메뉴 건너뛰기




Volumn 3, Issue November, 2014, Pages 1-21

Transcription mediated insulation and interference direct gene cluster expression switches

Author keywords

[No Author keywords available]

Indexed keywords

FK 506 BINDING PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR IIB; CARBON; COMPLEMENTARY RNA; MESSENGER RNA; SACCHAROMYCES CEREVISIAE PROTEIN;

EID: 84928719564     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.03635     Document Type: Article
Times cited : (34)

References (60)
  • 1
    • 34848825637 scopus 로고    scopus 로고
    • Chromatin remodelling is a major source of coexpression of linked genes in yeast
    • Batada NN, Urrutia AO, Hurst LD. 2007. Chromatin remodelling is a major source of coexpression of linked genes in yeast. Trends in Genetics 23:480-484. doi: 10.1016/j.tig.2007.08.003.
    • (2007) Trends in Genetics , vol.23 , pp. 480-484
    • Batada, N.N.1    Urrutia, A.O.2    Hurst, L.D.3
  • 2
    • 40349116304 scopus 로고    scopus 로고
    • A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae
    • Berretta J, Pinskaya M, Morillon A. 2008. A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae. Genes & Development 22:615-626. doi: 10.1101/gad.458008.
    • (2008) Genes & Development , vol.22 , pp. 615-626
    • Berretta, J.1    Pinskaya, M.2    Morillon, A.3
  • 5
    • 36048951040 scopus 로고    scopus 로고
    • Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae
    • Camblong J, Iglesias N, Fickentscher C, Dieppois G, Stutz F. 2007. Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae. Cell 131:706-717. doi: 10.1016/j. cell.2007.09.014.
    • (2007) Cell , vol.131 , pp. 706-717
    • Camblong, J.1    Iglesias, N.2    Fickentscher, C.3    Dieppois, G.4    Stutz, F.5
  • 7
    • 78751659330 scopus 로고    scopus 로고
    • Nascent transcript sequencing visualizes transcription at nucleotide resolution
    • Churchman LS, Weissman JS. 2011. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 469:368-373. doi: 10.1038/nature09652.
    • (2011) Nature , vol.469 , pp. 368-373
    • Churchman, L.S.1    Weissman, J.S.2
  • 8
    • 0033780450 scopus 로고    scopus 로고
    • A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression
    • Cohen BA, Mitra RD, Hughes JD, Church GM. 2000. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nature Genetics 26:183-186. doi: 10.1038/79896.
    • (2000) Nature Genetics , vol.26 , pp. 183-186
    • Cohen, B.A.1    Mitra, R.D.2    Hughes, J.D.3    Church, G.M.4
  • 9
    • 69949173145 scopus 로고    scopus 로고
    • Gene looping is conferred by activator-dependent interaction of transcription initiation and termination machineries
    • El Kaderi B, Medler S, Raghunayakula S, Ansari A. 2009. Gene looping is conferred by activator-dependent interaction of transcription initiation and termination machineries. The Journal of Biological Chemistry 284:25015-25025. doi: 10.1074/jbc.M109.007948.
    • (2009) The Journal of Biological Chemistry , vol.284 , pp. 25015-25025
    • El Kaderi, B.1    Medler, S.2    Raghunayakula, S.3    Ansari, A.4
  • 10
    • 84864309100 scopus 로고    scopus 로고
    • Clocks, metabolism, and the epigenome
    • Feng D, Lazar MA. 2012. Clocks, metabolism, and the epigenome. Molecular Cell 47:158-167. doi: 10.1016/j. molcel.2012.06.026.
    • (2012) Molecular Cell , vol.47 , pp. 158-167
    • Feng, D.1    Lazar, M.A.2
  • 13
    • 52049084405 scopus 로고    scopus 로고
    • The anchor-away technique: Rapid, conditional establishment of yeast mutant phenotypes
    • Haruki H, Nishikawa J, Laemmli UK. 2008. The anchor-away technique: rapid, conditional establishment of yeast mutant phenotypes. Molecular Cell 31:925-932. doi: 10.1016/j.molcel.2008.07.020.
    • (2008) Molecular Cell , vol.31 , pp. 925-932
    • Haruki, H.1    Nishikawa, J.2    Laemmli, U.K.3
  • 14
    • 33750814968 scopus 로고    scopus 로고
    • Antisense transcription controls cell fate in Saccharomyces cerevisiae
    • Hongay CF, Grisafi PL, Galitski T, Fink GR. 2006. Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell 127:735-745. doi: 10.1016/j.cell.2006.09.038.
    • (2006) Cell , vol.127 , pp. 735-745
    • Hongay, C.F.1    Grisafi, P.L.2    Galitski, T.3    Fink, G.R.4
  • 15
    • 56849093493 scopus 로고    scopus 로고
    • A nc RNA modulates histone modification and m RNA induction in the yeast GAL gene cluster
    • Houseley J, Rubbi L, Grunstein M, Tollervey D, Vogelauer M. 2008. A nc RNA modulates histone modification and m RNA induction in the yeast GAL gene cluster. Molecular Cell 32:685-695. doi: 10.1016/j.molcel. 2008.09.027.
    • (2008) Molecular Cell , vol.32 , pp. 685-695
    • Houseley, J.1    Rubbi, L.2    Grunstein, M.3    Tollervey, D.4    Vogelauer, M.5
  • 16
    • 34249088350 scopus 로고    scopus 로고
    • Genome-wide transcription and the implications for genomic organization
    • Kapranov P, Willingham AT, Gingeras TR. 2007. Genome-wide transcription and the implications for genomic organization. Nature Reviews. Genetics 8:413-423. doi: 10.1038/nrg2083.
    • (2007) Nature Reviews. Genetics , vol.8 , pp. 413-423
    • Kapranov, P.1    Willingham, A.T.2    Gingeras, T.R.3
  • 17
    • 0028017601 scopus 로고
    • Chromatin structure modulation in Saccharomyces cerevisiae by centromere and promoter factor 1
    • Kent NA, Tsang JS, Crowther DJ, Mellor J. 1994. Chromatin structure modulation in Saccharomyces cerevisiae by centromere and promoter factor 1. Molecular and Cellular Biology 14:5229-5241.
    • (1994) Molecular and Cellular Biology , vol.14 , pp. 5229-5241
    • Kent, N.A.1    Tsang, J.S.2    Crowther, D.J.3    Mellor, J.4
  • 19
    • 0242669950 scopus 로고    scopus 로고
    • Role for antisense RNA in regulating circadian clock function in Neurospora crassa
    • Kramer C, Loros JJ, Dunlap JC, Crosthwaite SK. 2003. Role for antisense RNA in regulating circadian clock function in Neurospora crassa. Nature 421:948-952. doi: 10.1038/nature01427.
    • (2003) Nature , vol.421 , pp. 948-952
    • Kramer, C.1    Loros, J.J.2    Dunlap, J.C.3    Crosthwaite, S.K.4
  • 20
    • 34547844064 scopus 로고    scopus 로고
    • SCEPTRANS: An online tool for analyzing periodic transcription in yeast
    • Kudlicki A, Rowicka M, Otwinowski Z. 2007. SCEPTRANS: an online tool for analyzing periodic transcription in yeast. Bioinformatics 23:1559-1561. doi: 10.1093/bioinformatics/btm126.
    • (2007) Bioinformatics , vol.23 , pp. 1559-1561
    • Kudlicki, A.1    Rowicka, M.2    Otwinowski, Z.3
  • 21
    • 77958559009 scopus 로고    scopus 로고
    • Behavior of a metabolic cycling population at the single cell level as visualized by fluorescent gene expression reporters
    • Laxman S, Sutter BM, Tu BP. 2010. Behavior of a metabolic cycling population at the single cell level as visualized by fluorescent gene expression reporters. PLOS ONE 5:e12595. doi: 10.1371/journal.pone.0012595.
    • (2010) PLOS ONE , vol.5
    • Laxman, S.1    Sutter, B.M.2    Tu, B.P.3
  • 22
    • 0038104857 scopus 로고    scopus 로고
    • Genomic gene clustering analysis of pathways in eukaryotes
    • Lee JM, Sonnhammer EL. 2003. Genomic gene clustering analysis of pathways in eukaryotes. Genome Research 13:875-882. doi: 10.1101/gr.737703.
    • (2003) Genome Research , vol.13 , pp. 875-882
    • Lee, J.M.1    Sonnhammer, E.L.2
  • 23
    • 0031820288 scopus 로고    scopus 로고
    • Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae
    • Longtine MS, McKenzie A, Demarini DJ, Shah NG, Wach A, Brachat A, Philippsen P, Pringle JR. 1998. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14:953-961. doi: 10.1002/(SICI)1097-0061(199807)14:103.0.CO;2-U.
    • (1998) Yeast , vol.14 , pp. 953-961
    • Longtine, M.S.1    McKenzie, A.2    Demarini, D.J.3    Shah, N.G.4    Wach, A.5    Brachat, A.6    Philippsen, P.7    Pringle, J.R.8
  • 25
    • 2942560254 scopus 로고    scopus 로고
    • Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene
    • Martens JA, Laprade L, Winston F. 2004. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429:571-574. doi: 10.1038/nature02538.
    • (2004) Nature , vol.429 , pp. 571-574
    • Martens, J.A.1    Laprade, L.2    Winston, F.3
  • 26
    • 33846930357 scopus 로고    scopus 로고
    • Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript
    • Martianov I, Ramadass A, Serra Barros A, Chow N, Akoulitchev A. 2007. Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 445:666-670. doi: 10.1038/nature05519.
    • (2007) Nature , vol.445 , pp. 666-670
    • Martianov, I.1    Ramadass, A.2    Serra Barros, A.3    Chow, N.4    Akoulitchev, A.5
  • 27
    • 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. 2011. Evidence for a complex of transcription factor IIB with poly(A) polymerase and cleavage factor 1 subunits required for gene looping. The Journal of Biological Chemistry 286:33709-33718. doi: 10.1074/jbc.M110.193870.
    • (2011) The Journal of Biological Chemistry , vol.286 , pp. 33709-33718
    • Medler, S.1    Al Husini, N.2    Raghunayakula, S.3    Mukundan, B.4    Aldea, A.5    Ansari, A.6
  • 29
    • 0021706678 scopus 로고
    • Regulation of glutamine-repressible gene products by the GLN3 function in Saccharomyces cerevisiae
    • Mitchell AP, Magasanik B. 1984. Regulation of glutamine-repressible gene products by the GLN3 function in Saccharomyces cerevisiae. Molecular and Cellular Biology 4:2758-2766.
    • (1984) Molecular and Cellular Biology , vol.4 , pp. 2758-2766
    • Mitchell, A.P.1    Magasanik, B.2
  • 30
    • 20444375490 scopus 로고    scopus 로고
    • Dynamic lysine methylation on histone H3 defines the regulatory phase of gene transcription
    • Morillon A, Karabetsou N, Nair A, Mellor J. 2005. Dynamic lysine methylation on histone H3 defines the regulatory phase of gene transcription. Molecular Cell 18:723-734. doi: 10.1016/j.molcel.2005.05.009.
    • (2005) Molecular Cell , vol.18 , pp. 723-734
    • Morillon, A.1    Karabetsou, N.2    Nair, A.3    Mellor, J.4
  • 31
    • 0242584447 scopus 로고    scopus 로고
    • Regulation of elongating RNA polymerase II by forkhead transcription factors in yeast
    • Morillon A, O'Sullivan J, Azad A, Proudfoot N, Mellor J. 2003. Regulation of elongating RNA polymerase II by forkhead transcription factors in yeast. Science 300:492-495. doi: 10.1126/science.1081379.
    • (2003) Science , vol.300 , pp. 492-495
    • Morillon, A.1    O'Sullivan, J.2    Azad, A.3    Proudfoot, N.4    Mellor, J.5
  • 32
    • 77955452809 scopus 로고    scopus 로고
    • Long antisense non-coding RNAs and their role in transcription and oncogenesis
    • Morris KV, Vogt PK. 2010. Long antisense non-coding RNAs and their role in transcription and oncogenesis. Cell Cycle 9:2544-2547. doi: 10.4161/cc.9.13.12145.
    • (2010) Cell Cycle , vol.9 , pp. 2544-2547
    • Morris, K.V.1    Vogt, P.K.2
  • 33
    • 84859335229 scopus 로고    scopus 로고
    • A pre-initiation complex at the 3'-end of genes drives antisense transcription independent of divergent sense transcription
    • Murray SC, Serra Barros A, Brown DA, Dudek P, Ayling J, Mellor J. 2012. A pre-initiation complex at the 3'-end of genes drives antisense transcription independent of divergent sense transcription. Nucleic Acids Research 40:2432-2444. doi: 10.1093/nar/gkr1121.
    • (2012) Nucleic Acids Research , vol.40 , pp. 2432-2444
    • Murray, S.C.1    Serra Barros, A.2    Brown, D.A.3    Dudek, P.4    Ayling, J.5    Mellor, J.6
  • 35
    • 84877574893 scopus 로고    scopus 로고
    • Extensive transcriptional heterogeneity revealed by isoform profiling
    • Pelechano V, Wei W, Steinmetz LM. 2013. Extensive transcriptional heterogeneity revealed by isoform profiling. Nature 497:127-131. doi: 10.1038/nature12121.
    • (2013) Nature , vol.497 , pp. 127-131
    • Pelechano, V.1    Wei, W.2    Steinmetz, L.M.3
  • 36
    • 36148972085 scopus 로고    scopus 로고
    • Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D
    • Perocchi F, Xu Z, Clauder-Munster S, Steinmetz LM. 2007. Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Research 35:e128.
    • (2007) Nucleic Acids Research , vol.35
    • Perocchi, F.1    Xu, Z.2    Clauder-Munster, S.3    Steinmetz, L.M.4
  • 37
    • 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. 2009. H3 lysine 4 di-and tri-methylation deposited by cryptic transcription attenuates promoter activation. The EMBO Journal 28:1697-1707. doi: 10.1038/emboj.2009.108.
    • (2009) The EMBO Journal , vol.28 , pp. 1697-1707
    • Pinskaya, M.1    Gourvennec, S.2    Morillon, A.3
  • 38
    • 0028019848 scopus 로고
    • Characterization of sua7 mutations defines a domain of TFIIB involved in transcription start site selection in yeast
    • Pinto I, Wu WH, Na JG, Hampsey M. 1994. Characterization of sua7 mutations defines a domain of TFIIB involved in transcription start site selection in yeast. The Journal of Biological Chemistry 269:30569-30573.
    • (1994) The Journal of Biological Chemistry , vol.269 , pp. 30569-30573
    • Pinto, I.1    Wu, W.H.2    Na, J.G.3    Hampsey, M.4
  • 42
    • 64249090531 scopus 로고    scopus 로고
    • m RNA stability and the unfolding of gene expression in the long-period yeast metabolic cycle
    • Soranzo N, Zampieri M, Farina L, Altafini C. 2009. m RNA stability and the unfolding of gene expression in the long-period yeast metabolic cycle. BMC Systems Biology 3:18. doi: 10.1186/1752-0509-3-18.
    • (2009) BMC Systems Biology , vol.3 , pp. 18
    • Soranzo, N.1    Zampieri, M.2    Farina, L.3    Altafini, C.4
  • 43
    • 0027972417 scopus 로고
    • Sequence and promoter analysis of the highly expressed TEF gene of the filamentous fungus Ashbya gossypii
    • Steiner S, Philippsen P. 1994. Sequence and promoter analysis of the highly expressed TEF gene of the filamentous fungus Ashbya gossypii. Molecular & General Genetics 242:263-271. doi: 10.1007/BF00280415.
    • (1994) Molecular & General Genetics , vol.242 , pp. 263-271
    • Steiner, S.1    Philippsen, P.2
  • 45
    • 84875634162 scopus 로고    scopus 로고
    • Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration
    • Thorvaldsdottir H, Robinson JT, Mesirov JP. 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in Bioinformatics 14:178-192. doi: 10.1093/bib/bbs017.
    • (2013) Briefings in Bioinformatics , vol.14 , pp. 178-192
    • Thorvaldsdottir, H.1    Robinson, J.T.2    Mesirov, J.P.3
  • 46
    • 43749088127 scopus 로고    scopus 로고
    • Two strategies for gene regulation by promoter nucleosomes
    • Tirosh I, Barkai N. 2008. Two strategies for gene regulation by promoter nucleosomes. Genome Research 18:1084-1091. doi: 10.1101/gr.076059.108.
    • (2008) Genome Research , vol.18 , pp. 1084-1091
    • Tirosh, I.1    Barkai, N.2
  • 47
    • 84455200588 scopus 로고    scopus 로고
    • Single-molecule m RNA decay measurements reveal promoter-regulated m RNA stability in yeast
    • Trcek T, Larson DR, Moldón A, Query CC, Singer RH. 2011. Single-molecule m RNA decay measurements reveal promoter-regulated m RNA stability in yeast. Cell 147:1484-1497. doi: 10.1016/j.cell.2011.11.051.
    • (2011) Cell , vol.147 , pp. 1484-1497
    • Trcek, T.1    Larson, D.R.2    Moldón, A.3    Query, C.C.4    Singer, R.H.5
  • 48
    • 80555156654 scopus 로고    scopus 로고
    • Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization
    • Tsankov A, Yanagisawa Y, Rhind N, Regev A, Rando OJ. 2011. Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. Genome Research 21:1851-1862. doi: 10.1101/gr.122267.111.
    • (2011) Genome Research , vol.21 , pp. 1851-1862
    • Tsankov, A.1    Yanagisawa, Y.2    Rhind, N.3    Regev, A.4    Rando, O.J.5
  • 49
    • 27944487902 scopus 로고    scopus 로고
    • Logic of the yeast metabolic cycle: Temporal compartmentalization of cellular processes
    • Tu BP, Kudlicki A, Rowicka M, McKnight SL. 2005. Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science 310:1152-1158. doi: 10.1126/science.1120499.
    • (2005) Science , vol.310 , pp. 1152-1158
    • Tu, B.P.1    Kudlicki, A.2    Rowicka, M.3    McKnight, S.L.4
  • 50
    • 33747591416 scopus 로고    scopus 로고
    • Metabolic cycles as an underlying basis of biological oscillations
    • Tu BP, McKnight SL. 2006. Metabolic cycles as an underlying basis of biological oscillations. Nature Reviews. Molecular Cell Biology 7:696-701. doi: 10.1038/nrm1980.
    • (2006) Nature Reviews. Molecular Cell Biology , vol.7 , pp. 696-701
    • Tu, B.P.1    McKnight, S.L.2
  • 53
  • 54
    • 60349122111 scopus 로고    scopus 로고
    • A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome
    • Venters BJ, Pugh BF. 2009. A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome. Genome Research 19:360-371. doi: 10.1101/gr.084970.108.
    • (2009) Genome Research , vol.19 , pp. 360-371
    • Venters, B.J.1    Pugh, B.F.2
  • 59
    • 77956027418 scopus 로고    scopus 로고
    • Analyzing m RNA expression using single m RNA resolution fluorescent in situ hybridization
    • Zenklusen D, Singer RH. 2010. Analyzing m RNA expression using single m RNA resolution fluorescent in situ hybridization. Methods Enzymology 470:641-659. doi: 10.1016/S0076-6879(10)70026-4.
    • (2010) Methods Enzymology , vol.470 , pp. 641-659
    • Zenklusen, D.1    Singer, R.H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.