, P., Arlt, M. F., and Glover, T. W. (2002). ATR regulates fragile site stability. Cell 111, 779-789. doi: 10.1016/S0092-8674(02)01113-3.
    • (2002) Cell , vol.111 , pp. 779-789
    • Casper, A.M.1    Nghiem, P.2    Arlt, M.F.3    Glover, T.W.4
  • 15
    • 84908282370 scopus 로고    scopus 로고
    • Dicer promotes transcription termination at sites of replication stress to maintain genome stability
    • Castel, S. E., Ren, J., Bhattacharjee, S., Chang, A. Y., Sanchez, M., Valbuena, A., et al. (2014). Dicer promotes transcription termination at sites of replication stress to maintain genome stability. Cell 159, 572-583. doi: 10.1016/j.cell.2014.09.031.
    • (2014) Cell , vol.159 , pp. 572-583
    • Castel, S.E.1    Ren, J.2    Bhattacharjee, S.3    Chang, A.Y.4    Sanchez, M.5    Valbuena, A.6
  • 17
    • 79957813857 scopus 로고    scopus 로고
    • Human DHX9 helicase preferentially unwinds RNA-containing displacement loops (R-loops) and G-quadruplexes
    • Chakraborty, P., and Grosse, F. (2011). Human DHX9 helicase preferentially unwinds RNA-containing displacement loops (R-loops) and G-quadruplexes. DNA Repair (Amst) 10, 654-665. doi: 10.1016/j.dnarep.2011.04.013.
    • (2011) DNA Repair (Amst) , vol.10 , pp. 654-665
    • Chakraborty, P.1    Grosse, F.2
  • 18
    • 84901360066 scopus 로고    scopus 로고
    • Genome-wide profiling of yeast DNA:RNA hybrid prone sites with DRIP-chip
    • Chan, Y. A., Aristizabal, M. J., Lu, P. Y., Luo, Z., Hamza, A., Kobor, M. S., et al. (2014). Genome-wide profiling of yeast DNA:RNA hybrid prone sites with DRIP-chip. PLoS Genet. 10:e1004288. doi: 10.1371/journal.pgen.1004288.
    • (2014) PLoS Genet , vol.10
    • Chan, Y.A.1    Aristizabal, M.J.2    Lu, P.Y.3    Luo, Z.4    Hamza, A.5    Kobor, M.S.6
  • 19
    • 2442658908 scopus 로고    scopus 로고
    • DNA/RNA helicase gene mutations in a form of juvenile amyotrophic lateral sclerosis (ALS4)
    • Chen, Y. Z., Bennett, C. L., Huynh, H. M., Blair, I. P., Puls, I., Irobi, J., et al. (2004). DNA/RNA helicase gene mutations in a form of juvenile amyotrophic lateral sclerosis (ALS4). Am. J. Hum. Genet. 74, 1128-1135. doi: 10.1086/421054.
    • (2004) Am. J. Hum. Genet , vol.74 , pp. 1128-1135
    • Chen, Y.Z.1    Bennett, C.L.2    Huynh, H.M.3    Blair, I.P.4    Puls, I.5    Irobi, J.6
  • 20
    • 84876363526 scopus 로고    scopus 로고
    • RNase H2 roles in genome integrity revealed by unlinking its activities
    • Chon, H., Sparks, J. L., Rychlik, M., Nowotny, M., Burgers, P. M., Crouch, R. J., et al. (2013). RNase H2 roles in genome integrity revealed by unlinking its activities. Nucleic Acids Res. 41, 3130-3143. doi: 10.1093/nar/gkt027.
    • (2013) Nucleic Acids Res , vol.41 , pp. 3130-3143
    • Chon, H.1    Sparks, J.L.2    Rychlik, M.3    Nowotny, M.4    Burgers, P.M.5    Crouch, R.J.6
  • 21
    • 33746522835 scopus 로고    scopus 로고
    • Mutations in genes encoding ribonuclease H2 subunits cause Aicardi-Goutieres syndrome and mimic congenital viral brain infection
    • Crow, Y. J., Leitch, A., Hayward, B. E., Garner, A., Parmar, R., Griffith, E., et al. (2006). Mutations in genes encoding ribonuclease H2 subunits cause Aicardi-Goutieres syndrome and mimic congenital viral brain infection. Nat. Genet. 38, 910-916. doi: 10.1038/ng1842.
    • (2006) Nat. Genet , vol.38 , pp. 910-916
    • Crow, Y.J.1    Leitch, A.2    Hayward, B.E.3    Garner, A.4    Parmar, R.5    Griffith, E.6
  • 22
    • 0029740114 scopus 로고    scopus 로고
    • DNA replication fork pause sites dependent on transcription
    • Deshpande, A. M., and Newlon, C. S. (1996). DNA replication fork pause sites dependent on transcription. Science 272, 1030-1033. doi: 10.1126/science.272.5264.1030.
    • (1996) Science , vol.272 , pp. 1030-1033
    • Deshpande, A.M.1    Newlon, C.S.2
  • 23
    • 33845269825 scopus 로고    scopus 로고
    • Oncogene-induced senescence is a DNA damage response triggered by DNA hyper-replication
    • Di Micco, R., Fumagalli, M., Cicalese, A., Piccinin, S., Gasparini, P., Luise, C., et al. (2006). Oncogene-induced senescence is a DNA damage response triggered by DNA hyper-replication. Nature 444, 638-642. doi: 10.1038/nature05327.
    • (2006) Nature , vol.444 , pp. 638-642
    • Di Micco, R.1    Fumagalli, M.2    Cicalese, A.3    Piccinin, S.4    Gasparini, P.5    Luise, C.6
  • 24
    • 33645052194 scopus 로고    scopus 로고
    • Growth inhibition mediated by excess negative supercoiling: the interplay between transcription elongation, R-loop formation and DNA topology
    • Drolet, M. (2006). Growth inhibition mediated by excess negative supercoiling: the interplay between transcription elongation, R-loop formation and DNA topology. Mol. Microbiol. 59, 723-730. doi: 10.1111/j.1365-2958.2005.05006.x.
    • (2006) Mol. Microbiol , vol.59 , pp. 723-730
    • Drolet, M.1
  • 25
    • 84871740379 scopus 로고    scopus 로고
    • Coordinated control of replication and transcription by a SAPK protects genomic integrity
    • Duch, A., Felipe-Abrio, I., Barroso, S., Yaakov, G., Garcia-Rubio, M., Aguilera, A., et al. (2013). Coordinated control of replication and transcription by a SAPK protects genomic integrity. Nature 493, 116-119. doi: 10.1038/nature11675.
    • (2013) Nature , vol.493 , pp. 116-119
    • Duch, A.1    Felipe-Abrio, I.2    Barroso, S.3    Yaakov, G.4    Garcia-Rubio, M.5    Aguilera, A.6
  • 26
    • 80052008241 scopus 로고    scopus 로고
    • Linking RNA polymerase backtracking to genome instability in E. coli
    • Dutta, D., Shatalin, K., Epshtein, V., Gottesman, M. E., and Nudler, E. (2011). Linking RNA polymerase backtracking to genome instability in E. coli. Cell 146, 533-543. doi: 10.1016/j.cell.2011.07.034.
    • (2011) Cell , vol.146 , pp. 533-543
    • Dutta, D.1    Shatalin, K.2    Epshtein, V.3    Gottesman, M.E.4    Nudler, E.5
  • 27
    • 84859087611 scopus 로고    scopus 로고
    • R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters
    • Ginno, P. A., Lott, P. L., Christensen, H. C., Korf, I., and Chedin, F. (2012). R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol. Cell 45, 814-825. doi: 10.1016/j.molcel.2012.01.017.
    • (2012) Mol. Cell , vol.45 , pp. 814-825
    • Ginno, P.A.1    Lott, P.L.2    Christensen, H.C.3    Korf, I.4    Chedin, F.5
  • 28
    • 70349335582 scopus 로고    scopus 로고
    • The S-phase checkpoint is required to respond to R-loops accumulated in THO mutants
    • Gomez-Gonzalez, B., Felipe-Abrio, I., and Aguilera, A. (2009). The S-phase checkpoint is required to respond to R-loops accumulated in THO mutants. Mol. Cell. Biol. 29, 5203-5213. doi: 10.1128/MCB.00402-09.
    • (2009) Mol. Cell. Biol , vol.29 , pp. 5203-5213
    • Gomez-Gonzalez, B.1    Felipe-Abrio, I.2    Aguilera, A.3
  • 29
    • 79961031438 scopus 로고    scopus 로고
    • Genome-wide function of THO/TREX in active genes prevents R-loop-dependent replication obstacles
    • Gomez-Gonzalez, B., Garcia-Rubio, M., Bermejo, R., Gaillard, H., Shirahige, K., Marin, A., et al. (2011). Genome-wide function of THO/TREX in active genes prevents R-loop-dependent replication obstacles. EMBO J. 30, 3106-3119.
    • (2011) EMBO J , vol.30 , pp. 3106-3119
    • Gomez-Gonzalez, B.1    Garcia-Rubio, M.2    Bermejo, R.3    Gaillard, H.4    Shirahige, K.5    Marin, A.6
  • 30
    • 37549026516 scopus 로고    scopus 로고
    • Transcription-associated recombination is dependent on replication in Mammalian cells
    • Gottipati, P., Cassel, T. N., Savolainen, L., and Helleday, T. (2008). Transcription-associated recombination is dependent on replication in Mammalian cells. Mol. Cell. Biol. 28, 154-164. doi: 10.1128/MCB.00816-07.
    • (2008) Mol. Cell. Biol , vol.28 , pp. 154-164
    • Gottipati, P.1    Cassel, T.N.2    Savolainen, L.3    Helleday, T.4
  • 31
  • 32
    • 84901626668 scopus 로고    scopus 로고
    • R-loops associated with triplet repeat expansions promote gene silencing in Friedreich ataxia and fragile X syndrome
    • Groh, M., Lufino, M. M., Wade-Martins, R., and Gromak, N. (2014). R-loops associated with triplet repeat expansions promote gene silencing in Friedreich ataxia and fragile X syndrome. PLoS Genet. 10:e1004318. doi: 10.1371/journal.pgen.1004318.
    • (2014) PLoS Genet , vol.10
    • Groh, M.1    Lufino, M.M.2    Wade-Martins, R.3    Gromak, N.4
  • 33
    • 84896259966 scopus 로고    scopus 로고
    • C9orf72 nucleotide repeat structures initiate molecular cascades of disease
    • Haeusler, A. R., Donnelly, C. J., Periz, G., Simko, E. A., Shaw, P. G., Kim, M. S., et al. (2014). C9orf72 nucleotide repeat structures initiate molecular cascades of disease. Nature 507, 195-200. doi: 10.1038/nature13124.
    • (2014) Nature , vol.507 , pp. 195-200
    • Haeusler, A.R.1    Donnelly, C.J.2    Periz, G.3    Simko, E.A.4    Shaw, P.G.5    Kim, M.S.6
  • 34
    • 84922181550 scopus 로고    scopus 로고
    • Balancing the innate immune system in tumor development
    • Hagerling, C., Casbon, A. J., and Werb, Z. (2014). Balancing the innate immune system in tumor development. Trends Cell Biol. 25, 214-220. doi: 10.1016/j.tcb.2014.11.001.
    • (2014) Trends Cell Biol , vol.25 , pp. 214-220
    • Hagerling, C.1    Casbon, A.J.2    Werb, Z.3
  • 35
    • 84923848772 scopus 로고    scopus 로고
    • BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair
    • Hatchi, E., Skourti-Stathaki, K., Ventz, S., Pinello, L., Yen, A., Kamieniarz-Gdula, K., et al. (2015). BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair. Mol. Cell 57, 636-647. doi: 10.1016/j.molcel.2015.01.011.
    • (2015) Mol. Cell , vol.57 , pp. 636-647
    • Hatchi, E.1    Skourti-Stathaki, K.2    Ventz, S.3    Pinello, L.4    Yen, A.5    Kamieniarz-Gdula, K.6
  • 36
    • 84255198334 scopus 로고    scopus 로고
    • Collisions between replication and transcription complexes cause common fragile site instability at the longest human genes
    • Helmrich, A., Ballarino, M., and Tora, L. (2011). Collisions between replication and transcription complexes cause common fragile site instability at the longest human genes. Mol. Cell 44, 966-977. doi: 10.1016/j.molcel.2011.10.013.
    • (2011) Mol. Cell , vol.44 , pp. 966-977
    • Helmrich, A.1    Ballarino, M.2    Tora, L.3
  • 37
    • 84898841862 scopus 로고    scopus 로고
    • The yeast and human FACT chromatin-reorganizing complexes solve R-loop-mediated transcription-replication conflicts
    • Herrera-Moyano, E., Mergui, X., Garcia-Rubio, M. L., Barroso, S., and Aguilera, A. (2014). The yeast and human FACT chromatin-reorganizing complexes solve R-loop-mediated transcription-replication conflicts. Genes Dev. 28, 735-748. doi: 10.1101/gad.234070.113.
    • (2014) Genes Dev , vol.28 , pp. 735-748
    • Herrera-Moyano, E.1    Mergui, X.2    Garcia-Rubio, M.L.3    Barroso, S.4    Aguilera, A.5
  • 38
    • 84906857430 scopus 로고    scopus 로고
    • Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage
    • Hill, S. J., Rolland, T., Adelmant, G., Xia, X., Owen, M. S., Dricot, A., et al. (2014). Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage. Genes Dev. 28, 1957-1975. doi: 10.1101/gad.241620.114.
    • (2014) Genes Dev , vol.28 , pp. 1957-1975
    • Hill, S.J.1    Rolland, T.2    Adelmant, G.3    Xia, X.4    Owen, M.S.5    Dricot, A.6
  • 39
    • 34548396264 scopus 로고    scopus 로고
    • Human gene organization driven by the coordination of replication and transcription
    • Huvet, M., Nicolay, S., Touchon, M., Audit, B., d'Aubenton-Carafa, Y., Arneodo, A., et al. (2007). Human gene organization driven by the coordination of replication and transcription. Genome Res. 17, 1278-1285. doi: 10.1101/gr.6533407.
    • (2007) Genome Res , vol.17 , pp. 1278-1285
    • Huvet, M.1    Nicolay, S.2    Touchon, M.3    Audit, B.4    d'Aubenton-Carafa, Y.5    Arneodo, A.6
  • 40
    • 84898863608 scopus 로고    scopus 로고
    • ATR checkpoint kinase and CRL1betaTRCP collaborate to degrade ASF1a and thus repress genes overlapping with clusters of stalled replication forks
    • Im, J. S., Keaton, M., Lee, K. Y., Kumar, P., Park, J., and Dutta, A. (2014). ATR checkpoint kinase and CRL1betaTRCP collaborate to degrade ASF1a and thus repress genes overlapping with clusters of stalled replication forks. Genes Dev. 28, 875-887. doi: 10.1101/gad.239194.114.
    • (2014) Genes Dev , vol.28 , pp. 875-887
    • Im, J.S.1    Keaton, M.2    Lee, K.Y.3    Kumar, P.4    Park, J.5    Dutta, A.6
  • 41
    • 0348047594 scopus 로고    scopus 로고
    • The Saccharomyces cerevisiae helicase Rrm3p facilitates replication past nonhistone protein-DNA complexes
    • Ivessa, A. S., Lenzmeier, B. A., Bessler, J. B., Goudsouzian, L. K., Schnakenberg, S. L., and Zakian, V. A. (2003). The Saccharomyces cerevisiae helicase Rrm3p facilitates replication past nonhistone protein-DNA complexes. Mol. Cell 12, 1525-1536. doi: 10.1016/S1097-2765(03)00456-8.
    • (2003) Mol. Cell , vol.12 , pp. 1525-1536
    • Ivessa, A.S.1    Lenzmeier, B.A.2    Bessler, J.B.3    Goudsouzian, L.K.4    Schnakenberg, S.L.5    Zakian, V.A.6
  • 42
    • 84881480253 scopus 로고    scopus 로고
    • Increased replication initiation and conflicts with transcription underlie Cyclin E-induced replication stress
    • Jones, R. M., Mortusewicz, O., Afzal, I., Lorvellec, M., Garcia, P., Helleday, T., et al. (2012). Increased replication initiation and conflicts with transcription underlie Cyclin E-induced replication stress. Oncogene 32, 3744-3753. doi: 10.1038/onc.2012.387.
    • (2012) Oncogene , vol.32 , pp. 3744-3753
    • Jones, R.M.1    Mortusewicz, O.2    Afzal, I.3    Lorvellec, M.4    Garcia, P.5    Helleday, T.6
  • 44
    • 84901452746 scopus 로고    scopus 로고
    • The annealing helicase and branch migration activities of Drosophila HARP
    • Kassavetis, G. A., and Kadonaga, J. T. (2014). The annealing helicase and branch migration activities of Drosophila HARP. PLoS ONE 9:e98173. doi: 10.1371/journal.pone.0098173.
    • (2014) PLoS ONE , vol.9
    • Kassavetis, G.A.1    Kadonaga, J.T.2
  • 45
    • 0033517855 scopus 로고    scopus 로고
    • The sen1(+) gene of Schizosaccharomyces pombe, a homologue of budding yeast SEN1, encodes an RNA and DNA helicase
    • Kim, H. D., Choe, J., and Seo, Y. S. (1999). The sen1(+) gene of Schizosaccharomyces pombe, a homologue of budding yeast SEN1, encodes an RNA and DNA helicase. Biochemistry 38, 14697-14710. doi: 10.1021/bi991470c.
    • (1999) Biochemistry , vol.38 , pp. 14697-14710
    • Kim, H.D.1    Choe, J.2    Seo, Y.S.3
  • 46
    • 34547789312 scopus 로고    scopus 로고
    • Transcription-associated mutagenesis in yeast is directly proportional to the level of gene expression and influenced by the direction of DNA replication
    • Kim, N., Abdulovic, A. L., Gealy, R., Lippert, M. J., and Jinks-Robertson, S. (2007). Transcription-associated mutagenesis in yeast is directly proportional to the level of gene expression and influenced by the direction of DNA replication. DNA Repair (Amst) 6, 1285-1296. doi: 10.1016/j.dnarep.2007.02.023.
    • (2007) DNA Repair (Amst) , vol.6 , pp. 1285-1296
    • Kim, N.1    Abdulovic, A.L.2    Gealy, R.3    Lippert, M.J.4    Jinks-Robertson, S.5
  • 47
    • 84888259361 scopus 로고    scopus 로고
    • RNA:DNA hybrids initiate quasi-palindrome-associated mutations in highly transcribed yeast DNA
    • Kim, N., Cho, J. E., Li, Y. C., and Jinks-Robertson, S. (2013). RNA:DNA hybrids initiate quasi-palindrome-associated mutations in highly transcribed yeast DNA. PLoS Genet. 9:e1003924. doi: 10.1371/journal.pgen.1003924.
    • (2013) PLoS Genet , vol.9
    • Kim, N.1    Cho, J.E.2    Li, Y.C.3    Jinks-Robertson, S.4
  • 48
    • 84899806551 scopus 로고    scopus 로고
    • Ribosomal RNA gene repeats, their stability and cellular senescence
    • Kobayashi, T. (2014). Ribosomal RNA gene repeats, their stability and cellular senescence. Proc. Jpn Acad. Ser. B Phys. Biol. Sci. 90, 119-129. doi: 10.2183/pjab.90.119.
    • (2014) Proc. Jpn Acad. Ser. B Phys. Biol. Sci , vol.90 , pp. 119-129
    • Kobayashi, T.1
  • 49
    • 23744455164 scopus 로고    scopus 로고
    • Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability
    • Li, X., and Manley, J. L. (2005). Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability. Cell 122, 365-378. doi: 10.1016/j.cell.2005.06.008.
    • (2005) Cell , vol.122 , pp. 365-378
    • Li, X.1    Manley, J.L.2
  • 51
    • 0023433855 scopus 로고
    • Supercoiling of the DNA template during transcription
    • Liu, L. F., and Wang, J. C. (1987). Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. U.S.A. 84, 7024-7027. doi: 10.1073/pnas.84.20.7024.
    • (1987) Proc. Natl. Acad. Sci. U.S.A , vol.84 , pp. 7024-7027
    • Liu, L.F.1    Wang, J.C.2
  • 52
    • 35549006420 scopus 로고    scopus 로고
    • Glial cells as intrinsic components of non-cell-autonomous neurodegenerative disease
    • Lobsiger, C. S., and Cleveland, D. W. (2007). Glial cells as intrinsic components of non-cell-autonomous neurodegenerative disease. Nat. Neurosci. 10, 1355-1360. doi: 10.1038/nn1988.
    • (2007) Nat. Neurosci , vol.10 , pp. 1355-1360
    • Lobsiger, C.S.1    Cleveland, D.W.2
  • 53
    • 84901346090 scopus 로고    scopus 로고
    • Transcription-associated R-loop formation across the human FMR1 CGG-repeat region
    • Loomis, E. W., Sanz, L. A., Chedin, F., and Hagerman, P. J. (2014). Transcription-associated R-loop formation across the human FMR1 CGG-repeat region. PLoS Genet. 10:e1004294. doi: 10.1371/journal.pgen.1004294.
    • (2014) PLoS Genet , vol.10
    • Loomis, E.W.1    Sanz, L.A.2    Chedin, F.3    Hagerman, P.J.4
  • 54
    • 84918823623 scopus 로고    scopus 로고
    • Cytosolic RNA:DNA hybrids activate the cGAS-STING axis
    • Mankan, A. K., Schmidt, T., Chauhan, D., Goldeck, M., Honing, K., Gaidt, M., et al. (2014). Cytosolic RNA:DNA hybrids activate the cGAS-STING axis. EMBO J. 33, 2937-2946. doi: 10.15252/embj.201488726.
    • (2014) EMBO J , vol.33 , pp. 2937-2946
    • Mankan, A.K.1    Schmidt, T.2    Chauhan, D.3    Goldeck, M.4    Honing, K.5    Gaidt, M.6
  • 55
    • 79952126098 scopus 로고    scopus 로고
    • Co-directional replication-transcription conflicts lead to replication restart
    • Merrikh, H., Machon, C., Grainger, W. H., Grossman, A. D., and Soultanas, P. (2011). Co-directional replication-transcription conflicts lead to replication restart. Nature 470, 554-557. doi: 10.1038/nature09758.
    • (2011) Nature , vol.470 , pp. 554-557
    • Merrikh, H.1    Machon, C.2    Grainger, W.H.3    Grossman, A.D.4    Soultanas, P.5
  • 56
    • 84862490443 scopus 로고    scopus 로고
    • Replication-transcription conflicts in bacteria
    • Merrikh, H., Zhang, Y., Grossman, A. D., and Wang, J. D. (2012). Replication-transcription conflicts in bacteria. Nat. Rev. Microbiol. 10, 449-458. doi: 10.1038/nrmicro2800.
    • (2012) Nat. Rev. Microbiol , vol.10 , pp. 449-458
    • Merrikh, H.1    Zhang, Y.2    Grossman, A.D.3    Wang, J.D.4
  • 57
    • 12844265439 scopus 로고    scopus 로고
    • Mechanisms of transcription-replication collisions in bacteria
    • Mirkin, E. V., and Mirkin, S. M. (2005). Mechanisms of transcription-replication collisions in bacteria. Mol. Cell. Biol. 25, 888-895. doi: 10.1128/MCB.25.3.888-895.2005.
    • (2005) Mol. Cell. Biol , vol.25 , pp. 888-895
    • Mirkin, E.V.1    Mirkin, S.M.2
  • 58
    • 78650727733 scopus 로고    scopus 로고
    • Yeast Sen1 helicase protects the genome from transcription-associated instability
    • Mischo, H. E., Gomez-Gonzalez, B., Grzechnik, P., Rondon, A. G., Wei, W., Steinmetz, L., et al. (2011). Yeast Sen1 helicase protects the genome from transcription-associated instability. Mol. Cell 41, 21-32. doi: 10.1016/j.molcel.2010.12.007.
    • (2011) Mol. Cell , vol.41 , pp. 21-32
    • Mischo, H.E.1    Gomez-Gonzalez, B.2    Grzechnik, P.3    Rondon, A.G.4    Wei, W.5    Steinmetz, L.6
  • 59
    • 10744230604 scopus 로고    scopus 로고
    • Senataxin, the ortholog of a yeast RNA helicase, is mutant in ataxia-ocular apraxia 2
    • Moreira, M. C., Klur, S., Watanabe, M., Nemeth, A. H., Le Ber, I., Moniz, J. C., et al. (2004). Senataxin, the ortholog of a yeast RNA helicase, is mutant in ataxia-ocular apraxia 2. Nat. Genet. 36, 225-227. doi: 10.1038/ng1303ng1303.
    • (2004) Nat. Genet , vol.36 , pp. 225-227
    • Moreira, M.C.1    Klur, S.2    Watanabe, M.3    Nemeth, A.H.4    Le Ber, I.5    Moniz, J.C.6
  • 60
    • 84857237196 scopus 로고    scopus 로고
    • DNA-RNA hybrid formation mediates RNAi-directed heterochromatin formation
    • Nakama, M., Kawakami, K., Kajitani, T., Urano, T., and Murakami, Y. (2012). DNA-RNA hybrid formation mediates RNAi-directed heterochromatin formation. Genes Cells 17, 218-233. doi: 10.1111/j.1365-2443.2012.01583.x.
    • (2012) Genes Cells , vol.17 , pp. 218-233
    • Nakama, M.1    Kawakami, K.2    Kajitani, T.3    Urano, T.4    Murakami, Y.5
  • 63
    • 79957556530 scopus 로고    scopus 로고
    • DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase
    • Paeschke, K., Capra, J. A., and Zakian, V. A. (2011). DNA replication through G-quadruplex motifs is promoted by the Saccharomyces cerevisiae Pif1 DNA helicase. Cell 145, 678-691. doi: 10.1016/j.cell.2011.04.015.
    • (2011) Cell , vol.145 , pp. 678-691
    • Paeschke, K.1    Capra, J.A.2    Zakian, V.A.3
  • 64
    • 84875609978 scopus 로고    scopus 로고
    • Accelerated gene evolution through replication-transcription conflicts
    • Paul, S., Million-Weaver, S., Chattopadhyay, S., Sokurenko, E., and Merrikh, H. (2012). Accelerated gene evolution through replication-transcription conflicts. Nature 495, 512-515. doi: 10.1038/nature11989.
    • (2012) Nature , vol.495 , pp. 512-515
    • Paul, S.1    Million-Weaver, S.2    Chattopadhyay, S.3    Sokurenko, E.4    Merrikh, H.5
  • 65
    • 57649129186 scopus 로고    scopus 로고
    • The replisome uses mRNA as a primer after colliding with RNA polymerase
    • Pomerantz, R. T., and O'Donnell, M. (2008). The replisome uses mRNA as a primer after colliding with RNA polymerase. Nature 456, 762-766. doi: 10.1038/nature07527.
    • (2008) Nature , vol.456 , pp. 762-766
    • Pomerantz, R.T.1    O'Donnell, M.2
  • 66
    • 49649099084 scopus 로고    scopus 로고
    • The human RecQ helicases, BLM and RECQ1, display distinct DNA substrate specificities
    • Popuri, V., Bachrati, C. Z., Muzzolini, L., Mosedale, G., Costantini, S., Giacomini, E., et al. (2008). The human RecQ helicases, BLM and RECQ1, display distinct DNA substrate specificities. J. Biol. Chem. 283, 17766-17776. doi: 10.1074/jbc.M709749200.
    • (2008) J. Biol. Chem , vol.283 , pp. 17766-17776
    • Popuri, V.1    Bachrati, C.Z.2    Muzzolini, L.3    Mosedale, G.4    Costantini, S.5    Giacomini, E.6
  • 67
    • 17144426028 scopus 로고    scopus 로고
    • Impairment of replication fork progression mediates RNA polII transcription-associated recombination
    • Prado, F., and Aguilera, A. (2005). Impairment of replication fork progression mediates RNA polII transcription-associated recombination. EMBO J. 24, 1267-1276. doi: 10.1038/sj.emboj.7600602.
    • (2005) EMBO J , vol.24 , pp. 1267-1276
    • Prado, F.1    Aguilera, A.2
  • 68
    • 84921417056 scopus 로고    scopus 로고
    • Processing of double-R-loops in (CAG).(CTG) and C9orf72 (GGGGCC).(GGCCCC) repeats causes instability
    • Reddy, K., Schmidt, M. H., Geist, J. M., Thakkar, N. P., Panigrahi, G. B., Wang, Y. H., et al. (2010). Processing of double-R-loops in (CAG).(CTG) and C9orf72 (GGGGCC).(GGCCCC) repeats causes instability. Nucleic Acids Res. 42, 10473-10487. doi: 10.1093/nar/gku658.
    • (2010) Nucleic Acids Res , vol.42 , pp. 10473-10487
    • Reddy, K.1    Schmidt, M.H.2    Geist, J.M.3    Thakkar, N.P.4    Panigrahi, G.B.5    Wang, Y.H.6
  • 69
    • 84885926733 scopus 로고    scopus 로고
    • A SUMO-dependent interaction between Senataxin and the exosome, disrupted in the neurodegenerative disease AOA2, targets the exosome to sites of transcription-induced DNA damage
    • Richard, P., Feng, S., and Manley, J. L. (2013). A SUMO-dependent interaction between Senataxin and the exosome, disrupted in the neurodegenerative disease AOA2, targets the exosome to sites of transcription-induced DNA damage. Genes Dev. 27, 2227-2232. doi: 10.1101/gad.224923.113.
    • (2013) Genes Dev , vol.27 , pp. 2227-2232
    • Richard, P.1    Feng, S.2    Manley, J.L.3
  • 70
    • 84898636091 scopus 로고    scopus 로고
    • RNA:DNA hybrids are a novel molecular pattern sensed by TLR9
    • Rigby, R. E., Webb, L. M., Mackenzie, K. J., Li, Y., Leitch, A., Reijns, M. A., et al. (2014). RNA:DNA hybrids are a novel molecular pattern sensed by TLR9. EMBO J. 33, 542-558. doi: 10.1002/embj.201386117.
    • (2014) EMBO J , vol.33 , pp. 542-558
    • Rigby, R.E.1    Webb, L.M.2    Mackenzie, K.J.3    Li, Y.4    Leitch, A.5    Reijns, M.A.6
  • 71
    • 58449118337 scopus 로고    scopus 로고
    • The organization of the bacterial genome
    • Rocha, E. P. (2008). The organization of the bacterial genome. Annu. Rev. Genet. 42, 211-233. doi: 10.1146/annurev.genet.42.110807.091653.
    • (2008) Annu. Rev. Genet , vol.42 , pp. 211-233
    • Rocha, E.P.1
  • 72
    • 84901408644 scopus 로고    scopus 로고
    • RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress
    • Saponaro, M., Kantidakis, T., Mitter, R., Kelly, G. P., Heron, M., Williams, H., et al. (2014). RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress. Cell 157, 1037-1049. doi: 10.1016/j.cell.2014.03.048.
    • (2014) Cell , vol.157 , pp. 1037-1049
    • Saponaro, M.1    Kantidakis, T.2    Mitter, R.3    Kelly, G.P.4    Heron, M.5    Williams, H.6
  • 73
    • 84927694211 scopus 로고    scopus 로고
    • Determinants of G quadruplex-induced epigenetic instability in REV1-deficient cells
    • Schiavone, D., Guilbaud, G., Murat, P., Papadopoulou, C., Sarkies, P., Prioleau, M. N., et al. (2014). Determinants of G quadruplex-induced epigenetic instability in REV1-deficient cells. EMBO J. 33, 2507-2520. doi: 10.15252/embj.201488398.
    • (2014) EMBO J , vol.33 , pp. 2507-2520
    • Schiavone, D.1    Guilbaud, G.2    Murat, P.3    Papadopoulou, C.4    Sarkies, P.5    Prioleau, M.N.6
  • 74
    • 84923172195 scopus 로고    scopus 로고
    • R-loops induce repressive chromatin marks over mammalian gene terminators
    • Skourti-Stathaki, K., Kamieniarz-Gdula, K., and Proudfoot, N. J. (2014). R-loops induce repressive chromatin marks over mammalian gene terminators. Nature 516, 436-439. doi: 10.1038/nature13787.
    • (2014) Nature , vol.516 , pp. 436-439
    • Skourti-Stathaki, K.1    Kamieniarz-Gdula, K.2    Proudfoot, N.J.3
  • 75
    • 84903795949 scopus 로고    scopus 로고
    • A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression
    • Skourti-Stathaki, K., and Proudfoot, N. J. (2014). A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression. Genes Dev. 28, 1384-1396. doi: 10.1101/gad.242990.114.
    • (2014) Genes Dev , vol.28 , pp. 1384-1396
    • Skourti-Stathaki, K.1    Proudfoot, N.J.2
  • 76
    • 79959345878 scopus 로고    scopus 로고
    • Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination
    • Skourti-Stathaki, K., Proudfoot, N. J., and Gromak, N. (2011). Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination. Mol. Cell 42, 794-805. doi: 10.1016/j.molcel.2011.04.026.
    • (2011) Mol. Cell , vol.42 , pp. 794-805
    • Skourti-Stathaki, K.1    Proudfoot, N.J.2    Gromak, N.3
  • 77
    • 84918791689 scopus 로고    scopus 로고
    • Transcription-coupled nucleotide excision repair factors promote R-loop-induced genome instability
    • Sollier, J., Stork, C. T., Garcia-Rubio, M. L., Paulsen, R. D., Aguilera, A., and Cimprich, K. A. (2014). Transcription-coupled nucleotide excision repair factors promote R-loop-induced genome instability. Mol. Cell 56, 777-785. doi: 10.1016/j.molcel.2014.10.020.
    • (2014) Mol. Cell , vol.56 , pp. 777-785
    • Sollier, J.1    Stork, C.T.2    Garcia-Rubio, M.L.3    Paulsen, R.D.4    Aguilera, A.5    Cimprich, K.A.6
  • 78
    • 84856253456 scopus 로고    scopus 로고
    • R-loop-mediated genome instability in mRNA cleavage and polyadenylation mutants
    • Stirling, P. C., Chan, Y. A., Minaker, S. W., Aristizabal, M. J., Barrett, I., Sipahimalani, P., et al. (2012). R-loop-mediated genome instability in mRNA cleavage and polyadenylation mutants. Genes Dev. 26, 163-175. doi: 10.1101/gad.179721.111.
    • (2012) Genes Dev , vol.26 , pp. 163-175
    • Stirling, P.C.1    Chan, Y.A.2    Minaker, S.W.3    Aristizabal, M.J.4    Barrett, I.5    Sipahimalani, P.6
  • 79
    • 70449522304 scopus 로고    scopus 로고
    • Topoisomerase I suppresses genomic instability by preventing interference between replication and transcription
    • Tuduri, S., Crabbe, L., Conti, C., Tourriere, H., Holtgreve-Grez, H., Jauch, A., et al. (2009). Topoisomerase I suppresses genomic instability by preventing interference between replication and transcription. Nat. Cell Biol. 11, 1315-1324. doi: 10.1038/ncb1984.
    • (2009) Nat. Cell Biol , vol.11 , pp. 1315-1324
    • Tuduri, S.1    Crabbe, L.2    Conti, C.3    Tourriere, H.4    Holtgreve-Grez, H.5    Jauch, A.6
  • 80
    • 77953634888 scopus 로고    scopus 로고
    • Does interference between replication and transcription contribute to genomic instability in cancer cells?
    • Tuduri, S., Crabbe, L., Tourriere, H., Coquelle, A., and Pasero, P. (2010). Does interference between replication and transcription contribute to genomic instability in cancer cells? Cell Cycle 9, 1886-1892. doi: 10.4161/cc.9.10.11539.
    • (2010) Cell Cycle , vol.9 , pp. 1886-1892
    • Tuduri, S.1    Crabbe, L.2    Tourriere, H.3    Coquelle, A.4    Pasero, P.5
  • 81
    • 84255177502 scopus 로고    scopus 로고
    • RNase H and multiple RNA biogenesis factors cooperate to prevent RNA:DNA hybrids from generating genome instability
    • Wahba, L., Amon, J. D., Koshland, D., and Vuica-Ross, M. (2011). RNase H and multiple RNA biogenesis factors cooperate to prevent RNA:DNA hybrids from generating genome instability. Mol. Cell 44, 978-988. doi: 10.1016/j.molcel.2011.10.017.
    • (2011) Mol. Cell , vol.44 , pp. 978-988
    • Wahba, L.1    Amon, J.D.2    Koshland, D.3    Vuica-Ross, M.4
  • 82
    • 84871861757 scopus 로고    scopus 로고
    • Senataxin, defective in the neurodegenerative disorder ataxia with oculomotor apraxia 2, lies at the interface of transcription and the DNA damage response
    • Yuce, O., and West, S. C. (2013). Senataxin, defective in the neurodegenerative disorder ataxia with oculomotor apraxia 2, lies at the interface of transcription and the DNA damage response. Mol. Cell. Biol. 33, 406-417. doi: 10.1128/MCB.01195-12.
    • (2013) Mol. Cell. Biol , vol.33 , pp. 406-417
    • Yuce, O.1    West, S.C.2
  • 83
    • 80455176844 scopus 로고    scopus 로고
    • RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II
    • Zaratiegui, M., Castel, S. E., Irvine, D. V., Kloc, A., Ren, J., Li, F., et al. (2011). RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II. Nature 479, 135-138. doi: 10.1038/nature10501.
    • (2011) Nature , vol.479 , pp. 135-138
    • Zaratiegui, M.1    Castel, S.E.2    Irvine, D.V.3    Kloc, A.4    Ren, J.5    Li, F.6
  • 84
    • 84868100119 scopus 로고    scopus 로고
    • Genome-wide screen identifies pathways that govern GAA/TTC repeat fragility and expansions in dividing and nondividing yeast cells
    • Zhang, Y., Shishkin, A. A., Nishida, Y., Marcinkowski-Desmond, D., Saini, N., Volkov, K. V., et al. (2012). Genome-wide screen identifies pathways that govern GAA/TTC repeat fragility and expansions in dividing and nondividing yeast cells. Mol. Cell 48, 254-265. doi: 10.1016/j.molcel.2012.08.002.
    • (2012) Mol. Cell , vol.48 , pp. 254-265
    • Zhang, Y.1    Shishkin, A.A.2    Nishida, Y.3    Marcinkowski-Desmond, D.4    Saini, N.5    Volkov, K.V.6


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