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Volumn 39, Issue 4, 2011, Pages 1501-1509

Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL RNA; MESSENGER RNA; PROTEIN GBP2; PROTEIN HRB1; PROTEIN MRN1; PROTEIN NSR1; PROTEIN PIN4; PROTEIN PUF3; PROTEIN SGN1; PROTEIN SHE2; PROTEIN VTS1; PROTEIN WHI3; RNA BINDING PROTEIN; TRANSCRIPTOME; UNCLASSIFIED DRUG;

EID: 79952351662     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq920     Document Type: Article
Times cited : (58)

References (40)
  • 1
    • 54949148332 scopus 로고    scopus 로고
    • Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system
    • Hogan, D.J., Riordan, D.P., Gerber, A.P., Herschlag, D. and Brown, P.O. (2008) Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol., 6, e255.
    • (2008) PLoS Biol. , vol.6
    • Hogan, D.J.1    Riordan, D.P.2    Gerber, A.P.3    Herschlag, D.4    Brown, P.O.5
  • 2
    • 34250735674 scopus 로고    scopus 로고
    • RNA regulons: Coordination of post-transcriptional events
    • DOI 10.1038/nrg2111, PII NRG2111
    • Keene, J.D. (2007) RNA regulons: coordination of post-transcriptional events. Nat. Rev. Genet., 8, 533-543. (Pubitemid 46955210)
    • (2007) Nature Reviews Genetics , vol.8 , Issue.7 , pp. 533-543
    • Keene, J.D.1
  • 3
    • 19344365947 scopus 로고    scopus 로고
    • Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
    • Gerber, A.P., Herschlag, D. and Brown, P.O. (2004) Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol., 2, E79.
    • (2004) PLoS Biol. , vol.2
    • Gerber, A.P.1    Herschlag, D.2    Brown, P.O.3
  • 4
    • 0037313537 scopus 로고    scopus 로고
    • Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery
    • DOI 10.1038/ng1080
    • Hieronymus, H. and Silver, P.A. (2003) Genome-wide analysis of RNA-protein interactions illustrates specificity of the mRNA export machinery. Nat. Genet., 33, 155-161. (Pubitemid 36177066)
    • (2003) Nature Genetics , vol.33 , Issue.2 , pp. 155-161
    • Hieronymus, H.1    Silver, P.A.2
  • 6
    • 0036289532 scopus 로고    scopus 로고
    • Eukaryotic mRNPs may represent posttranscriptional operons
    • DOI 10.1016/S1097-2765(02)00559-2
    • Keene, J.D. and Tenenbaum, S.A. (2002) Eukaryotic mRNPs may represent posttranscriptional operons. Mol. Cell, 9, 1161-1167. (Pubitemid 34722296)
    • (2002) Molecular Cell , vol.9 , Issue.6 , pp. 1161-1167
    • Keene, J.D.1    Tenenbaum, S.A.2
  • 8
    • 0002759539 scopus 로고
    • Unsupervised learning of multiple motifs in biopolymers using expectation maximization
    • Bailey, T.L. and Elkan, C. (1995) Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Mach. Learn., 21, 51-80.
    • (1995) Mach. Learn. , vol.21 , pp. 51-80
    • Bailey, T.L.1    Elkan, C.2
  • 9
    • 35348955882 scopus 로고    scopus 로고
    • A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types
    • DOI 10.1016/j.molcel.2007.09.027, PII S1097276507006661
    • Elemento, O., Slonim, N. and Tavazoie, S. (2007) A universal framework for regulatory element discovery across all genomes and data types. Mol. Cell, 28, 337-350. (Pubitemid 47600005)
    • (2007) Molecular Cell , vol.28 , Issue.2 , pp. 337-350
    • Elemento, O.1    Slonim, N.2    Tavazoie, S.3
  • 10
    • 0027912333 scopus 로고
    • Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
    • Lawrence, C.E., Altschul, S.F., Boguski, M.S., Liu, J.S., Neuwald, A.F. and Wootton, J.C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
    • (1993) Science , vol.262 , pp. 208-214
    • Lawrence, C.E.1    Altschul, S.F.2    Boguski, M.S.3    Liu, J.S.4    Neuwald, A.F.5    Wootton, J.C.6
  • 11
    • 0031787969 scopus 로고    scopus 로고
    • Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
    • DOI 10.1038/nbt1098-939
    • Roth, F.P., Hughes, J.D., Estep, P.W. and Church, G.M. (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol., 16, 939-945. (Pubitemid 28483622)
    • (1998) Nature Biotechnology , vol.16 , Issue.10 , pp. 939-945
    • Roth, F.P.1    Hughes, J.D.2    Estep, P.W.3    Church, G.M.4
  • 13
    • 0042490664 scopus 로고    scopus 로고
    • The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators
    • DOI 10.1038/nsb956
    • Aviv, T., Lin, Z., Lau, S., Rendl, L.M., Sicheri, F. and Smibert, C.A. (2003) The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators. Nat. Struct. Biol., 10, 614-621. (Pubitemid 36944714)
    • (2003) Nature Structural Biology , vol.10 , Issue.8 , pp. 614-621
    • Aviv, T.1    Lin, Z.2    Lau, S.3    Rendl, L.M.4    Sicheri, F.5    Smibert, C.A.6
  • 14
    • 55549092781 scopus 로고    scopus 로고
    • Distinct roles for Khd1p in the localization and expression of bud-localized mRNAs in yeast
    • Hasegawa, Y., Irie, K. and Gerber, A.P. (2008) Distinct roles for Khd1p in the localization and expression of bud-localized mRNAs in yeast. RNA, 14, 2333-2347.
    • (2008) RNA , vol.14 , pp. 2333-2347
    • Hasegawa, Y.1    Irie, K.2    Gerber, A.P.3
  • 15
    • 0038487811 scopus 로고    scopus 로고
    • Poly(A)-binding proteins: Multifunctional scaffolds for the post-transcriptional control of gene expression
    • Mangus, D.A., Evans, M.C. and Jacobson, A. (2003) Poly(A)-binding proteins: multifunctional scaffolds for the post-transcriptional control of gene expression. Genome Biol., 4, 223.
    • (2003) Genome Biol. , vol.4 , pp. 223
    • Mangus, D.A.1    Evans, M.C.2    Jacobson, A.3
  • 16
    • 45549088326 scopus 로고    scopus 로고
    • The transcriptional landscape of the yeast genome defined by RNA sequencing
    • DOI 10.1126/science.1158441
    • 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. (Pubitemid 351929471)
    • (2008) Science , vol.320 , Issue.5881 , pp. 1344-1349
    • Nagalakshmi, U.1    Wang, Z.2    Waern, K.3    Shou, C.4    Raha, D.5    Gerstein, M.6    Snyder, M.7
  • 17
    • 0035921929 scopus 로고    scopus 로고
    • RNA-binding protein Nrd1 directs poly(A)-independent 3-end formation of RNA polymerase II transcripts
    • DOI 10.1038/35095090
    • 0-end formation of RNA polymerase II transcripts. Nature, 413, 327-331. (Pubitemid 32905855)
    • (2001) Nature , vol.413 , Issue.6853 , pp. 327-331
    • Steinmetz, E.J.1    Conrad, N.K.2    Brow, D.A.3    Corden, J.L.4
  • 18
    • 33744790273 scopus 로고    scopus 로고
    • Prediction of RNA secondary structure by free energy minimization
    • DOI 10.1016/j.sbi.2006.05.010, PII S0959440X06000819
    • Mathews, D.H. and Turner, D.H. (2006) Prediction of RNA secondary structure by free energy minimization. Curr. Opin. Struct. Biol., 16, 270-278. (Pubitemid 43831654)
    • (2006) Current Opinion in Structural Biology , vol.16 , Issue.3 , pp. 270-278
    • Mathews, D.H.1    Turner, D.H.2
  • 19
    • 0025074907 scopus 로고
    • Vitro selection of RNA molecules that bind specific ligands
    • Ellington, A.D. and Szostak, J.W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature, 346, 818-822.
    • (1990) Nature , vol.346 , pp. 818-822
    • Ellington, A.D.1    Szostak, J.W.2
  • 20
    • 0025194307 scopus 로고
    • Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
    • Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249, 505-510.
    • (1990) Science , vol.249 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 22
    • 0034388021 scopus 로고    scopus 로고
    • The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast
    • Olivas, W. and Parker, R. (2000) The Puf3 protein is a transcript-specific regulator of mRNA degradation in yeast. EMBO J., 19, 6602-6611.
    • (2000) EMBO J. , vol.19 , pp. 6602-6611
    • Olivas, W.1    Parker, R.2
  • 23
    • 32244436130 scopus 로고    scopus 로고
    • Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p
    • DOI 10.1038/nsmb1053, PII NSMB1053
    • Aviv, T., Lin, Z., Ben-Ari, G., Smibert, C.A. and Sicheri, F. (2006) Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p. Nat. Struct. Mol. Biol., 13, 168-176. (Pubitemid 43214721)
    • (2006) Nature Structural and Molecular Biology , vol.13 , Issue.2 , pp. 168-176
    • Aviv, T.1    Lin, Z.2    Ben-Ari, G.3    Smibert, C.A.4    Sicheri, F.5
  • 24
    • 66249108559 scopus 로고    scopus 로고
    • Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs
    • Foat, B.C. and Stormo, G.D. (2009) Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs. Mol. Syst. Biol., 5, 268.
    • (2009) Mol. Syst. Biol. , vol.5 , pp. 268
    • Foat, B.C.1    Stormo, G.D.2
  • 25
    • 57649137957 scopus 로고    scopus 로고
    • Whi3, a developmental regulator of budding yeast, binds a large set of mRNAs functionally related to the endoplasmic reticulum
    • Colomina, N., Ferrezuelo, F., Wang, H., Aldea, M. and Gari, E. (2008) Whi3, a developmental regulator of budding yeast, binds a large set of mRNAs functionally related to the endoplasmic reticulum. J. Biol. Chem., 283, 28670-28679.
    • (2008) J. Biol. Chem. , vol.283 , pp. 28670-28679
    • Colomina, N.1    Ferrezuelo, F.2    Wang, H.3    Aldea, M.4    Gari, E.5
  • 27
    • 18944388902 scopus 로고    scopus 로고
    • Identification of a conserved RNA motif essential for She2p recognition and mRNA localization to the yeast bud
    • DOI 10.1128/MCB.25.11.4752-4766.2005
    • Olivier, C., Poirier, G., Gendron, P., Boisgontier, A., Major, F. and Chartrand, P. (2005) Identification of a conserved RNA motif essential for She2p recognition and mRNA localization to the yeast bud. Mol. Cell Biol., 25, 4752-4766. (Pubitemid 40705777)
    • (2005) Molecular and Cellular Biology , vol.25 , Issue.11 , pp. 4752-4766
    • Olivier, C.1    Poirier, G.2    Gendron, P.3    Boisgontier, A.4    Major, F.5    Chartrand, P.6
  • 30
    • 0035261381 scopus 로고    scopus 로고
    • Genomic strategies to identify mammalian regulatory sequences
    • DOI 10.1038/35052548
    • Pennacchio, L.A. and Rubin, E.M. (2001) Genomic strategies to identify mammalian regulatory sequences. Nat. Rev. Genet., 2, 100-109. (Pubitemid 33674001)
    • (2001) Nature Reviews Genetics , vol.2 , Issue.2 , pp. 100-109
    • Pennacchio, L.A.1    Rubin, E.M.2
  • 32
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • DOI 10.1038/nature01644
    • Kellis, M., Patterson, N., Endrizzi, M., Birren, B. and Lander, E.S. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature, 423, 241-254. (Pubitemid 40852689)
    • (2003) Nature , vol.423 , Issue.6937 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 34
    • 23144463134 scopus 로고    scopus 로고
    • T-profiler: Scoring the activity of predefined groups of genes using gene expression data
    • DOI 10.1093/nar/gki484
    • Boorsma, A., Foat, B.C., Vis, D., Klis, F. and Bussemaker, H.J. (2005) T-profiler: scoring the activity of predefined groups of genes using gene expression data. Nucleic Acids Res., 33, W592-W595. (Pubitemid 44529991)
    • (2005) Nucleic Acids Research , vol.33 , Issue.WEB. SERV. ISS.
    • Boorsma, A.1    Foat, B.C.2    Vis, D.3    Klis, F.4    Bussemaker, H.J.5
  • 35
    • 24744453533 scopus 로고    scopus 로고
    • The promise and peril of continuous in vitro evolution
    • DOI 10.1007/s00239-004-0307-1
    • Johns, G.C. and Joyce, G.F. (2005) The promise and peril of continuous in vitro evolution. J. Mol. Evol., 61, 253-263. (Pubitemid 41298109)
    • (2005) Journal of Molecular Evolution , vol.61 , Issue.2 , pp. 253-263
    • Johns, G.C.1    Joyce, G.F.2
  • 36
    • 0032514717 scopus 로고    scopus 로고
    • Functional requirements for specific ligand recognition by a biotin- binding rna pseudoknot
    • DOI 10.1021/bi981371j
    • Wilson, C., Nix, J. and Szostak, J. (1998) Functional requirements for specific ligand recognition by a biotin-binding RNA pseudoknot. Biochemistry, 37, 14410-14419. (Pubitemid 28489047)
    • (1998) Biochemistry , vol.37 , Issue.41 , pp. 14410-14419
    • Wilson, C.1    Nix, J.2    Szostak, J.3
  • 37
    • 43349093418 scopus 로고    scopus 로고
    • RNA secondary structure analysis using the Vienna RNA package
    • Chapter 12, Unit
    • Hofacker, I.L. (2004) RNA secondary structure analysis using the Vienna RNA package. Curr. Protoc. Bioinformatics, Chapter 12, Unit 12, 12.
    • (2004) Curr. Protoc. Bioinformatics , vol.12 , pp. 12
    • Hofacker, I.L.1
  • 38
    • 67649854477 scopus 로고    scopus 로고
    • Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs
    • Granneman, S., Kudla, G., Petfalski, E. and Tollervey, D. (2009) Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs. Proc. Natl Acad. Sci. USA, 106, 9613-9618.
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 9613-9618
    • Granneman, S.1    Kudla, G.2    Petfalski, E.3    Tollervey, D.4


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