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Volumn 32, Issue 4, 2014, Pages 387-391

Massively parallel functional annotation of 3' untranslated regions

Author keywords

[No Author keywords available]

Indexed keywords

PROTEINS;

EID: 84900841403     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.2851     Document Type: Article
Times cited : (81)

References (40)
  • 1
    • 80051764752 scopus 로고    scopus 로고
    • Toward a systematic understanding of mRNA 3 untranslated regions
    • Zhao, W., Blagev, D., Pollack, J.L. & Erle, D.J. Toward a systematic understanding of mRNA 3? untranslated regions. Proc. Am. Thorac. Soc. 8, 163-166 (2011).
    • (2011) Proc. Am. Thorac. Soc , vol.8 , pp. 163-166
    • Zhao, W.1    Blagev, D.2    Pollack, J.L.3    Erle, D.J.4
  • 2
    • 31144448042 scopus 로고    scopus 로고
    • AU-rich elements and associated factors: Are there unifying principles?
    • Barreau, C., Paillard, L. & Osborne, H.B. AU-rich elements and associated factors: are there unifying principles? Nucleic Acids Res. 33, 7138-7150 (2005).
    • (2005) Nucleic Acids Res , vol.33 , pp. 7138-7150
    • Barreau, C.1    Paillard, L.2    Osborne, H.B.3
  • 3
    • 0036498828 scopus 로고    scopus 로고
    • A PUF family portrait: 3UTR regulation as a way of life
    • Wickens, M., Bernstein, D.S., Kimble, J. & Parker, R. A PUF family portrait: 3?UTR regulation as a way of life. Trends Genet. 18, 150-157 (2002).
    • (2002) Trends Genet , vol.18 , pp. 150-157
    • Wickens, M.1    Bernstein, D.S.2    Kimble, J.3    Parker, R.4
  • 4
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: Target recognition and regulatory functions
    • Bartel, D.P. MicroRNAs: target recognition and regulatory functions. Cell 136, 215-233 (2009).
    • (2009) Cell , vol.136 , pp. 215-233
    • Bartel, D.P.1
  • 5
    • 65249141709 scopus 로고    scopus 로고
    • Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells
    • Sharova, L.V. et al. Database for mRNA half-life of 19 977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells. DNA Res. 16, 45-58 (2009).
    • (2009) DNA Res , vol.16 , pp. 45-58
    • Sharova, L.V.1
  • 6
    • 0028788194 scopus 로고
    • AU-rich elements: Characterization and importance in mRNA degradation
    • Chen, C.Y. & Shyu, A.B. AU-rich elements: characterization and importance in mRNA degradation. Trends Biochem. Sci. 20, 465-470 (1995).
    • (1995) Trends Biochem. Sci , vol.20 , pp. 465-470
    • Chen, C.Y.1    Shyu, A.B.2
  • 7
    • 15244358503 scopus 로고    scopus 로고
    • Systematic discovery of regulatory motifs in human promoters and 3? UTRs by comparison of several mammals
    • Xie, X. et al. Systematic discovery of regulatory motifs in human promoters and 3? UTRs by comparison of several mammals. Nature 434, 338-345 (2005).
    • (2005) Nature , vol.434 , pp. 338-345
    • Xie, X.1
  • 8
    • 84860765680 scopus 로고    scopus 로고
    • Systematic discovery of structural elements governing stability of mammalian messenger RNAs
    • Goodarzi, H. et al. Systematic discovery of structural elements governing stability of mammalian messenger RNAs. Nature 485, 264-268 (2012).
    • (2012) Nature , vol.485 , pp. 264-268
    • Goodarzi, H.1
  • 9
    • 77950920903 scopus 로고    scopus 로고
    • Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
    • Hafner, M. et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141, 129-141 (2010).
    • (2010) Cell , vol.141 , pp. 129-141
    • Hafner, M.1
  • 11
    • 71849118573 scopus 로고    scopus 로고
    • High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis
    • Patwardhan, R.P. et al. High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nat. Biotechnol. 27, 1173-1175 (2009).
    • (2009) Nat. Biotechnol , vol.27 , pp. 1173-1175
    • Patwardhan, R.P.1
  • 12
    • 84863230316 scopus 로고    scopus 로고
    • Massively parallel functional dissection of mammalian enhancers in vivo
    • Patwardhan, R.P. et al. Massively parallel functional dissection of mammalian enhancers in vivo. Nat. Biotechnol. 30, 265-270 (2012).
    • (2012) Nat. Biotechnol , vol.30 , pp. 265-270
    • Patwardhan, R.P.1
  • 13
    • 84863229330 scopus 로고    scopus 로고
    • Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay
    • Melnikov, A. et al. Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nat. Biotechnol. 30, 271-277 (2012).
    • (2012) Nat. Biotechnol , vol.30 , pp. 271-277
    • Melnikov, A.1
  • 14
    • 0344586094 scopus 로고    scopus 로고
    • Analysis of the mechanism regulating the stability of rat macrophage inflammatory protein-2 mRNA in RBL-2H3 cells
    • Numahata, K. et al. Analysis of the mechanism regulating the stability of rat macrophage inflammatory protein-2 mRNA in RBL-2H3 cells. J. Cell. Biochem. 90, 976-986 (2003).
    • (2003) J. Cell. Biochem , vol.90 , pp. 976-986
    • Numahata, K.1
  • 15
    • 84862778053 scopus 로고    scopus 로고
    • Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish
    • Bazzini, A.A., Lee, M.T. & Giraldez, A.J. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 336, 233-237 (2012).
    • (2012) Science , vol.336 , pp. 233-237
    • Bazzini, A.A.1    Lee, M.T.2    Giraldez, A.J.3
  • 16
    • 84859632747 scopus 로고    scopus 로고
    • MiRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay
    • Djuranovic, S., Nahvi, A. & Green, R. miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science 336, 237-240 (2012).
    • (2012) Science , vol.336 , pp. 237-240
    • Djuranovic, S.1    Nahvi, A.2    Green, R.3
  • 17
    • 77955644289 scopus 로고    scopus 로고
    • Mammalian microRNAs predominantly act to decrease target mRNA levels
    • Guo, H., Ingolia, N.T., Weissman, J.S. & Bartel, D.P. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466, 835-840 (2010).
    • (2010) Nature , vol.466 , pp. 835-840
    • Guo, H.1    Ingolia, N.T.2    Weissman, J.S.3    Bartel, D.P.4
  • 18
    • 33745139539 scopus 로고    scopus 로고
    • Nitric oxide activation of Erk1/2 regulates the stability and translation of mRNA transcripts containing CU-rich elements
    • Wang, S. et al. Nitric oxide activation of Erk1/2 regulates the stability and translation of mRNA transcripts containing CU-rich elements. Nucleic Acids Res. 34, 3044-3056 (2006).
    • (2006) Nucleic Acids Res , vol.34 , pp. 3044-3056
    • Wang, S.1
  • 19
    • 52349122355 scopus 로고    scopus 로고
    • Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system
    • Galgano, A. et al. Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system. PLoS ONE 3, e3164 (2008).
    • (2008) PLoS ONE , vol.3
    • Galgano, A.1
  • 20
    • 44949255018 scopus 로고    scopus 로고
    • Ribonomic analysis of human Pum1 reveals cis-trans conservation across species despite evolution of diverse mRNA target sets
    • Morris, A.R., Mukherjee, N. & Keene, J.D. Ribonomic analysis of human Pum1 reveals cis-trans conservation across species despite evolution of diverse mRNA target sets. Mol. Cell. Biol. 28, 4093-4103 (2008).
    • (2008) Mol. Cell. Biol , vol.28 , pp. 4093-4103
    • Morris, A.R.1    Mukherjee, N.2    Keene, J.D.3
  • 21
    • 84880427394 scopus 로고    scopus 로고
    • A compendium of RNA-binding motifs for decoding gene regulation
    • Ray, D. et al. A compendium of RNA-binding motifs for decoding gene regulation. Nature 499, 172-177 (2013).
    • (2013) Nature , vol.499 , pp. 172-177
    • Ray, D.1
  • 22
    • 33646272409 scopus 로고    scopus 로고
    • Identification and classification of conserved RNA secondary structures in the human genome
    • Pedersen, J.S. et al. Identification and classification of conserved RNA secondary structures in the human genome. PLOS Comput. Biol. 2, e33 (2006).
    • (2006) PLOS Comput. Biol , vol.2
    • Pedersen, J.S.1
  • 23
    • 80455154984 scopus 로고    scopus 로고
    • Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs
    • Garcia, D.M. et al. Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat. Struct. Mol. Biol. 18, 1139-1146 (2011).
    • (2011) Nat. Struct. Mol. Biol , vol.18 , pp. 1139-1146
    • Garcia, D.M.1
  • 24
    • 46249092601 scopus 로고    scopus 로고
    • Proliferating cells express mRNAs with shortened 3 untranslated regions and fewer microRNA target sites
    • Sandberg, R., Neilson, J.R., Sarma, A., Sharp, P.A. & Burge, C.B. Proliferating cells express mRNAs with shortened 3? untranslated regions and fewer microRNA target sites. Science 320, 1643-1647 (2008).
    • (2008) Science , vol.320 , pp. 1643-1647
    • Sandberg, R.1    Neilson, J.R.2    Sarma, A.3    Sharp, P.A.4    Burge, C.B.5
  • 25
    • 68749113985 scopus 로고    scopus 로고
    • Widespread shortening of 3UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells
    • Mayr, C. & Bartel, D.P. Widespread shortening of 3?UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138, 673-684 (2009).
    • (2009) Cell , vol.138 , pp. 673-684
    • Mayr, C.1    Bartel, D.P.2
  • 26
    • 84890494960 scopus 로고    scopus 로고
    • 3? UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts
    • Spies, N., Burge, C.B. & Bartel, D.P. 3? UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts. Genome Res. 23, 2078-2090 (2013).
    • (2013) Genome Res , vol.23 , pp. 2078-2090
    • Spies, N.1    Burge, C.B.2    Bartel, D.P.3
  • 27
    • 84887053121 scopus 로고    scopus 로고
    • Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression
    • Lianoglou, S., Garg, V., Yang, J.L., Leslie, C.S. & Mayr, C. Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression. Genes Dev. 27, 2380-2396 (2013).
    • (2013) Genes Dev. , vol.27 , pp. 2380-2396
    • Lianoglou, S.1    Garg, V.2    Yang, J.L.3    Leslie, C.S.4    Mayr, C.5
  • 28
    • 84876847154 scopus 로고    scopus 로고
    • All SNPs are not created equal: Genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs
    • Schork, A.J. et al. All SNPs are not created equal: genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs. PLoS Genet. 9, e1003449 (2013).
    • (2013) PLoS Genet , vol.9
    • Schork, A.J.1
  • 29
    • 15244351083 scopus 로고    scopus 로고
    • Coordinate dual-gene transgenesis by lentiviral vectors carrying synthetic bidirectional promoters
    • Amendola, M., Venneri, M.A., Biffi, A., Vigna, E. & Naldini, L. Coordinate dual-gene transgenesis by lentiviral vectors carrying synthetic bidirectional promoters. Nat. Biotechnol. 23, 108-116 (2005).
    • (2005) Nat. Biotechnol , vol.23 , pp. 108-116
    • Amendola, M.1    Venneri, M.A.2    Biffi, A.3    Vigna, E.4    Naldini, L.5
  • 30
    • 0026720075 scopus 로고
    • Tight control of gene expression in mammalian cells by tetracycline-responsive promoters
    • Gossen, M. & Bujard, H. Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proc. Natl. Acad. Sci. USA 89, 5547-5551 (1992).
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 5547-5551
    • Gossen, M.1    Bujard, H.2
  • 31
    • 34748872768 scopus 로고    scopus 로고
    • Versatile applications of transcriptional pulsing to study mRNA turnover in mammalian cells
    • Chen, C.Y. et al. Versatile applications of transcriptional pulsing to study mRNA turnover in mammalian cells. RNA 13, 1775-1786 (2007).
    • (2007) RNA , vol.13 , pp. 1775-1786
    • Chen, C.Y.1
  • 33
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B. & Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 34
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and SAMtools
    • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 35
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European molecular biology open software suite
    • Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16, 276-277 (2000).
    • (2000) Trends Genet , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 36
    • 79958090979 scopus 로고    scopus 로고
    • DREME: Motif discovery in transcription factor ChIP-seq data
    • Bailey, T.L. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics 27, 1653-1659 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 1653-1659
    • Bailey, T.L.1
  • 37
    • 84877708543 scopus 로고    scopus 로고
    • Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs
    • Leppek, K. et al. Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs. Cell 153, 869-881 (2013).
    • (2013) Cell , vol.153 , pp. 869-881
    • Leppek, K.1
  • 38
    • 0030987239 scopus 로고    scopus 로고
    • Four highly stable eukaryotic mRNAs assemble 3 untranslated region RNA-protein complexes sharing cis and trans components
    • Holcik, M. & Liebhaber, S.A. Four highly stable eukaryotic mRNAs assemble 3? untranslated region RNA-protein complexes sharing cis and trans components. Proc. Natl. Acad. Sci. USA 94, 2410-2414 (1997).
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 2410-2414
    • Holcik, M.1    Liebhaber, S.A.2
  • 39
    • 79953300078 scopus 로고    scopus 로고
    • FIMO: Scanning for occurrences of a given motif
    • Grant, C.E., Bailey, T.L. & Noble, W.S. FIMO: scanning for occurrences of a given motif. Bioinformatics 27, 1017-1018 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 1017-1018
    • Grant, C.E.1    Bailey, T.L.2    Noble, W.S.3
  • 40
    • 0041523923 scopus 로고    scopus 로고
    • Decay rates of human mRNAs: Correlation with functional characteristics and sequence attributes
    • Yang, E. et al. Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. Genome Res. 13, 1863-1872 (2003).
    • (2003) Genome Res , vol.13 , pp. 1863-1872
    • Yang, E.1


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