메뉴 건너뛰기




Volumn 22, Issue 5, 2012, Pages 947-956

Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals

Author keywords

[No Author keywords available]

Indexed keywords

BROXURIDINE; MESSENGER RNA; RETINOIC ACID; UNTRANSLATED RNA;

EID: 84860575639     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.130559.111     Document Type: Article
Times cited : (322)

References (54)
  • 1
    • 60549115605 scopus 로고    scopus 로고
    • Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs
    • Affymetrix/Cold Spring Harbor Laboratory ENCODE Transcriptome Project
    • Affymetrix/Cold Spring Harbor Laboratory ENCODE Transcriptome Project. 2009. Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Nature 457: 1028-1032.
    • (2009) Nature , vol.457 , pp. 1028-1032
  • 2
    • 2342456308 scopus 로고    scopus 로고
    • Nonsense-mediated mRNA decay: Terminating erroneous gene expression
    • DOI 10.1016/j.ceb.2004.03.003, PII S0955067404000419
    • Baker KE, Parker R. 2004. Nonsense-mediated mRNA decay: Terminating erroneous gene expression. Curr Opin Cell Biol 16: 293-299. (Pubitemid 38610410)
    • (2004) Current Opinion in Cell Biology , vol.16 , Issue.3 , pp. 293-299
    • Baker, K.E.1    Parker, R.2
  • 6
    • 38849117246 scopus 로고    scopus 로고
    • RNA-protein interactions and control of mRNA stability in neurons
    • DOI 10.1002/jnr.21473
    • Bolognani F, Perrone-Bizzozero NI. 2008. RNA-protein interactions and control of mRNA stability in neurons. J Neurosci Res 86: 481-489. (Pubitemid 351204460)
    • (2008) Journal of Neuroscience Research , vol.86 , Issue.3 , pp. 481-489
    • Bolognani, F.1    Perrone-Bizzozero, N.I.2
  • 7
    • 0023277545 scopus 로고
    • Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction
    • DOI 10.1006/abio.1987.9999
    • Chomczynski P, Sacchi N. 1987. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162: 156-159. (Pubitemid 17064313)
    • (1987) Analytical Biochemistry , vol.162 , Issue.1 , pp. 156-159
    • Chomczynski, P.1    Sacchi, N.2
  • 8
  • 9
    • 57849109058 scopus 로고    scopus 로고
    • Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    • Core LJ, Waterfall JJ, Lis JT. 2008. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322: 1845-1848.
    • (2008) Science , vol.322 , pp. 1845-1848
    • Core, L.J.1    Waterfall, J.J.2    Lis, J.T.3
  • 10
    • 0021332093 scopus 로고
    • Detection of mRNAs in sea urchin embryos by in situ hybridization using asymmetric RNA probes
    • Cox KH, DeLeon DV, Angerer LM, Angerer RC. 1984. Detection of mRNAs in sea urchin embryos by in situ hybridization using asymmetric RNA probes. Dev Biol 101: 485-502. (Pubitemid 14196080)
    • (1984) Developmental Biology , vol.101 , Issue.2 , pp. 485-502
    • Cox, K.H.1    DeLeon, D.V.2    Angerer, L.M.3    Angerer, R.C.4
  • 11
    • 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
    • 0347416978 scopus 로고    scopus 로고
    • Genome-Wide Analysis of mRNAs Regulated by the Nonsense-Mediated and 5′ to 3′ mRNA Decay Pathways in Yeast
    • DOI 10.1016/S1097-2765(03)00446-5
    • He F, Li X, Spatrick P, Casillo R, Dong S, Jacobson A. 2003. Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5′ to 3′ mRNA decay pathways in yeast. Mol Cell 12: 1439-1452. (Pubitemid 38037013)
    • (2003) Molecular Cell , vol.12 , Issue.6 , pp. 1439-1452
    • He, F.1    Li, X.2    Spatrick, P.3    Casillo, R.4    Dong, S.5    Jacobson, A.6
  • 15
    • 33847185603 scopus 로고    scopus 로고
    • A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains
    • doi: 10.1186/1471-2164-8-39
    • Hutchinson JN, Ensminger AW, Clemson CM, Lynch CR, Lawrence JB, Chess A. 2007. A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics 8: 39. doi: 10.1186/1471-2164-8-39.
    • (2007) BMC Genomics , vol.8 , pp. 39
    • Hutchinson, J.N.1    Ensminger, A.W.2    Clemson, C.M.3    Lynch, C.R.4    Lawrence, J.B.5    Chess, A.6
  • 16
    • 67651002028 scopus 로고    scopus 로고
    • Efficient oligonucleotide-mediated degradation of nuclear noncoding RNAs in mammalian cultured cells
    • Ideue T, Hino K, Kitao S, Yokoi T, Hirose T. 2009. Efficient oligonucleotide-mediated degradation of nuclear noncoding RNAs in mammalian cultured cells. RNA 15: 1578-1587.
    • (2009) RNA , vol.15 , pp. 1578-1587
    • Ideue, T.1    Hino, K.2    Kitao, S.3    Yokoi, T.4    Hirose, T.5
  • 17
    • 0035253857 scopus 로고    scopus 로고
    • A small nucleolar guide RNA functions both in 2′-O-ribose methylation and pseudouridylation of the U5 spliceosomal RNA
    • DOI 10.1093/emboj/20.3.541
    • Jády BE, Kiss TA. 2001. Small nucleolar guide RNA functions both in 2′-O-ribose methylation and pseudouridylation of the U5 spliceosomal RNA. EMBO J 20: 541-551. (Pubitemid 32126989)
    • (2001) EMBO Journal , vol.20 , Issue.3 , pp. 541-551
    • Jady, B.E.1    Kiss, T.2
  • 18
    • 57349121991 scopus 로고    scopus 로고
    • Exploring RNA transcription and turnover in vivo by using click chemistry
    • Jao CY, Salic A. 2008. Exploring RNA transcription and turnover in vivo by using click chemistry. Proc Natl Acad Sci 105: 15779-15784.
    • (2008) Proc Natl Acad Sci , vol.105 , pp. 15779-15784
    • Jao, C.Y.1    Salic, A.2
  • 19
    • 0028169728 scopus 로고
    • Elongation factor-1 a mRNA is selectively translated following mitogenic stimulation
    • Jefferies HB, Thomas G, Thomas G. 1994. Elongation factor-1 a mRNA is selectively translated following mitogenic stimulation. J Biol Chem 269: 4367-4372.
    • (1994) J Biol Chem , vol.269 , pp. 4367-4372
    • Jefferies, H.B.1    Thomas, G.2    Thomas, G.3
  • 20
    • 77955110979 scopus 로고    scopus 로고
    • Genome-wide computational identification and manual annotation of human long noncoding RNA genes
    • Jia H, Osak M, Bogu GK, Stanton LW, Johnson R, Lipovich L. 2010. Genome-wide computational identification and manual annotation of human long noncoding RNA genes. RNA 16: 1478-1487.
    • (2010) RNA , vol.16 , pp. 1478-1487
    • Jia, H.1    Osak, M.2    Bogu, G.K.3    Stanton, L.W.4    Johnson, R.5    Lipovich, L.6
  • 21
    • 77950295790 scopus 로고    scopus 로고
    • Minireview: Global regulation and dynamics of ribonucleic Acid
    • Keene JD. 2010. Minireview: Global regulation and dynamics of ribonucleic Acid. Endocrinology 151: 1391-1397.
    • (2010) Endocrinology , vol.151 , pp. 1391-1397
    • Keene, J.D.1
  • 23
    • 77951638287 scopus 로고    scopus 로고
    • Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor
    • doi: 10.1126/scisignal.2000568
    • Kino T, Hurt DE, Ichijo T, Nader N, Chrousos GP. 2010. Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci Signal 3: ra8. doi: 10.1126/scisignal.2000568.
    • (2010) Sci Signal , vol.3
    • Kino, T.1    Hurt, D.E.2    Ichijo, T.3    Nader, N.4    Chrousos, G.P.5
  • 26
    • 1842584883 scopus 로고    scopus 로고
    • RNA regulation: A new genetics?
    • DOI 10.1038/nrg1321
    • Mattick JS. 2004. RNA regulation: A new genetics? Nat Rev Genet 5: 316-323. (Pubitemid 38435628)
    • (2004) Nature Reviews Genetics , vol.5 , Issue.4 , pp. 316-323
    • Mattick, J.S.1
  • 27
    • 6944256813 scopus 로고    scopus 로고
    • Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise
    • DOI 10.1038/ng1429
    • Mendell JT, Sharifi NA, Meyers JL, Martinez-Murillo F, Dietz HC. 2004. Nonsense surveillance regulates expression of diverse classes ofmammalian transcripts and mutes genomic noise. Nat Genet 36: 1073-1078. (Pubitemid 41184468)
    • (2004) Nature Genetics , vol.36 , Issue.10 , pp. 1073-1078
    • Mendell, J.T.1    Sharifi, N.A.2    Meyers, J.L.3    Martinez-Murillo, F.4    Dietz, H.C.5
  • 29
    • 84858630963 scopus 로고    scopus 로고
    • Identification of cis- and trans-acting factors involved in the localization of MALAT-1 noncoding RNA to nuclear speckles
    • doi: 10.1261/rna.028639.111
    • Miyagawa R, Tano K, Mizuno R, Nakamura Y, Ijiri K, Rakwal R, Shibato J, Masuo Y, Mayeda A, Hirose T, et al. 2012. Identification of cis- and trans-acting factors involved in the localization of MALAT-1 noncoding RNA to nuclear speckles. RNA doi: 10.1261/rna.028639.111.
    • (2012) RNA
    • Miyagawa, R.1    Tano, K.2    Mizuno, R.3    Nakamura, Y.4    Ijiri, K.5    Rakwal, R.6    Shibato, J.7    Masuo, Y.8    Mayeda, A.9    Hirose, T.10
  • 30
    • 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
  • 31
    • 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, 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
  • 33
    • 33846169089 scopus 로고    scopus 로고
    • Eukaryotic regulatory RNAs: An answer to the 'genome complexity' conundrum
    • DOI 10.1101/gad.1484207
    • Prasanth KV, Spector DL. 2007. Eukaryotic regulatory RNAs: An answer to the 'genome complexity' conundrum. Genes Dev 21: 11-42. (Pubitemid 46089704)
    • (2007) Genes and Development , vol.21 , Issue.1 , pp. 11-42
    • Prasanth, K.V.1    Spector, D.L.2
  • 36
    • 4644288309 scopus 로고    scopus 로고
    • Microarray-based analyses of mRNA decay in the regulation of mammalian gene expression
    • Raghavan A, Bohjanen PR. 2004. Microarray-based analyses of mRNA decay in the regulation of mammalian gene expression. Brief Funct Genomics Proteomics 3: 112-124.
    • (2004) Brief Funct Genomics Proteomics , vol.3 , pp. 112-124
    • Raghavan, A.1    Bohjanen, P.R.2
  • 39
    • 62449319486 scopus 로고    scopus 로고
    • MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles
    • Sasaki YT, Ideue T, Sano M, Mituyama T, Hirose T. 2009. MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc Natl Acad Sci 106: 2525-2530.
    • (2009) Proc Natl Acad Sci , vol.106 , pp. 2525-2530
    • Sasaki, Y.T.1    Ideue, T.2    Sano, M.3    Mituyama, T.4    Hirose, T.5
  • 43
    • 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 LV, Sharov AA, Nedorezov T, Piao Y, Shaik N, Ko MS. 2009. 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) DNA Res , vol.16 , pp. 45-58
    • Sharova, L.V.1    Sharov, A.A.2    Nedorezov, T.3    Piao, Y.4    Shaik, N.5    Ko, M.S.6
  • 44
    • 0031756336 scopus 로고    scopus 로고
    • Classification of gas5 as a multi-small-nucleolar-RNA (snoRNA) host gene and a member of the 5'-terminal oligopyrimidine gene family reveals common features of snoRNA host genes
    • Smith CM, Steitz JA. 1998. Classification of gas5 as a multi-small-nucleolar-RNA (snoRNA) host gene and a member of the 5′-terminal oligopyrimidine gene family reveals common features of snoRNA host genes. Mol Cell Biol 18: 6897-6909. (Pubitemid 28533011)
    • (1998) Molecular and Cellular Biology , vol.18 , Issue.12 , pp. 6897-6909
    • Smith, C.M.1    Steitz, J.A.2
  • 45
    • 34548291568 scopus 로고    scopus 로고
    • The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons
    • DOI 10.1242/jcs.009357
    • Sone M, Hayashi T, Tarui H, Agata K, Takeichi M, Nakagawa S. 2007. The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. J Cell Sci 120: 2498-2506. (Pubitemid 47323859)
    • (2007) Journal of Cell Science , vol.120 , Issue.15 , pp. 2498-2506
    • Sone, M.1    Hayashi, T.2    Tarui, H.3    Agata, K.4    Takeichi, M.5    Nakagawa, S.6
  • 46
    • 61849113891 scopus 로고    scopus 로고
    • MEN ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles
    • Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL. 2009. MEN ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 19: 347-359.
    • (2009) Genome Res , vol.19 , pp. 347-359
    • Sunwoo, H.1    Dinger, M.E.2    Wilusz, J.E.3    Amaral, P.P.4    Mattick, J.S.5    Spector, D.L.6
  • 47
    • 78249258719 scopus 로고    scopus 로고
    • MALAT-1 enhances cell motility of lung adenocarcinoma cells by influencing the expression of motility-related genes
    • Tano K, Mizuno R, Okada T, Rakwal R, Shibato J, Masuo Y, Ijiri K, Akimitsu N. 2010. MALAT-1 enhances cell motility of lung adenocarcinoma cells by influencing the expression of motility-related genes. FEBS Lett 584: 4575-4580.
    • (2010) FEBS Lett , vol.584 , pp. 4575-4580
    • Tano, K.1    Mizuno, R.2    Okada, T.3    Rakwal, R.4    Shibato, J.5    Masuo, Y.6    Ijiri, K.7    Akimitsu, N.8
  • 48
    • 75349083571 scopus 로고    scopus 로고
    • Identification and functional analyses of 11,769 full-length human cDNAs focused on alternative splicing
    • Wakamatsu A, Kimura K, Yamamoto J, Nishikawa T, Nomura N, Sugano S, Isogai T. 2009. Identification and functional analyses of 11,769 full-length human cDNAs focused on alternative splicing. DNA Res 16: 371-383.
    • (2009) DNA Res , vol.16 , pp. 371-383
    • Wakamatsu, A.1    Kimura, K.2    Yamamoto, J.3    Nishikawa, T.4    Nomura, N.5    Sugano, S.6    Isogai, T.7
  • 53
    • 81055140863 scopus 로고    scopus 로고
    • NcRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs
    • Yang L, Lin C, Liu W, Zhang J, Ohgi KA, Grinstein JD, Dorrestein PC, Rosenfeld MG. 2011. ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs. Cell 147: 773-788.
    • (2011) Cell , vol.147 , pp. 773-788
    • Yang, L.1    Lin, C.2    Liu, W.3    Zhang, J.4    Ohgi, K.A.5    Grinstein, J.D.6    Dorrestein, P.C.7    Rosenfeld, M.G.8
  • 54
    • 77953096072 scopus 로고    scopus 로고
    • Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by Polycomb CBX7 in transcriptional silencing of INK4a
    • Yap KL, Li S, Muñoz-Cabello AM, Raguz S, Zeng L, Mujtaba S, Gil J, Walsh MJ, Zhou MM. 2010. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by Polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell 38: 662-674.
    • (2010) Mol Cell , vol.38 , pp. 662-674
    • Yap, K.L.1    Li, S.2    Muñoz-Cabello, A.M.3    Raguz, S.4    Zeng, L.5    Mujtaba, S.6    Gil, J.7    Walsh, M.J.8    Zhou, M.M.9


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.