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Volumn 22, Issue 10, 2012, Pages 2031-2042

Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution

Author keywords

[No Author keywords available]

Indexed keywords

RNA; SMALL NUCLEOLAR RNA;

EID: 84866171651     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.131847.111     Document Type: Article
Times cited : (119)

References (41)
  • 1
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 57: 289-300.
    • (1995) J R Stat Soc ser B Methodol , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 3
    • 77953798171 scopus 로고    scopus 로고
    • Down-regulation of a host microRNA by a Herpesvirus saimiri noncoding RNA
    • Cazalla D, Yario T, Steitz JA. 2010. Down-regulation of a host microRNA by a Herpesvirus saimiri noncoding RNA. Science 328: 1563-1566.
    • (2010) Science , vol.328 , pp. 1563-1566
    • Cazalla, D.1    Yario, T.2    Steitz, J.A.3
  • 4
    • 0029461958 scopus 로고
    • Modification of the TRI ReagentT procedure for isolation of RNA from polysaccharide- and proteoglycan-rich sources
    • Chomczynski P, Mackey K. 1995. Short technical reports. Modification of the TRI reagent procedure for isolation of RNA from polysaccharide- and proteoglycan-rich sources. Biotechniques 19: 942-945. (Pubitemid 3021405)
    • (1995) BioTechniques , vol.19 , Issue.6 , pp. 942-945
    • Chomczynski, P.1    Mackey, K.2
  • 5
    • 13844281888 scopus 로고    scopus 로고
    • Biosynthetic labeling of RNA with uracil phosphoribosyltransferase allows cell-specific microarray analysis of mRNA synthesis and decay
    • DOI 10.1038/nbt1061
    • Cleary MD, Meiering CD, Jan E, Guymon R, Boothroyd JC. 2005. Biosynthetic labeling of RNA with uracil phosphoribosyltransferase allows cell-specific microarray analysis of mRNA synthesis and decay. Nat Biotechnol 23: 232-237. (Pubitemid 40255335)
    • (2005) Nature Biotechnology , vol.23 , Issue.2 , pp. 232-237
    • Cleary, M.D.1    Meiering, C.D.2    Jan, E.3    Guymon, R.4    Boothroyd, J.C.5
  • 6
    • 0033064680 scopus 로고    scopus 로고
    • The stability and fate of a spliced intron from vertebrate cells
    • DOI 10.1017/S1355838299981190
    • Clement JQ, Qian L, Kaplinsky N, Wilkinson MF. 1999. The stability and fate of a spliced intron from vertebrate cells. RNA 5: 206-220. (Pubitemid 29079281)
    • (1999) RNA , vol.5 , Issue.2 , pp. 206-220
    • Clement, J.Q.1    Qian, L.2    Kaplinsky, N.3    Wilkinson, M.F.4
  • 7
    • 67649933366 scopus 로고    scopus 로고
    • Eukaryotic snoRNAs: A paradigm for gene expression flexibility
    • Dieci G, Preti M, Montanini B. 2009. Eukaryotic snoRNAs: A paradigm for gene expression flexibility. Genomics 94: 83-88.
    • (2009) Genomics , vol.94 , pp. 83-88
    • Dieci, G.1    Preti, M.2    Montanini, B.3
  • 10
    • 33644856084 scopus 로고    scopus 로고
    • Exon tethering in transcription by RNA polymerase II
    • DOI 10.1016/j.molcel.2006.01.032, PII S1097276506000803
    • Dye MJ, Gromak N, Proudfoot NJ. 2006. Exon tethering in transcription by RNA polymerase II. Mol Cell 21: 849-859. (Pubitemid 43376134)
    • (2006) Molecular Cell , vol.21 , Issue.6 , pp. 849-859
    • Dye, M.J.1    Gromak, N.2    Proudfoot, N.J.3
  • 11
    • 70350035567 scopus 로고    scopus 로고
    • Metabolic tagging and purification of nascent RNA: Implications for transcriptomics
    • Friedel CC, Dölken L. 2009. Metabolic tagging and purification of nascent RNA: Implications for transcriptomics. Mol Biosyst 5: 1271-1278.
    • (2009) Mol Biosyst , vol.5 , pp. 1271-1278
    • Friedel, C.C.1    Dölken, L.2
  • 12
    • 73049097101 scopus 로고    scopus 로고
    • Conserved principles of mammalian transcriptional regulation revealed by RNA half-life
    • doi: 10.1093/nar/gkp542
    • Friedel CC, Dölken L, Ruzsics Z, Koszinowski UH, Zimmer R. 2009. Conserved principles of mammalian transcriptional regulation revealed by RNA half-life. Nucleic Acids Res 37: e115. doi: 10.1093/nar/gkp542.
    • (2009) Nucleic Acids Res , vol.37
    • Friedel, C.C.1    Dölken, L.2    Ruzsics, Z.3    Koszinowski, U.H.4    Zimmer, R.5
  • 14
    • 0043172414 scopus 로고    scopus 로고
    • Splicing-dependent and -independent modes of assembly for intron-encoded box C/D snoRNPs in mammalian cells
    • DOI 10.1016/S1097-2765(03)00267-3
    • Hirose T, Shu MD, Steitz JA. 2003. Splicing-dependent and -independent modes of assembly for intron-encoded box C/D snoRNPs in mammalian cells. Mol Cell 12: 113-123. (Pubitemid 36945040)
    • (2003) Molecular Cell , vol.12 , Issue.1 , pp. 113-123
    • Hirose, T.1    Shu, M.-D.2    Steitz, J.A.3
  • 15
  • 18
    • 67749113808 scopus 로고    scopus 로고
    • Transcriptional regulatory circuits: Predicting numbers from alphabets
    • Kim HD, Shay T, O'Shea EK, Regev A. 2009. Transcriptional regulatory circuits: Predicting numbers from alphabets. Science 325: 429-432.
    • (2009) Science , vol.325 , pp. 429-432
    • Kim, H.D.1    Shay, T.2    O'Shea, E.K.3    Regev, A.4
  • 19
    • 0037133942 scopus 로고    scopus 로고
    • Small nucleolar RNAs: An abundant group of noncoding RNAs with diverse cellular functions
    • DOI 10.1016/S0092-8674(02)00718-3
    • Kiss T. 2002. Small nucleolar RNAs: An abundant group of noncoding RNAs with diverse cellular functions. Cell 109: 145-148. (Pubitemid 34518252)
    • (2002) Cell , vol.109 , Issue.2 , pp. 145-148
    • Kiss, T.1
  • 20
    • 0023672447 scopus 로고
    • Spliceosome assembly involves the binding and release of U4 small nuclear ribonucleoprotein
    • Lamond AI, Konarska MM, Grabowski PJ, Sharp PA. 1988. Spliceosome assembly involves the binding and release of U4 small nuclear ribonucleoprotein. Proc Natl Acad Sci 85: 411-415.
    • (1988) Proc Natl Acad Sci , vol.85 , pp. 411-415
    • Lamond, A.I.1    Konarska, M.M.2    Grabowski, P.J.3    Sharp, P.A.4
  • 21
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • doi: 10.1186/gb-2009-10-3-r25
    • Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25. doi: 10.1186/gb-2009-10-3-r25.
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 22
    • 0018063623 scopus 로고
    • Incorporation of 6-thioguanosine and 4-thiouridine into RNA. Application to isolation of newly synthesised RNA by affinity chromatography
    • Melvin WT, Milne HB, Slater AA, Allen HJ, Keir HM. 1978. Incorporation of 6-thioguanosine and 4-thiouridine into RNA. Application to isolation of newly synthesised RNA by affinity chromatography. Eur J Biochem 92: 373-379.
    • (1978) Eur J Biochem , vol.92 , pp. 373-379
    • Melvin, W.T.1    Milne, H.B.2    Slater, A.A.3    Allen, H.J.4    Keir, H.M.5
  • 23
    • 67349288523 scopus 로고    scopus 로고
    • TU-tagging: Cell type-specific RNA isolation from intact complex tissues
    • Miller MR, Robinson KJ, Cleary MD, Doe CQ. 2009. TU-tagging: Cell type-specific RNA isolation from intact complex tissues. Nat Methods 6: 439-441.
    • (2009) Nat Methods , vol.6 , pp. 439-441
    • Miller, M.R.1    Robinson, K.J.2    Cleary, M.D.3    Doe, C.Q.4
  • 25
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • DOI 10.1038/nmeth.1226, PII NMETH.1226
    • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628. (Pubitemid 351911867)
    • (2008) Nature Methods , vol.5 , Issue.7 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 26
    • 0031053705 scopus 로고    scopus 로고
    • Severe growth defect in a Schizosaccharomyces pombe mutant defective in intron lariat degradation
    • Nam K, Lee G, Trambley J, Devine SE, Boeke JD. 1997. Severe growth defect in a Schizosaccharomyces pombe mutant defective in intron lariat degradation. Mol Cell Biol 17: 809-818. (Pubitemid 27044380)
    • (1997) Molecular and Cellular Biology , vol.17 , Issue.2 , pp. 809-818
    • Nam, K.1    Lee, G.2    Trambley, J.3    Devine, S.E.4    Boeke, J.D.5
  • 27
    • 75849145292 scopus 로고    scopus 로고
    • Expansion of the eukaryotic proteome by alternative splicing
    • Nilsen TW, Graveley BR. 2010. Expansion of the eukaryotic proteome by alternative splicing. Nature 463: 457-463.
    • (2010) Nature , vol.463 , pp. 457-463
    • Nilsen, T.W.1    Graveley, B.R.2
  • 28
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    • Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. 2008. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40: 1413-1415.
    • (2008) Nat Genet , vol.40 , pp. 1413-1415
    • Pan, Q.1    Shai, O.2    Lee, L.J.3    Frey, B.J.4    Blencowe, B.J.5
  • 30
    • 40649106258 scopus 로고    scopus 로고
    • Non-coding RNAs in imprinted gene clusters
    • DOI 10.1042/BC20070126
    • Royo H, Cavaille J. 2008. Non-coding RNAs in imprinted gene clusters. Biol Cell 100: 149-166. (Pubitemid 351372674)
    • (2008) Biology of the Cell , vol.100 , Issue.3 , pp. 149-166
    • Royo, H.1    Cavaille, J.2
  • 31
    • 0035509699 scopus 로고    scopus 로고
    • The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A
    • Runte M, Huttenhofer A, Gross S, Kiefmann M, Horsthemke B, Buiting K. 2001. The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A. Hum Mol Genet 10: 2687-2700. (Pubitemid 33133410)
    • (2001) Human Molecular Genetics , vol.10 , Issue.23 , pp. 2687-2700
    • Runte, M.1    Huttenhofer, A.2    Gross, S.3    Kiefmann, M.4    Horsthemke, B.5    Buiting, K.6
  • 33
    • 53949098609 scopus 로고    scopus 로고
    • Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation
    • doi: 10.1038/msb.2008.59
    • Shalem O, Dahan O, Levo M, Martinez MR, Furman I, Segal E, Pilpel Y. 2008. Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Mol Syst Biol 4: 223. doi: 10.1038/msb.2008.59.
    • (2008) Mol Syst Biol , vol.4 , pp. 223
    • Shalem, O.1    Dahan, O.2    Levo, M.3    Martinez, M.R.4    Furman, I.5    Segal, E.6    Pilpel, Y.7
  • 36
    • 0242497663 scopus 로고    scopus 로고
    • CLIP Identifies Nova-Regulated RNA Networks in the Brain
    • DOI 10.1126/science.1090095
    • Ule J, Jensen KB, Ruggiu M, Mele A, Ule A, Darnell RB. 2003. CLIP identifies Nova-regulated RNA networks in the brain. Science 302: 1212-1215. (Pubitemid 37421026)
    • (2003) Science , vol.302 , Issue.5648 , pp. 1212-1215
    • Ule, J.1    Jensen, K.B.2    Ruggiu, M.3    Mele, A.4    Ule, A.5    Darnell, R.B.6
  • 38
    • 72449205602 scopus 로고    scopus 로고
    • Long nuclear-retained non-coding RNAs and allele-specific higher-order chromatin organization at imprinted snoRNA gene arrays
    • Vitali P, Royo H, Marty V, Bortolin-Cavaille ML, Cavaille J. 2010. Long nuclear-retained non-coding RNAs and allele-specific higher-order chromatin organization at imprinted snoRNA gene arrays. J Cell Sci 123: 70-83.
    • (2010) J Cell Sci , vol.123 , pp. 70-83
    • Vitali, P.1    Royo, H.2    Marty, V.3    Bortolin-Cavaille, M.L.4    Cavaille, J.5
  • 41
    • 2442441507 scopus 로고    scopus 로고
    • Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
    • DOI 10.1089/1066527041410418
    • Yeo G, Burge CB. 2004. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 11: 377-394. (Pubitemid 38901668)
    • (2004) Journal of Computational Biology , vol.11 , Issue.2-3 , pp. 377-394
    • Yeo, G.1    Burge, C.B.2


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