메뉴 건너뛰기




Volumn 34, Issue , 2015, Pages 39-45

The Yin and Yang of R-loop biology

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME STRUCTURE; DNA REPAIR; GENE EXPRESSION; HUMAN; NONHUMAN; PRIORITY JOURNAL; REVIEW; RNA ANALYSIS; RNA PROCESSING; RNA STRUCTURE; RNA TRANSCRIPTION; ANIMAL; CHEMISTRY; GENETICS; GENOME; GENOMIC INSTABILITY;

EID: 84928716856     PISSN: 09550674     EISSN: 18790410     Source Type: Journal    
DOI: 10.1016/j.ceb.2015.04.008     Document Type: Review
Times cited : (102)

References (59)
  • 1
    • 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, 46:115-124.
    • (2012) Mol Cell , vol.46 , pp. 115-124
    • Aguilera, A.1    Garcia-Muse, T.2
  • 2
    • 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., Proudfoot N.J. A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression. Genes Dev 2014, 28:1384-1396.
    • (2014) Genes Dev , vol.28 , pp. 1384-1396
    • Skourti-Stathaki, K.1    Proudfoot, N.J.2
  • 3
    • 84902081933 scopus 로고    scopus 로고
    • The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability
    • Hamperl S., Cimprich K.A. The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability. DNA Repair (Amst) 2014, 19:84-94.
    • (2014) DNA Repair (Amst) , vol.19 , pp. 84-94
    • Hamperl, S.1    Cimprich, K.A.2
  • 4
    • 8344234112 scopus 로고    scopus 로고
    • Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center
    • Westover K.D., Bushnell D.A., Kornberg R.D. Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center. Cell 2004, 119:481-489.
    • (2004) Cell , vol.119 , pp. 481-489
    • Westover, K.D.1    Bushnell, D.A.2    Kornberg, R.D.3
  • 5
    • 0023433855 scopus 로고
    • Supercoiling of the DNA template during transcription
    • Liu L.F., Wang J.C. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci USA 1987, 84:7024-7027.
    • (1987) Proc Natl Acad Sci USA , vol.84 , pp. 7024-7027
    • Liu, L.F.1    Wang, J.C.2
  • 6
    • 0141819093 scopus 로고    scopus 로고
    • Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination
    • Huertas P., Aguilera A. Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination. Mol Cell 2003, 12:711-721.
    • (2003) Mol Cell , vol.12 , pp. 711-721
    • Huertas, P.1    Aguilera, A.2
  • 8
    • 84855286267 scopus 로고    scopus 로고
    • Genome instability and transcription elongation impairment in human cells depleted of THO/TREX
    • Dominguez-Sanchez M.S., Barroso S., Gomez-Gonzalez B., Luna R., Aguilera A. Genome instability and transcription elongation impairment in human cells depleted of THO/TREX. PLoS Genet 2011, 7:e1002386.
    • (2011) PLoS Genet , vol.7 , pp. e1002386
    • Dominguez-Sanchez, M.S.1    Barroso, S.2    Gomez-Gonzalez, B.3    Luna, R.4    Aguilera, A.5
  • 9
    • 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., Vuica-Ross M. RNase H and multiple RNA biogenesis factors cooperate to prevent RNA:DNA hybrids from generating genome instability. Mol Cell 2011, 44:978-988.
    • (2011) Mol Cell , vol.44 , pp. 978-988
    • Wahba, L.1    Amon, J.D.2    Koshland, D.3    Vuica-Ross, M.4
  • 10
    • 84879062475 scopus 로고    scopus 로고
    • The homologous recombination machinery modulates the formation of RNA-DNA hybrids and associated chromosome instability
    • Wahba L., Gore S.K., Koshland D. The homologous recombination machinery modulates the formation of RNA-DNA hybrids and associated chromosome instability. Elife 2013, 2:e00505.
    • (2013) Elife , vol.2 , pp. e00505
    • Wahba, L.1    Gore, S.K.2    Koshland, D.3
  • 11
    • 0034654617 scopus 로고    scopus 로고
    • A novel pairing process promoted by Escherichia coli RecA protein: inverse DNA and RNA strand exchange
    • Zaitsev E.N., Kowalczykowski S.C. A novel pairing process promoted by Escherichia coli RecA protein: inverse DNA and RNA strand exchange. Genes Dev 2000, 14:740-749.
    • (2000) Genes Dev , vol.14 , pp. 740-749
    • Zaitsev, E.N.1    Kowalczykowski, S.C.2
  • 12
    • 73649101345 scopus 로고    scopus 로고
    • Competition between the RNA transcript and the nontemplate DNA strand during R-loop formation in vitro: a nick can serve as a strong R-loop initiation site
    • Roy D., Zhang Z., Lu Z., Hsieh C.L., Lieber M.R. Competition between the RNA transcript and the nontemplate DNA strand during R-loop formation in vitro: a nick can serve as a strong R-loop initiation site. Mol Cell Biol 2010, 30:146-159.
    • (2010) Mol Cell Biol , vol.30 , pp. 146-159
    • Roy, D.1    Zhang, Z.2    Lu, Z.3    Hsieh, C.L.4    Lieber, M.R.5
  • 13
    • 84908343019 scopus 로고    scopus 로고
    • Genome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes, retrotransposons and mitochondria
    • El Hage A., Webb S., Kerr A., Tollervey D. Genome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes, retrotransposons and mitochondria. PLOS Genet 2014, 10:e1004716.
    • (2014) PLOS Genet , vol.10 , pp. e1004716
    • El Hage, A.1    Webb, S.2    Kerr, A.3    Tollervey, D.4
  • 15
    • 61349102407 scopus 로고    scopus 로고
    • Ribonuclease H: the enzymes in eukaryotes
    • Cerritelli S.M., Crouch R.J. Ribonuclease H: the enzymes in eukaryotes. FEBS J 2009, 276:1494-1505.
    • (2009) FEBS J , vol.276 , pp. 1494-1505
    • Cerritelli, S.M.1    Crouch, R.J.2
  • 16
    • 77950466824 scopus 로고    scopus 로고
    • The structure of the mammalian RNase H2 complex provides insight into RNA.NA hybrid processing to prevent immune dysfunction
    • Shaban N.M., Harvey S., Perrino F.W., Hollis T. The structure of the mammalian RNase H2 complex provides insight into RNA.NA hybrid processing to prevent immune dysfunction. J Biol Chem 2010, 285:3617-3624.
    • (2010) J Biol Chem , vol.285 , pp. 3617-3624
    • Shaban, N.M.1    Harvey, S.2    Perrino, F.W.3    Hollis, T.4
  • 17
    • 84866462296 scopus 로고    scopus 로고
    • Mammalian RNase H2 removes ribonucleotides from DNA to maintain genome integrity
    • Hiller B., Achleitner M., Glage S., Naumann R., Behrendt R., Roers A. Mammalian RNase H2 removes ribonucleotides from DNA to maintain genome integrity. J Exp Med 2012, 209:1419-1426.
    • (2012) J Exp Med , vol.209 , pp. 1419-1426
    • Hiller, B.1    Achleitner, M.2    Glage, S.3    Naumann, R.4    Behrendt, R.5    Roers, A.6
  • 18
    • 0033512305 scopus 로고    scopus 로고
    • Saccharomyces cerevisiae RNase H(35) functions in RNA primer removal during lagging-strand DNA synthesis, most efficiently in cooperation with Rad27 nuclease
    • Qiu J., Qian Y., Frank P., Wintersberger U., Shen B. Saccharomyces cerevisiae RNase H(35) functions in RNA primer removal during lagging-strand DNA synthesis, most efficiently in cooperation with Rad27 nuclease. Mol Cell Biol 1999, 19:8361-8371.
    • (1999) Mol Cell Biol , vol.19 , pp. 8361-8371
    • Qiu, J.1    Qian, Y.2    Frank, P.3    Wintersberger, U.4    Shen, B.5
  • 19
    • 0041696782 scopus 로고    scopus 로고
    • Loading Rho to terminate transcription
    • Richardson J.P. Loading Rho to terminate transcription. Cell 2003, 114:157-159.
    • (2003) Cell , vol.114 , pp. 157-159
    • Richardson, J.P.1
  • 20
    • 79957813857 scopus 로고    scopus 로고
    • Human DHX9 helicase preferentially unwinds RNA-containing displacement loops (R-loops) and G-quadruplexes
    • Chakraborty P., Grosse F. Human DHX9 helicase preferentially unwinds RNA-containing displacement loops (R-loops) and G-quadruplexes. DNA Repair (Amst) 2011, 10:654-665.
    • (2011) DNA Repair (Amst) , vol.10 , pp. 654-665
    • Chakraborty, P.1    Grosse, F.2
  • 23
    • 84859139467 scopus 로고    scopus 로고
    • Interactions of Sen1, Nrd1, and Nab3 with multiple phosphorylated forms of the Rpb1 C-terminal domain in Saccharomyces cerevisiae
    • Chinchilla K., Rodriguez-Molina J.B., Ursic D., Finkel J.S., Ansari A.Z., Culbertson M.R. Interactions of Sen1, Nrd1, and Nab3 with multiple phosphorylated forms of the Rpb1 C-terminal domain in Saccharomyces cerevisiae. Eukaryot Cell 2012, 11:417-429.
    • (2012) Eukaryot Cell , vol.11 , pp. 417-429
    • Chinchilla, K.1    Rodriguez-Molina, J.B.2    Ursic, D.3    Finkel, J.S.4    Ansari, A.Z.5    Culbertson, M.R.6
  • 24
    • 23744455164 scopus 로고    scopus 로고
    • Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability
    • Li X., Manley J.L. Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability. Cell 2005, 122:365-378.
    • (2005) Cell , vol.122 , pp. 365-378
    • Li, X.1    Manley, J.L.2
  • 25
    • 79951810510 scopus 로고    scopus 로고
    • Mutation: the perils of transcription
    • Muers M. Mutation: the perils of transcription. Nat Rev Genet 2011, 12:156.
    • (2011) Nat Rev Genet , vol.12 , pp. 156
    • Muers, M.1
  • 27
    • 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 A.S. Transcription-induced mutations: increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli. Proc Natl Acad Sci USA 1996, 93:13919-13924.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 13919-13924
    • Beletskii, A.1    Bhagwat, A.S.2
  • 28
    • 0037561998 scopus 로고    scopus 로고
    • AID mediates hypermutation by deaminating single stranded DNA
    • Dickerson S.K., Market E., Besmer E., Papavasiliou F.N. AID mediates hypermutation by deaminating single stranded DNA. J Exp Med 2003, 197:1291-1296.
    • (2003) J Exp Med , vol.197 , pp. 1291-1296
    • Dickerson, S.K.1    Market, E.2    Besmer, E.3    Papavasiliou, F.N.4
  • 29
    • 84892572836 scopus 로고    scopus 로고
    • Molecular targeting of mutagenic AID and APOBEC deaminases
    • Nabel C.S., Schutsky E.K., Kohli R.M. Molecular targeting of mutagenic AID and APOBEC deaminases. Cell Cycle 2014, 13:171-172.
    • (2014) Cell Cycle , vol.13 , pp. 171-172
    • Nabel, C.S.1    Schutsky, E.K.2    Kohli, R.M.3
  • 30
    • 80053645721 scopus 로고    scopus 로고
    • R-loop-mediated genomic instability is caused by impairment of replication fork progression
    • Gan W., Guan Z., Liu J., Gui T., Shen K., Manley J.L., Li X. R-loop-mediated genomic instability is caused by impairment of replication fork progression. Genes Dev 2011, 25:2041-2056.
    • (2011) Genes Dev , vol.25 , pp. 2041-2056
    • Gan, W.1    Guan, Z.2    Liu, J.3    Gui, T.4    Shen, K.5    Manley, J.L.6    Li, X.7
  • 31
    • 0030737725 scopus 로고    scopus 로고
    • Stable DNA replication: interplay between DNA replication, homologous recombination, and transcription
    • Kogoma T. Stable DNA replication: interplay between DNA replication, homologous recombination, and transcription. Microbiol Mol Biol Rev 1997, 61:212-238.
    • (1997) Microbiol Mol Biol Rev , vol.61 , pp. 212-238
    • Kogoma, T.1
  • 32
    • 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., Cimprich K.A. Transcription-coupled nucleotide excision repair factors promote R-loop-induced genome instability. Mol Cell 2014, 56:777-785.
    • (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
  • 34
    • 30144439370 scopus 로고    scopus 로고
    • Common fragile sites
    • Glover T.W. Common fragile sites. Cancer Lett 2006, 232:4-12.
    • (2006) Cancer Lett , vol.232 , pp. 4-12
    • Glover, T.W.1
  • 35
    • 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., Tora L. Collisions between replication and transcription complexes cause common fragile site instability at the longest human genes. Mol Cell 2011, 44:966-977.
    • (2011) Mol Cell , vol.44 , pp. 966-977
    • Helmrich, A.1    Ballarino, M.2    Tora, L.3
  • 36
    • 84875887504 scopus 로고    scopus 로고
    • Chromosome translocation, B cell lymphoma, and activation-induced cytidine deaminase
    • Robbiani D.F., Nussenzweig M.C. Chromosome translocation, B cell lymphoma, and activation-induced cytidine deaminase. Annu Rev Pathol 2013, 8:79-103.
    • (2013) Annu Rev Pathol , vol.8 , pp. 79-103
    • Robbiani, D.F.1    Nussenzweig, M.C.2
  • 37
    • 84555196106 scopus 로고    scopus 로고
    • BRCA1 and BRCA2: different roles in a common pathway of genome protection
    • Roy R., Chun J., Powell S.N. BRCA1 and BRCA2: different roles in a common pathway of genome protection. Nat Rev Cancer 2012, 12:68-78.
    • (2012) Nat Rev Cancer , vol.12 , pp. 68-78
    • Roy, R.1    Chun, J.2    Powell, S.N.3
  • 39
    • 42249115685 scopus 로고    scopus 로고
    • The consequences of Rad51 overexpression for normal and tumor cells
    • Klein H.L. The consequences of Rad51 overexpression for normal and tumor cells. DNA Repair (Amst) 2008, 7:686-693.
    • (2008) DNA Repair (Amst) , vol.7 , pp. 686-693
    • Klein, H.L.1
  • 40
    • 56249123594 scopus 로고    scopus 로고
    • Five years since the discovery of FIP1L1-PDGFRA: what we have learned about the fusion and other molecularly defined eosinophilias
    • Gotlib J., Cools J. Five years since the discovery of FIP1L1-PDGFRA: what we have learned about the fusion and other molecularly defined eosinophilias. Leukemia 2008, 22:1999-2010.
    • (2008) Leukemia , vol.22 , pp. 1999-2010
    • Gotlib, J.1    Cools, J.2
  • 41
    • 84907587725 scopus 로고    scopus 로고
    • Out of balance: R-loops in human disease
    • Groh M., Gromak N. Out of balance: R-loops in human disease. PLOS Genet 2014, 10:e1004630.
    • (2014) PLOS Genet , vol.10 , pp. e1004630
    • Groh, M.1    Gromak, N.2
  • 45
    • 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., Hagerman P.J. Transcription-associated R-loop formation across the human FMR1 CGG-repeat region. PLOS Genet 2014, 10:e1004294.
    • (2014) PLOS Genet , vol.10 , pp. e1004294
    • Loomis, E.W.1    Sanz, L.A.2    Chedin, F.3    Hagerman, P.J.4
  • 46
    • 77649144557 scopus 로고    scopus 로고
    • Repeat instability as the basis for human diseases and as a potential target for therapy
    • Lopez Castel A., Cleary J.D., Pearson C.E. Repeat instability as the basis for human diseases and as a potential target for therapy. Nat Rev Mol Cell Biol 2010, 11:165-170.
    • (2010) Nat Rev Mol Cell Biol , vol.11 , pp. 165-170
    • Lopez Castel, A.1    Cleary, J.D.2    Pearson, C.E.3
  • 48
    • 37549036739 scopus 로고    scopus 로고
    • Mechanism of R-loop formation at immunoglobulin class switch sequences
    • Roy D., Yu K., Lieber M.R. Mechanism of R-loop formation at immunoglobulin class switch sequences. Mol Cell Biol 2008, 28:50-60.
    • (2008) Mol Cell Biol , vol.28 , pp. 50-60
    • Roy, D.1    Yu, K.2    Lieber, M.R.3
  • 49
    • 84877354511 scopus 로고    scopus 로고
    • R-loop stabilization represses antisense transcription at the Arabidopsis FLC locus
    • Sun Q., Csorba T., Skourti-Stathaki K., Proudfoot N.J., Dean C. R-loop stabilization represses antisense transcription at the Arabidopsis FLC locus. Science 2013, 340:619-621.
    • (2013) Science , vol.340 , pp. 619-621
    • Sun, Q.1    Csorba, T.2    Skourti-Stathaki, K.3    Proudfoot, N.J.4    Dean, C.5
  • 50
    • 79956330964 scopus 로고    scopus 로고
    • CpG islands and the regulation of transcription
    • Deaton A.M., Bird A. CpG islands and the regulation of transcription. Genes Dev 2011, 25:1010-1022.
    • (2011) Genes Dev , vol.25 , pp. 1010-1022
    • Deaton, A.M.1    Bird, A.2
  • 51
    • 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., Chedin F. R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol Cell 2012, 45:814-825.
    • (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
  • 53
    • 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., Gromak N. Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination. Mol Cell 2011, 42:794-805.
    • (2011) Mol Cell , vol.42 , pp. 794-805
    • Skourti-Stathaki, K.1    Proudfoot, N.J.2    Gromak, N.3
  • 54
    • 84923172195 scopus 로고    scopus 로고
    • R-loops induce repressive chromatin marks over mammalian gene terminators
    • Skourti-Stathaki K., Kamieniarz-Gdula K., Proudfoot N.J. R-loops induce repressive chromatin marks over mammalian gene terminators. Nature 2014, 516:436-439.
    • (2014) Nature , vol.516 , pp. 436-439
    • Skourti-Stathaki, K.1    Kamieniarz-Gdula, K.2    Proudfoot, N.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.