메뉴 건너뛰기




Volumn 20, Issue 8, 2013, Pages 923-928

Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; PROMOTER UPSTREAM TRANSCRIPT; RNA POLYMERASE II; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

EID: 84881474625     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.2640     Document Type: Article
Times cited : (214)

References (38)
  • 1
    • 60549115605 scopus 로고    scopus 로고
    • Post-transcriptional processing generates a diversity of 5′-modi-fied long and short RNAs
    • Affymetrix ENCODE Transcriptome Project, Cold Spring Harbor Laboratory ENCODE Transcriptome Project.
    • Affymetrix ENCODE Transcriptome Project, Cold Spring Harbor Laboratory ENCODE Transcriptome Project. Post-transcriptional processing generates a diversity of 5′-modi-fied long and short RNAs. Nature 457, 1028-1032 (2009).
    • (2009) Nature , vol.457 , pp. 1028-1032
  • 2
    • 70449953975 scopus 로고    scopus 로고
    • The complex eukaryotic transcriptome: Unexpected pervasive transcription and novel small RNAs
    • Jacquier, A. The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat. Rev. Genet. 10, 833-844 (2009).
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 833-844
    • Jacquier, A.1
  • 3
    • 84858440747 scopus 로고    scopus 로고
    • Metazoan promoters: Emerging characteristics and insights into transcriptional regulation
    • Lenhard, B., Sandelin, A. & Carninci, P. Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat. Rev. Genet. 13, 233-245 (2012).
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 233-245
    • Lenhard, B.1    Sandelin, A.2    Carninci, P.3
  • 4
    • 57849140661 scopus 로고    scopus 로고
    • Divergent transcription from active promoters
    • Seila, A.C. et al. Divergent transcription from active promoters. Science 322, 1849-1851 (2008).
    • (2008) Science , vol.322 , pp. 1849-1851
    • Seila, A.C.1
  • 5
    • 80052458531 scopus 로고    scopus 로고
    • Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes
    • Valen, E. et al. Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes. Nat. Struct. Mol. Biol. 18, 1075-1082 (2011).
    • (2011) Nat. Struct. Mol. Biol. , vol.18 , pp. 1075-1082
    • Valen, E.1
  • 6
    • 67349157682 scopus 로고    scopus 로고
    • Tiny RNAs associated with transcription start sites in animals
    • Taft, R.J. et al. Tiny RNAs associated with transcription start sites in animals. Nat. Genet. 41, 572-578 (2009).
    • (2009) Nat. Genet. , vol.41 , pp. 572-578
    • Taft, R.J.1
  • 8
    • 84874248583 scopus 로고    scopus 로고
    • Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells
    • Sigova, A.A. et al. Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc. Natl. Acad. Sci. USA 110, 2876-2881 (2013).
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110 , pp. 2876-2881
    • Sigova, A.A.1
  • 9
    • 57849123049 scopus 로고    scopus 로고
    • RNA exosome depletion reveals transcription upstream of active human promoters
    • Preker, P. et al. RNA exosome depletion reveals transcription upstream of active human promoters. Science 322, 1851-1854 (2008).
    • (2008) Science , vol.322 , pp. 1851-1854
    • Preker, P.1
  • 10
    • 79960569959 scopus 로고    scopus 로고
    • Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome
    • Flynn, R.A., Almada, A.E., Zamudio, J.R. & Sharp, P.A. Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome. Proc. Natl. Acad. Sci. USA 108, 10460-10465 (2011).
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 10460-10465
    • Flynn, R.A.1    Almada, A.E.2    Zamudio, J.R.3    Sharp, P.A.4
  • 11
    • 80051764912 scopus 로고    scopus 로고
    • PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters
    • Preker, P. et al. PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters. Nucleic Acids Res. 39, 7179-7193 (2011).
    • (2011) Nucleic Acids Res. , vol.39 , pp. 7179-7193
    • Preker, P.1
  • 12
    • 78650566210 scopus 로고    scopus 로고
    • Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation
    • Nechaev, S. & Adelman, K. Pol II waiting in the starting gates: regulating the transition from transcription initiation into productive elongation. Biochim. Biophys. Acta 1809, 34-45 (2011).
    • (2011) Biochim. Biophys. Acta , vol.1809 , pp. 34-45
    • Nechaev, S.1    Adelman, K.2
  • 13
    • 84862229469 scopus 로고    scopus 로고
    • RNA polymerase II pausing downstream of core histone genes is different from genes producing polyadenylated transcripts
    • Anamika, K., Gyenis, A., Poidevin, L., Poch, O. & Tora, L. RNA polymerase II pausing downstream of core histone genes is different from genes producing polyadenylated transcripts. PLoS ONE 7, e38769 (2012).
    • (2012) PLoS ONE , vol.7
    • Anamika, K.1    Gyenis, A.2    Poidevin, L.3    Poch, O.4    Tora, L.5
  • 14
    • 79955475464 scopus 로고    scopus 로고
    • Unravelling the means to an end: RNA poly-merase II transcription termination
    • Kuehner, J.N., Pearson, E.L. & Moore, C. Unravelling the means to an end: RNA poly-merase II transcription termination. Nat. Rev. Mol. Cell Biol. 12, 283-294 (2011).
    • (2011) Nat. Rev. Mol. Cell Biol. , vol.12 , pp. 283-294
    • Kuehner, J.N.1    Pearson, E.L.2    Moore, C.3
  • 15
    • 84861903786 scopus 로고    scopus 로고
    • A quantitative atlas of polyadenylation in five mammals
    • Derti, A. et al. A quantitative atlas of polyadenylation in five mammals. Genome Res. 22, 1173-1183 (2012).
    • (2012) Genome Res. , vol.22 , pp. 1173-1183
    • Derti, A.1
  • 16
    • 0033858202 scopus 로고    scopus 로고
    • Patterns of variant polyadenylation signal usage in human genes
    • DOI 10.1101/gr.10.7.1001
    • Beaudoing, E., Freier, S., Wyatt, J.R., Claverie, J.M. & Gautheret, D. Patterns of variant polyadenylation signal usage in human genes. Genome Res. 10, 1001-1010 (2000). (Pubitemid 30608635)
    • (2000) Genome Research , vol.10 , Issue.7 , pp. 1001-1010
    • Beaudoing, E.1    Freier, S.2    Wyatt, J.R.3    Claverie, J.-M.4    Gautheret, D.5
  • 17
    • 33747353311 scopus 로고    scopus 로고
    • A multispecies comparison of the meta-zoan 3′-processing downstream elements and the CstF-64 RNA recognition motif
    • Salisbury, J., Hutchison, K.W. & Graber, J.H. A multispecies comparison of the meta-zoan 3′-processing downstream elements and the CstF-64 RNA recognition motif. BMC Genomics 7, 55 (2006).
    • (2006) BMC Genomics , vol.7 , pp. 55
    • Salisbury, J.1    Hutchison, K.W.2    Graber, J.H.3
  • 18
    • 84863093884 scopus 로고    scopus 로고
    • Genome-wide analysis of pre-mRNA 3′ end processing reveals a decisive role of human cleavage factor i in the regulation of 3′ UTR length
    • Martin, G., Gruber, A. R., Keller, W. & Zavolan, M. Genome-wide analysis of pre-mRNA 3′ end processing reveals a decisive role of human cleavage factor I in the regulation of 3′ UTR length. Cell Rep. 1, 753-763 (2012).
    • (2012) Cell Rep. , vol.1 , pp. 753-763
    • Martin, G.1    Gruber, A.R.2    Keller, W.3    Zavolan, M.4
  • 19
    • 84869228761 scopus 로고    scopus 로고
    • Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation
    • Yao, C. et al. Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation. Proc. Natl. Acad. Sci. USA 109, 18773-18778 (2012).
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 18773-18778
    • Yao, C.1
  • 20
    • 80052447253 scopus 로고    scopus 로고
    • Ending the message: Poly(A) signals then and now
    • Proudfoot, N.J. Ending the message: poly(A) signals then and now. Genes Dev. 25, 1770-1782 (2011).
    • (2011) Genes Dev. , vol.25 , pp. 1770-1782
    • Proudfoot, N.J.1
  • 21
    • 66149187105 scopus 로고    scopus 로고
    • Transcription termination by nuclear RNA polymerases
    • Richard, P. & Manley, J.L. Transcription termination by nuclear RNA polymerases. Genes Dev. 23, 1247-1269 (2009).
    • (2009) Genes Dev. , vol.23 , pp. 1247-1269
    • Richard, P.1    Manley, J.L.2
  • 22
    • 57849109058 scopus 로고    scopus 로고
    • Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    • Core, L.J., Waterfall, J.J. & Lis, J.T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845-1848 (2008).
    • (2008) Science , vol.322 , pp. 1845-1848
    • Core, L.J.1    Waterfall, J.J.2    Lis, J.T.3
  • 23
    • 78649847070 scopus 로고    scopus 로고
    • U1 snRNP protects pre-mRNAs from premature cleavage and polyad-enylation
    • Kaida, D. et al. U1 snRNP protects pre-mRNAs from premature cleavage and polyad-enylation. Nature 468, 664-668 (2010).
    • (2010) Nature , vol.468 , pp. 664-668
    • Kaida, D.1
  • 24
    • 84868139307 scopus 로고    scopus 로고
    • Defining the status of RNA polymerase at promoters
    • Core, L. J. et al. Defining the status of RNA polymerase at promoters. Cell Rep. 2, 1025-1035 (2012).
    • (2012) Cell Rep. , vol.2 , pp. 1025-1035
    • Core, L.J.1
  • 26
    • 49449105283 scopus 로고    scopus 로고
    • Phosphorylation of the RNA polymerase II C-terminal domain dictates transcription termination choice
    • Gudipati, R.K., Villa, T., Boulay, J. & Libri, D. Phosphorylation of the RNA polymerase II C-terminal domain dictates transcription termination choice. Nat. Struct. Mol. Biol. 15, 786-794 (2008).
    • (2008) Nat. Struct. Mol. Biol. , vol.15 , pp. 786-794
    • Gudipati, R.K.1    Villa, T.2    Boulay, J.3    Libri, D.4
  • 27
    • 70449641057 scopus 로고    scopus 로고
    • Progression through the RNA polymerase II CTD cycle
    • Buratowski, S. Progression through the RNA polymerase II CTD cycle. Mol. Cell 36, 541-546 (2009).
    • (2009) Mol. Cell , vol.36 , pp. 541-546
    • Buratowski, S.1
  • 28
    • 60549114880 scopus 로고    scopus 로고
    • Widespread bidirectional promoters are the major source of cryptic transcripts in yeast
    • Neil, H. et al. Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 457, 1038-1042 (2009).
    • (2009) Nature , vol.457 , pp. 1038-1042
    • Neil, H.1
  • 29
    • 60549108380 scopus 로고    scopus 로고
    • Bidirectional promoters generate pervasive transcription in yeast
    • Xu, Z. et al. Bidirectional promoters generate pervasive transcription in yeast. Nature 457, 1033-1037 (2009).
    • (2009) Nature , vol.457 , pp. 1033-1037
    • Xu, Z.1
  • 30
    • 0037335613 scopus 로고    scopus 로고
    • Downstream elements of mammalian pre-mRNA polyadenylation signals: Primary, secondary and higher-order structures
    • DOI 10.1093/nar/gkg241
    • Zarudnaya, M.I., Kolomiets, I.M., Potyahaylo, A.L. & Hovorun, D.M. Downstream elements of mammalian pre-mRNA polyadenylation signals: primary, secondary and higher-order structures. Nucleic Acids Res. 31, 1375-1386 (2003). (Pubitemid 36304898)
    • (2003) Nucleic Acids Research , vol.31 , Issue.5 , pp. 1375-1386
    • Zarudnaya, M.I.1    Kolomiets, I.M.2    Potyahaylo, A.L.3    Hovorun, D.M.4
  • 31
    • 84867154009 scopus 로고    scopus 로고
    • Promoter-proximal polyadenylation sites reduce transcription activity
    • Andersen, P.K., Lykke-Andersen, S. & Jensen, T.H. Promoter-proximal polyadenylation sites reduce transcription activity. Genes Dev. 26, 2169-2179 (2012).
    • (2012) Genes Dev. , vol.26 , pp. 2169-2179
    • Andersen, P.K.1    Lykke-Andersen, S.2    Jensen, T.H.3
  • 32
    • 80555139654 scopus 로고    scopus 로고
    • CAGE (cap analysis of gene expression): A protocol for the detection of promoter and transcriptional networks
    • Takahashi, H., Kato, S., Murata, M. & Carninci, P. CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks. Methods Mol. Biol. 786, 181-200 (2012).
    • (2012) Methods Mol. Biol. , vol.786 , pp. 181-200
    • Takahashi, H.1    Kato, S.2    Murata, M.3    Carninci, P.4
  • 33
    • 84871809302 scopus 로고    scopus 로고
    • STAR: Ultrafast universal RNA-seq aligner
    • Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 15-21
    • Dobin, A.1
  • 35
    • 84876385823 scopus 로고    scopus 로고
    • An efficient method for genome-wide polyadenylation site mapping and RNA quantification
    • Wilkening, S. et al. An efficient method for genome-wide polyadenylation site mapping and RNA quantification. Nucleic Acids Res. 41, e65 (2013).
    • (2013) Nucleic Acids Res. , vol.41
    • Wilkening, S.1
  • 36
    • 77951820899 scopus 로고    scopus 로고
    • Fast and SNP-tolerant detection of complex variants and splicing in short reads
    • Wu, T.D. & Nacu, S. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26, 873-881 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 873-881
    • Wu, T.D.1    Nacu, S.2
  • 37
    • 46049107540 scopus 로고    scopus 로고
    • Asap: A framework for over-representation statistics for transcription factor binding sites
    • Marstrand, T. T. et al. Asap: a framework for over-representation statistics for transcription factor binding sites. PloS One 3, e1623 (2008).
    • (2008) PloS One , vol.3
    • Marstrand, T.T.1
  • 38
    • 75549083247 scopus 로고    scopus 로고
    • JASPAR 2010: The greatly expanded open-access database of transcription factor binding profiles
    • Portales-Casamar, E. et al. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. 38, D105-D110 (2010).
    • (2010) Nucleic Acids Res. , vol.38
    • Portales-Casamar, E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.