메뉴 건너뛰기




Volumn 44, Issue 1, 2016, Pages 377-386

Epitope-tagged yeast strains reveal promoter driven changes to 3′-end formation and convergent antisense-transcription from common 3′ UTRs

Author keywords

[No Author keywords available]

Indexed keywords

3' UNTRANSLATED REGION; ADH1 GENE; ANTISENSE TRANSCRIPTION; ARTICLE; CONTROLLED STUDY; CYC1 GENE; FUNGAL STRAIN; GENE; GENE LOCUS; GENETIC TRANSCRIPTION; NONHUMAN; POLYADENYLATION; PRIORITY JOURNAL; PROMOTER REGION; SACCHAROMYCES CEREVISIAE; STEADY STATE; TRANSCRIPTION REGULATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; YEAST;

EID: 84959544574     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv1022     Document Type: Article
Times cited : (6)

References (46)
  • 1
    • 0033529707 scopus 로고    scopus 로고
    • Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis
    • Winzeler,E.A., Shoemaker,D.D. and Astromoff,A. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science, 285, 901-906.
    • (1999) Science , vol.285 , pp. 901-906
    • Winzeler, E.A.1    Shoemaker, D.D.2    Astromoff, A.3
  • 7
    • 60549114880 scopus 로고    scopus 로고
    • Widespread bidirectional promoters are the major source of cryptic transcripts in yeast
    • Neil,H., Malabat,C., d'Aubenton-Carafa,Y., Xu,Z., Steinmetz,L.M. and Jacquier,A. (2009) Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature, 457, 1038-1042.
    • (2009) Nature , vol.457 , pp. 1038-1042
    • Neil, H.1    Malabat, C.2    D'Aubenton-Carafa, Y.3    Xu, Z.4    Steinmetz, L.M.5    Jacquier, A.6
  • 9
    • 45549088326 scopus 로고    scopus 로고
    • The transcriptional landscape of the yeast genome defined by RNA sequencing
    • Nagalakshmi,U., Wang,Z., Waern,K., Shou,C., Raha,D., Gerstein,M. and Snyder,M. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 320, 1344-1349.
    • (2008) Science , vol.320 , pp. 1344-1349
    • Nagalakshmi, U.1    Wang, Z.2    Waern, K.3    Shou, C.4    Raha, D.5    Gerstein, M.6    Snyder, M.7
  • 10
    • 79953014914 scopus 로고    scopus 로고
    • Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq
    • Shepard,P.J., Choi,E.A., Lu,J., Flanagan,L.A., Hertel,K.J. and Shi,Y. (2011) Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. RNA, 17, 761-772.
    • (2011) RNA , vol.17 , pp. 761-772
    • Shepard, P.J.1    Choi, E.A.2    Lu, J.3    Flanagan, L.A.4    Hertel, K.J.5    Shi, Y.6
  • 12
    • 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. and Stutz,F. (2007) Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae. Cell, 131, 706-717.
    • (2007) Cell , vol.131 , pp. 706-717
    • Camblong, J.1    Iglesias, N.2    Fickentscher, C.3    Dieppois, G.4    Stutz, F.5
  • 14
    • 84908395055 scopus 로고    scopus 로고
    • ATP-dependent chromatin remodeling shapes the long noncoding RNA landscape
    • Alcid,E.A. and Tsukiyama,T. (2014) ATP-dependent chromatin remodeling shapes the long noncoding RNA landscape. Genes Dev., 28, 2348-2360.
    • (2014) Genes Dev. , vol.28 , pp. 2348-2360
    • Alcid, E.A.1    Tsukiyama, T.2
  • 15
    • 0037173089 scopus 로고    scopus 로고
    • Transcriptional collision between convergent genes in budding yeast
    • Prescott,E.M. and Proudfoot,N.J. (2002) Transcriptional collision between convergent genes in budding yeast. Proc. Natl. Acad. Sci. U.S.A., 99, 8796-8801.
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 8796-8801
    • Prescott, E.M.1    Proudfoot, N.J.2
  • 17
    • 84896692153 scopus 로고    scopus 로고
    • 3′ Untranslated regions mediate transcriptional interference between convergent genes both locally and ectopically in Saccharomyces cerevisiae
    • Wang,L., Jiang,N., Wang,L., Fang,O., Leach,L.J., Hu,X. and Luo,Z. (2014) 3′ Untranslated regions mediate transcriptional interference between convergent genes both locally and ectopically in Saccharomyces cerevisiae. PLoS Genet., 10, e1004021.
    • (2014) PLoS Genet. , vol.10
    • Wang, L.1    Jiang, N.2    Wang, L.3    Fang, O.4    Leach, L.J.5    Hu, X.6    Luo, Z.7
  • 19
    • 78649910014 scopus 로고    scopus 로고
    • Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation
    • Ozsolak,F., Kapranov,P., Foissac,S., Kim,S.W., Fishilevich,E., Monaghan,A.P., John,B. and Milos,P.M. (2010) Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell, 143, 1018-1029.
    • (2010) Cell , vol.143 , pp. 1018-1029
    • Ozsolak, F.1    Kapranov, P.2    Foissac, S.3    Kim, S.W.4    Fishilevich, E.5    Monaghan, A.P.6    John, B.7    Milos, P.M.8
  • 20
    • 84937908672 scopus 로고    scopus 로고
    • PAT-seq: A method to study the integration of 3′-UTR dynamics with gene expression in the eukaryotic transcriptome
    • Harrison,P.F., Powell,D.R., Clancy,J.L., Preiss,T., Boag,P.R., Traven,A., Seemann,T. and Beilharz,T.H. (2015) PAT-seq: a method to study the integration of 3′-UTR dynamics with gene expression in the eukaryotic transcriptome. RNA, 21, 1502-1510.
    • (2015) RNA , vol.21 , pp. 1502-1510
    • Harrison, P.F.1    Powell, D.R.2    Clancy, J.L.3    Preiss, T.4    Boag, P.R.5    Traven, A.6    Seemann, T.7    Beilharz, T.H.8
  • 21
    • 84861374632 scopus 로고    scopus 로고
    • ePAT: A simple method to tag adenylated RNA to measure poly(A)-tail length and other 3′ RACE applications
    • Janicke,A., Vancuylenberg,J., Boag,P.R., Traven,A. and Beilharz,T.H. (2012) ePAT: A simple method to tag adenylated RNA to measure poly(A)-tail length and other 3′ RACE applications. RNA, 18, 1289-1295.
    • (2012) RNA , vol.18 , pp. 1289-1295
    • Janicke, A.1    Vancuylenberg, J.2    Boag, P.R.3    Traven, A.4    Beilharz, T.H.5
  • 22
    • 84865083753 scopus 로고    scopus 로고
    • The mRNA decay pathway regulates the expression of the Flo11 adhesin and biofilm formation in Saccharomyces cerevisiae
    • Lo,T.L., Qu,Y., Uwamahoro,N., Quenault,T., Beilharz,T.H. and Traven,A. (2012) The mRNA decay pathway regulates the expression of the Flo11 adhesin and biofilm formation in Saccharomyces cerevisiae. Genetics, 191, 1387-1391.
    • (2012) Genetics , vol.191 , pp. 1387-1391
    • Lo, T.L.1    Qu, Y.2    Uwamahoro, N.3    Quenault, T.4    Beilharz, T.H.5    Traven, A.6
  • 24
    • 84867028082 scopus 로고    scopus 로고
    • Transcriptional profiling of a yeast colony provides new insight into the heterogeneity of multicellular fungal communities
    • Traven,A., Janicke,A., Harrison,P., Swaminathan,A., Seemann,T. and Beilharz,T.H. (2012) Transcriptional profiling of a yeast colony provides new insight into the heterogeneity of multicellular fungal communities. PloS One, 7, e46243.
    • (2012) PloS One , vol.7
    • Traven, A.1    Janicke, A.2    Harrison, P.3    Swaminathan, A.4    Seemann, T.5    Beilharz, T.H.6
  • 25
    • 34250895717 scopus 로고    scopus 로고
    • Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome
    • Beilharz,T.H. and Preiss,T. (2007) Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome. RNA, 13, 982-997.
    • (2007) RNA , vol.13 , pp. 982-997
    • Beilharz, T.H.1    Preiss, T.2
  • 26
    • 0024687518 scopus 로고
    • Mutational analysis of a yeast transcriptional terminator
    • Osborne,B.I. and Guarente,L. (1989) Mutational analysis of a yeast transcriptional terminator. Proc. Natl. Acad. Sci. U.S.A., 86, 4097-4101.
    • (1989) Proc. Natl. Acad. Sci. U.S.A. , vol.86 , pp. 4097-4101
    • Osborne, B.I.1    Guarente, L.2
  • 28
    • 34247629588 scopus 로고    scopus 로고
    • Genetic reconstruction of a functional transcriptional regulatory network
    • Hu,Z., Killion,P.J. and Iyer,V.R. (2007) Genetic reconstruction of a functional transcriptional regulatory network. Nat. Genet., 39, 683-687.
    • (2007) Nat. Genet. , vol.39 , pp. 683-687
    • Hu, Z.1    Killion, P.J.2    Iyer, V.R.3
  • 30
    • 84885784559 scopus 로고    scopus 로고
    • Yeast hEST1A/B (SMG5/6)-like proteins contribute to environment-sensing adaptive gene expression responses
    • Lai,X., Beilharz,T., Au,W.C., Hammet,A., Preiss,T., Basrai,M.A. and Heierhorst,J. (2013) Yeast hEST1A/B (SMG5/6)-like proteins contribute to environment-sensing adaptive gene expression responses. G3 (Bethesda), 3, 1649-1659.
    • (2013) G3 (Bethesda) , vol.3 , pp. 1649-1659
    • Lai, X.1    Beilharz, T.2    Au, W.C.3    Hammet, A.4    Preiss, T.5    Basrai, M.A.6    Heierhorst, J.7
  • 31
    • 81255198360 scopus 로고    scopus 로고
    • Exonucleases and endonucleases involved in polyadenylation-assisted RNA decay
    • Slomovic,S. and Schuster,G. (2011) Exonucleases and endonucleases involved in polyadenylation-assisted RNA decay. Wiley Interdisciplinary Rev. RNA, 2, 106-123.
    • (2011) Wiley Interdisciplinary Rev. RNA , vol.2 , pp. 106-123
    • Slomovic, S.1    Schuster, G.2
  • 32
    • 0037155584 scopus 로고    scopus 로고
    • Exosome-mediated recognition and degradation of mRNAs lacking a termination codon
    • van Hoof,A., Frischmeyer,P.A., Dietz,H.C. and Parker,R. (2002) Exosome-mediated recognition and degradation of mRNAs lacking a termination codon. Science, 295, 2262-2264.
    • (2002) Science , vol.295 , pp. 2262-2264
    • Van Hoof, A.1    Frischmeyer, P.A.2    Dietz, H.C.3    Parker, R.4
  • 33
    • 84871865476 scopus 로고    scopus 로고
    • Ribosome-associated complex and Ssb are required for translational repression induced by polylysine segments within nascent chains
    • Chiabudini,M., Conz,C., Reckmann,F. and Rospert,S. (2012) Ribosome-associated complex and Ssb are required for translational repression induced by polylysine segments within nascent chains. Mol. Cell. Biol., 32, 4769-4779.
    • (2012) Mol. Cell. Biol. , vol.32 , pp. 4769-4779
    • Chiabudini, M.1    Conz, C.2    Reckmann, F.3    Rospert, S.4
  • 34
    • 0036715205 scopus 로고    scopus 로고
    • Non-stop decay - A new mRNA surveillance pathway
    • Vasudevan,S., Peltz,S.W. and Wilusz,C.J. (2002) Non-stop decay - a new mRNA surveillance pathway. Bioessays, 24, 785-788.
    • (2002) Bioessays , vol.24 , pp. 785-788
    • Vasudevan, S.1    Peltz, S.W.2    Wilusz, C.J.3
  • 35
    • 33645277360 scopus 로고    scopus 로고
    • Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation
    • Doma,M.K. and Parker,R. (2006) Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature, 440, 561-564.
    • (2006) Nature , vol.440 , pp. 561-564
    • Doma, M.K.1    Parker, R.2
  • 37
    • 84887995915 scopus 로고    scopus 로고
    • Gene regulation by antisense transcription
    • Pelechano,V. and Steinmetz,L.M. (2013) Gene regulation by antisense transcription. Nat. Rev. Genet., 14, 880-893.
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 880-893
    • Pelechano, V.1    Steinmetz, L.M.2
  • 38
    • 33750814968 scopus 로고    scopus 로고
    • Antisense transcription controls cell fate in Saccharomyces cerevisiae
    • Hongay,C.F., Grisafi,P.L., Galitski,T. and Fink,G.R. (2006) Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell, 127, 735-745.
    • (2006) Cell , vol.127 , pp. 735-745
    • Hongay, C.F.1    Grisafi, P.L.2    Galitski, T.3    Fink, G.R.4
  • 39
    • 84876441383 scopus 로고    scopus 로고
    • Making ends meet: Coordination between RNA 3′-end processing and transcription initiation
    • Andersen,P.K., Jensen,T.H. and Lykke-Andersen,S. (2013) Making ends meet: coordination between RNA 3′-end processing and transcription initiation. Wiley Interdisciplinary Rev. RNA, 4, 233-246.
    • (2013) Wiley Interdisciplinary Rev. RNA , vol.4 , pp. 233-246
    • Andersen, P.K.1    Jensen, T.H.2    Lykke-Andersen, S.3
  • 40
    • 80053413109 scopus 로고    scopus 로고
    • Transcriptional activity regulates alternative cleavage and polyadenylation
    • Ji,Z., Luo,W., Li,W., Hoque,M., Pan,Z., Zhao,Y. and Tian,B. (2011) Transcriptional activity regulates alternative cleavage and polyadenylation. Mol. Syst. Biol., 7, 534-547.
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 534-547
    • Ji, Z.1    Luo, W.2    Li, W.3    Hoque, M.4    Pan, Z.5    Zhao, Y.6    Tian, B.7
  • 41
    • 81255210985 scopus 로고    scopus 로고
    • Transcriptional activators enhance polyadenylation of mRNA precursors
    • Nagaike,T. and Manley,J.L. (2011) Transcriptional activators enhance polyadenylation of mRNA precursors. RNA Biol., 8, 964-967.
    • (2011) RNA Biol. , vol.8 , pp. 964-967
    • Nagaike, T.1    Manley, J.L.2
  • 44
    • 79960445493 scopus 로고    scopus 로고
    • Localization of mRNAs coding for mitochondrial proteins in the yeast Saccharomyces cerevisiae
    • Gadir,N., Haim-Vilmovsky,L., Kraut-Cohen,J. and Gerst,J.E. (2011) Localization of mRNAs coding for mitochondrial proteins in the yeast Saccharomyces cerevisiae. RNA, 17, 1551-1565.
    • (2011) RNA , vol.17 , pp. 1551-1565
    • Gadir, N.1    Haim-Vilmovsky, L.2    Kraut-Cohen, J.3    Gerst, J.E.4
  • 45
    • 84937925237 scopus 로고    scopus 로고
    • MS2 coat proteins bound to yeast mRNAs block 5′ to 3′ degradation and trap mRNA decay products: Implications for the localization of mRNAs by MS2-MCP system
    • Garcia,J.F. and Parker,R. (2015) MS2 coat proteins bound to yeast mRNAs block 5′ to 3′ degradation and trap mRNA decay products: implications for the localization of mRNAs by MS2-MCP system. RNA, 21, 1393-1395.
    • (2015) RNA , vol.21 , pp. 1393-1395
    • Garcia, J.F.1    Parker, R.2
  • 46
    • 0032775010 scopus 로고    scopus 로고
    • Epitope tagging of yeast genes using a PCR-based strategy: More tags and improved practical routines
    • Knop,M., Siegers,K., Pereira,G., Zachariae,W., Winsor,B., Nasmyth,K. and Schiebel,E. (1999) Epitope tagging of yeast genes using a PCR-based strategy: more tags and improved practical routines. Yeast, 15, 963-972.
    • (1999) Yeast , vol.15 , pp. 963-972
    • Knop, M.1    Siegers, K.2    Pereira, G.3    Zachariae, W.4    Winsor, B.5    Nasmyth, K.6    Schiebel, E.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.