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Volumn 61, Issue 3, 2016, Pages 393-404

Regulated Formation of lncRNA-DNA Hybrids Enables Faster Transcriptional Induction and Environmental Adaptation

Author keywords

[No Author keywords available]

Indexed keywords

DBP2; DNA HYBRID; LONG UNTRANSLATED RNA; RNA HELICASE; UNCLASSIFIED DRUG; CYC8 PROTEIN, S CEREVISIAE; DBP2 PROTEIN, S CEREVISIAE; DEAD BOX PROTEIN; FUNGAL DNA; FUNGAL RNA; GALACTOSE; GLUCOSE; HPR1 PROTEIN, S CEREVISIAE; NUCLEAR PROTEIN; REPRESSOR PROTEIN; RIBONUCLEASE H; RIBONUCLEASE HI; SACCHAROMYCES CEREVISIAE PROTEIN;

EID: 84957654693     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2015.12.024     Document Type: Article
Times cited : (81)

References (69)
  • 1
    • 29144472375 scopus 로고    scopus 로고
    • A role for the CPF 3'-end processing machinery in RNAP II-dependent gene looping
    • Ansari A., Hampsey M. A role for the CPF 3'-end processing machinery in RNAP II-dependent gene looping. Genes Dev. 2005, 19:2969-2978.
    • (2005) Genes Dev. , vol.19 , pp. 2969-2978
    • Ansari, A.1    Hampsey, M.2
  • 2
    • 79956306617 scopus 로고    scopus 로고
    • Regulation of X-chromosome inactivation by the X-inactivation centre
    • Augui S., Nora E.P., Heard E. Regulation of X-chromosome inactivation by the X-inactivation centre. Nat. Rev. Genet. 2011, 12:429-442.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 429-442
    • Augui, S.1    Nora, E.P.2    Heard, E.3
  • 3
    • 0028080154 scopus 로고
    • A dynamic approach to predicting bacterial growth in food
    • Baranyi J., Roberts T.A. A dynamic approach to predicting bacterial growth in food. Int. J. Food Microbiol. 1994, 23:277-294.
    • (1994) Int. J. Food Microbiol. , vol.23 , pp. 277-294
    • Baranyi, J.1    Roberts, T.A.2
  • 4
    • 84908658486 scopus 로고    scopus 로고
    • Regulation of glucose-dependent gene expression by the RNA helicase Dbp2 in Saccharomyces cerevisiae
    • Beck Z.T., Cloutier S.C., Schipma M.J., Petell C.J., Ma W.K., Tran E.J. Regulation of glucose-dependent gene expression by the RNA helicase Dbp2 in Saccharomyces cerevisiae. Genetics 2014, 198:1001-1014.
    • (2014) Genetics , vol.198 , pp. 1001-1014
    • Beck, Z.T.1    Cloutier, S.C.2    Schipma, M.J.3    Petell, C.J.4    Ma, W.K.5    Tran, E.J.6
  • 9
    • 0031439267 scopus 로고    scopus 로고
    • The yeast HPR1 gene has a functional role in transcriptional elongation that uncovers a novel source of genome instability
    • Chávez S., Aguilera A. The yeast HPR1 gene has a functional role in transcriptional elongation that uncovers a novel source of genome instability. Genes Dev. 1997, 11:3459-3470.
    • (1997) Genes Dev. , vol.11 , pp. 3459-3470
    • Chávez, S.1    Aguilera, A.2
  • 10
    • 84864387173 scopus 로고    scopus 로고
    • The DEAD-box RNA helicase Dbp2 connects RNA quality control with repression of aberrant transcription
    • Cloutier S.C., Ma W.K., Nguyen L.T., Tran E.J. The DEAD-box RNA helicase Dbp2 connects RNA quality control with repression of aberrant transcription. J. Biol. Chem. 2012, 287:26155-26166.
    • (2012) J. Biol. Chem. , vol.287 , pp. 26155-26166
    • Cloutier, S.C.1    Ma, W.K.2    Nguyen, L.T.3    Tran, E.J.4
  • 11
    • 84888996303 scopus 로고    scopus 로고
    • Long noncoding RNAs promote transcriptional poising of inducible genes
    • Cloutier S.C., Wang S., Ma W.K., Petell C.J., Tran E.J. Long noncoding RNAs promote transcriptional poising of inducible genes. PLoS Biol. 2013, 11:e1001715.
    • (2013) PLoS Biol. , vol.11 , pp. e1001715
    • Cloutier, S.C.1    Wang, S.2    Ma, W.K.3    Petell, C.J.4    Tran, E.J.5
  • 13
    • 84927128325 scopus 로고    scopus 로고
    • Telomeric repeat-containing RNA TERRA: a noncoding RNA connecting telomere biology to genome integrity
    • Cusanelli E., Chartrand P. Telomeric repeat-containing RNA TERRA: a noncoding RNA connecting telomere biology to genome integrity. Front. Genet. 2015, 6:143.
    • (2015) Front. Genet. , vol.6 , pp. 143
    • Cusanelli, E.1    Chartrand, P.2
  • 14
    • 0030883032 scopus 로고    scopus 로고
    • Regulated nuclear translocation of the Mig1 glucose repressor
    • De Vit M.J., Waddle J.A., Johnston M. Regulated nuclear translocation of the Mig1 glucose repressor. Mol. Biol. Cell 1997, 8:1603-1618.
    • (1997) Mol. Biol. Cell , vol.8 , pp. 1603-1618
    • De Vit, M.J.1    Waddle, J.A.2    Johnston, M.3
  • 15
  • 16
    • 77954841539 scopus 로고    scopus 로고
    • Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis
    • El Hage A., French S.L., Beyer A.L., Tollervey D. Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis. Genes Dev. 2010, 24:1546-1558.
    • (2010) Genes Dev. , vol.24 , pp. 1546-1558
    • El Hage, A.1    French, S.L.2    Beyer, A.L.3    Tollervey, D.4
  • 17
    • 84872676459 scopus 로고    scopus 로고
    • Analysis of interactions between genomic loci through Chromosome Conformation Capture (3C)
    • Unit22 15
    • El Kaderi B., Medler S., Ansari A. Analysis of interactions between genomic loci through Chromosome Conformation Capture (3C). Curr. Protoc. Cell Biol. 2012, Chapter 22. Unit22 15. 10.1002/0471143030.cb2215s56.
    • (2012) Curr. Protoc. Cell Biol. , vol.Chapter 22
    • El Kaderi, B.1    Medler, S.2    Ansari, A.3
  • 19
    • 84856782922 scopus 로고    scopus 로고
    • Decapping of long noncoding RNAs regulates inducible genes
    • Geisler S., Lojek L., Khalil A.M., Baker K.E., Coller J. Decapping of long noncoding RNAs regulates inducible genes. Mol. Cell 2012, 45:279-291.
    • (2012) Mol. Cell , vol.45 , pp. 279-291
    • Geisler, S.1    Lojek, L.2    Khalil, A.M.3    Baker, K.E.4    Coller, J.5
  • 20
    • 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., Chédin 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    Chédin, F.5
  • 21
    • 84885081625 scopus 로고    scopus 로고
    • GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination
    • Ginno P.A., Lim Y.W., Lott P.L., Korf I., Chédin F. GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination. Genome Res. 2013, 23:1590-1600.
    • (2013) Genome Res. , vol.23 , pp. 1590-1600
    • Ginno, P.A.1    Lim, Y.W.2    Lott, P.L.3    Korf, I.4    Chédin, F.5
  • 26
    • 52049084405 scopus 로고    scopus 로고
    • The anchor-away technique: rapid, conditional establishment of yeast mutant phenotypes
    • Haruki H., Nishikawa J., Laemmli U.K. The anchor-away technique: rapid, conditional establishment of yeast mutant phenotypes. Mol. Cell 2008, 31:925-932.
    • (2008) Mol. Cell , vol.31 , pp. 925-932
    • Haruki, H.1    Nishikawa, J.2    Laemmli, U.K.3
  • 28
    • 56849093493 scopus 로고    scopus 로고
    • A ncRNA modulates histone modification and mRNA induction in the yeast GAL gene cluster
    • Houseley J., Rubbi L., Grunstein M., Tollervey D., Vogelauer M. A ncRNA modulates histone modification and mRNA induction in the yeast GAL gene cluster. Mol. Cell 2008, 32:685-695.
    • (2008) Mol. Cell , vol.32 , pp. 685-695
    • Houseley, J.1    Rubbi, L.2    Grunstein, M.3    Tollervey, D.4    Vogelauer, M.5
  • 30
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
    • Huang W., Sherman B.T., Lempicki R.A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009, 37:1-13.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 1-13
    • Huang, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 31
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang W., Sherman B.T., Lempicki R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009, 4:44-57.
    • (2009) Nat. Protoc. , vol.4 , pp. 44-57
    • Huang, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 32
    • 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
  • 33
    • 79959948197 scopus 로고    scopus 로고
    • YY1 tethers Xist RNA to the inactive X nucleation center
    • Jeon Y., Lee J.T. YY1 tethers Xist RNA to the inactive X nucleation center. Cell 2011, 146:119-133.
    • (2011) Cell , vol.146 , pp. 119-133
    • Jeon, Y.1    Lee, J.T.2
  • 34
    • 0028230982 scopus 로고
    • Multiple mechanisms provide rapid and stringent glucose repression of GAL gene expression in Saccharomyces cerevisiae
    • Johnston M., Flick J.S., Pexton T. Multiple mechanisms provide rapid and stringent glucose repression of GAL gene expression in Saccharomyces cerevisiae. Mol. Cell. Biol. 1994, 14:3834-3841.
    • (1994) Mol. Cell. Biol. , vol.14 , pp. 3834-3841
    • Johnston, M.1    Flick, J.S.2    Pexton, T.3
  • 36
    • 84874368349 scopus 로고    scopus 로고
    • Activating RNAs associate with Mediator to enhance chromatin architecture and transcription
    • Lai F., Orom U.A., Cesaroni M., Beringer M., Taatjes D.J., Blobel G.A., Shiekhattar R. Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature 2013, 494:497-501.
    • (2013) Nature , vol.494 , pp. 497-501
    • Lai, F.1    Orom, U.A.2    Cesaroni, M.3    Beringer, M.4    Taatjes, D.J.5    Blobel, G.A.6    Shiekhattar, R.7
  • 38
    • 84947785608 scopus 로고    scopus 로고
    • Single-Molecule Imaging Reveals a Switch between Spurious and Functional ncRNA Transcription
    • Lenstra T.L., Coulon A., Chow C.C., Larson D.R. Single-Molecule Imaging Reveals a Switch between Spurious and Functional ncRNA Transcription. Mol. Cell 2015, 60:597-610.
    • (2015) Mol. Cell , vol.60 , pp. 597-610
    • Lenstra, T.L.1    Coulon, A.2    Chow, C.C.3    Larson, D.R.4
  • 40
    • 0029058555 scopus 로고
    • Transcriptional regulation in the yeast GAL gene family: a complex genetic network
    • Lohr D., Venkov P., Zlatanova J. Transcriptional regulation in the yeast GAL gene family: a complex genetic network. FASEB J. 1995, 9:777-787.
    • (1995) FASEB J. , vol.9 , pp. 777-787
    • Lohr, D.1    Venkov, P.2    Zlatanova, J.3
  • 41
    • 84885172341 scopus 로고    scopus 로고
    • The DEAD-box protein Dbp2 functions with the RNA-binding protein Yra1 to promote mRNP assembly
    • Ma W.K., Cloutier S.C., Tran E.J. The DEAD-box protein Dbp2 functions with the RNA-binding protein Yra1 to promote mRNP assembly. J. Mol. Biol. 2013, 425:3824-3838. 10.1016/j.jmb.2013.1005.1016.
    • (2013) J. Mol. Biol. , vol.425 , pp. 3824-3838
    • Ma, W.K.1    Cloutier, S.C.2    Tran, E.J.3
  • 43
    • 80053190826 scopus 로고    scopus 로고
    • Evidence for a complex of transcription factor IIB with poly(A) polymerase and cleavage factor 1 subunits required for gene looping
    • Medler S., Al Husini N., Raghunayakula S., Mukundan B., Aldea A., Ansari A. Evidence for a complex of transcription factor IIB with poly(A) polymerase and cleavage factor 1 subunits required for gene looping. J. Biol. Chem. 2011, 286:33709-33718.
    • (2011) J. Biol. Chem. , vol.286 , pp. 33709-33718
    • Medler, S.1    Al Husini, N.2    Raghunayakula, S.3    Mukundan, B.4    Aldea, A.5    Ansari, A.6
  • 47
    • 2442486948 scopus 로고    scopus 로고
    • The Snf1 kinase controls glucose repression in yeast by modulating interactions between the Mig1 repressor and the Cyc8-Tup1 co-repressor
    • Papamichos-Chronakis M., Gligoris T., Tzamarias D. The Snf1 kinase controls glucose repression in yeast by modulating interactions between the Mig1 repressor and the Cyc8-Tup1 co-repressor. EMBO Rep. 2004, 5:368-372.
    • (2004) EMBO Rep. , vol.5 , pp. 368-372
    • Papamichos-Chronakis, M.1    Gligoris, T.2    Tzamarias, D.3
  • 49
    • 67649550089 scopus 로고    scopus 로고
    • H3 lysine 4 di- and tri-methylation deposited by cryptic transcription attenuates promoter activation
    • Pinskaya M., Gourvennec S., Morillon A. H3 lysine 4 di- and tri-methylation deposited by cryptic transcription attenuates promoter activation. EMBO J. 2009, 28:1697-1707.
    • (2009) EMBO J. , vol.28 , pp. 1697-1707
    • Pinskaya, M.1    Gourvennec, S.2    Morillon, A.3
  • 50
    • 0030959070 scopus 로고    scopus 로고
    • Recombination between DNA repeats in yeast hpr1delta cells is linked to transcription elongation
    • Prado F., Piruat J.I., Aguilera A. Recombination between DNA repeats in yeast hpr1delta cells is linked to transcription elongation. EMBO J. 1997, 16:2826-2835.
    • (1997) EMBO J. , vol.16 , pp. 2826-2835
    • Prado, F.1    Piruat, J.I.2    Aguilera, A.3
  • 51
    • 83255164884 scopus 로고    scopus 로고
    • Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution
    • Rhee H.S., Pugh B.F. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 2011, 147:1408-1419.
    • (2011) Cell , vol.147 , pp. 1408-1419
    • Rhee, H.S.1    Pugh, B.F.2
  • 52
    • 84861904178 scopus 로고    scopus 로고
    • Genome regulation by long noncoding RNAs
    • Rinn J.L., Chang H.Y. Genome regulation by long noncoding RNAs. Annu. Rev. Biochem. 2012, 81:145-166.
    • (2012) Annu. Rev. Biochem. , vol.81 , pp. 145-166
    • Rinn, J.L.1    Chang, H.Y.2
  • 54
    • 54449085117 scopus 로고    scopus 로고
    • Galactose metabolism in yeast-structure and regulation of the leloir pathway enzymes and the genes encoding them
    • Sellick C.A., Campbell R.N., Reece R.J. Galactose metabolism in yeast-structure and regulation of the leloir pathway enzymes and the genes encoding them. Int. Rev. Cell Mol. Biol. 2008, 269:111-150.
    • (2008) Int. Rev. Cell Mol. Biol. , vol.269 , pp. 111-150
    • Sellick, C.A.1    Campbell, R.N.2    Reece, R.J.3
  • 55
    • 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
  • 56
    • 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
  • 59
    • 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
  • 60
    • 72749098124 scopus 로고    scopus 로고
    • Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complex
    • Tan-Wong S.M., Wijayatilake H.D., Proudfoot N.J. Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complex. Genes Dev. 2009, 23:2610-2624.
    • (2009) Genes Dev. , vol.23 , pp. 2610-2624
    • Tan-Wong, S.M.1    Wijayatilake, H.D.2    Proudfoot, N.J.3
  • 61
    • 84884550965 scopus 로고    scopus 로고
    • The nuclear pore regulates GAL1 gene transcription by controlling the localization of the SUMO protease Ulp1
    • Texari L., Dieppois G., Vinciguerra P., Contreras M.P., Groner A., Letourneau A., Stutz F. The nuclear pore regulates GAL1 gene transcription by controlling the localization of the SUMO protease Ulp1. Mol. Cell 2013, 51:807-818.
    • (2013) Mol. Cell , vol.51 , pp. 807-818
    • Texari, L.1    Dieppois, G.2    Vinciguerra, P.3    Contreras, M.P.4    Groner, A.5    Letourneau, A.6    Stutz, F.7
  • 63
    • 84883377142 scopus 로고    scopus 로고
    • A transcriptome-wide atlas of RNP composition reveals diverse classes of mRNAs and lncRNAs
    • Tuck A.C., Tollervey D. A transcriptome-wide atlas of RNP composition reveals diverse classes of mRNAs and lncRNAs. Cell 2013, 154:996-1009.
    • (2013) Cell , vol.154 , pp. 996-1009
    • Tuck, A.C.1    Tollervey, D.2
  • 65
    • 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
  • 66
    • 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
  • 67
    • 84894045085 scopus 로고    scopus 로고
    • Unexpected functions of lncRNAs in gene regulation
    • Wang S., Tran E.J. Unexpected functions of lncRNAs in gene regulation. Commun. Integr. Biol. 2013, 6:e27610.
    • (2013) Commun. Integr. Biol. , vol.6 , pp. e27610
    • Wang, S.1    Tran, E.J.2
  • 69
    • 0036889334 scopus 로고    scopus 로고
    • Stable mRNP formation and export require cotranscriptional recruitment of the mRNA export factors Yra1p and Sub2p by Hpr1p
    • Zenklusen D., Vinciguerra P., Wyss J.C., Stutz F. Stable mRNP formation and export require cotranscriptional recruitment of the mRNA export factors Yra1p and Sub2p by Hpr1p. Mol. Cell. Biol. 2002, 22:8241-8253.
    • (2002) Mol. Cell. Biol. , vol.22 , pp. 8241-8253
    • Zenklusen, D.1    Vinciguerra, P.2    Wyss, J.C.3    Stutz, F.4


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