메뉴 건너뛰기




Volumn 12, Issue 2, 2011, Pages

Genomewide characterization of non-polyadenylated RNAs

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H1; MESSENGER RNA; POLYADENYLATED RNA; UNTRANSLATED RNA; HISTONE; ISOPROTEIN; POLYADENYLIC ACID; RNA; TRANSCRIPTOME;

EID: 79951551684     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2011-12-2-r16     Document Type: Article
Times cited : (327)

References (38)
  • 1
    • 60149110358 scopus 로고    scopus 로고
    • Pre-mRNA processing reaches back to transcription and ahead to translation.
    • 10.1016/j.cell.2009.02.001, 19239889
    • Moore MJ, Proudfoot NJ. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 2009, 136:688-700. 10.1016/j.cell.2009.02.001, 19239889.
    • (2009) Cell , vol.136 , pp. 688-700
    • Moore, M.J.1    Proudfoot, N.J.2
  • 2
    • 0024836575 scopus 로고
    • RNA 3'-end formation.
    • 10.1101/gad.3.12b.2218, 2628168
    • Manley JL, Proudfoot NJ, Platt T. RNA 3'-end formation. Genes Dev 1989, 3:2218-2244. 10.1101/gad.3.12b.2218, 2628168.
    • (1989) Genes Dev , vol.3 , pp. 2218-2244
    • Manley, J.L.1    Proudfoot, N.J.2    Platt, T.3
  • 3
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing.
    • 10.1038/ng.259, 18978789
    • Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008, 40:1413-1415. 10.1038/ng.259, 18978789.
    • (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
  • 5
    • 66349122954 scopus 로고    scopus 로고
    • Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing.
    • 10.1126/science.1170995, 19478186
    • Li JB, Levanon EY, Yoon JK, Aach J, Xie B, Leproust E, Zhang K, Gao Y, Church GM. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 2009, 324:1210-1213. 10.1126/science.1170995, 19478186.
    • (2009) Science , vol.324 , pp. 1210-1213
    • Li, J.B.1    Levanon, E.Y.2    Yoon, J.K.3    Aach, J.4    Xie, B.5    Leproust, E.6    Zhang, K.7    Gao, Y.8    Church, G.M.9
  • 6
    • 46249096804 scopus 로고    scopus 로고
    • Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution.
    • 10.1038/nature07002, 18488015
    • Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bahler J. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 2008, 453:1239-1243. 10.1038/nature07002, 18488015.
    • (2008) Nature , vol.453 , pp. 1239-1243
    • Wilhelm, B.T.1    Marguerat, S.2    Watt, S.3    Schubert, F.4    Wood, V.5    Goodhead, I.6    Penkett, C.J.7    Rogers, J.8    Bahler, J.9
  • 7
    • 54149091257 scopus 로고    scopus 로고
    • Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail.
    • 10.1038/nrg2438, 2715827, 18927579
    • Marzluff WF, Wagner EJ, Duronio RJ. Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail. Nat Rev Genet 2008, 9:843-854. 10.1038/nrg2438, 2715827, 18927579.
    • (2008) Nat Rev Genet , vol.9 , pp. 843-854
    • Marzluff, W.F.1    Wagner, E.J.2    Duronio, R.J.3
  • 8
    • 56349113455 scopus 로고    scopus 로고
    • 3' end processing of a long nuclear-retained non-coding RNA yields a tRNA-like cytoplasmic RNA.
    • 10.1016/j.cell.2008.10.012, 2722846, 19041754
    • Wilusz JE, Freier SM, Spector DL. 3' end processing of a long nuclear-retained non-coding RNA yields a tRNA-like cytoplasmic RNA. Cell 2008, 135:919-932. 10.1016/j.cell.2008.10.012, 2722846, 19041754.
    • (2008) Cell , vol.135 , pp. 919-932
    • Wilusz, J.E.1    Freier, S.M.2    Spector, D.L.3
  • 9
    • 61849113891 scopus 로고    scopus 로고
    • MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles.
    • 10.1101/gr.087775.108, 2661813, 19106332
    • Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL. MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 2009, 19:347-359. 10.1101/gr.087775.108, 2661813, 19106332.
    • (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
  • 10
    • 0016283394 scopus 로고
    • The metabolism of a poly(A) minus mRNA fraction in HeLa cells.
    • 10.1016/0092-8674(74)90030-0, 4213457
    • Milcarek C, Price R, Penman S. The metabolism of a poly(A) minus mRNA fraction in HeLa cells. Cell 1974, 3:1-10. 10.1016/0092-8674(74)90030-0, 4213457.
    • (1974) Cell , vol.3 , pp. 1-10
    • Milcarek, C.1    Price, R.2    Penman, S.3
  • 11
    • 0019524412 scopus 로고
    • Large heterogeneous nuclear ribonucleic acid has three times as many 5' caps as polyadenylic acid segments, and most caps do not enter polyribosomes.
    • 369657, 6152852
    • Salditt-Georgieff M, Harpold MM, Wilson MC, Darnell JE. Large heterogeneous nuclear ribonucleic acid has three times as many 5' caps as polyadenylic acid segments, and most caps do not enter polyribosomes. Mol Cell Biol 1981, 1:179-187. 369657, 6152852.
    • (1981) Mol Cell Biol , vol.1 , pp. 179-187
    • Salditt-Georgieff, M.1    Harpold, M.M.2    Wilson, M.C.3    Darnell, J.E.4
  • 12
    • 0019194020 scopus 로고
    • Non-polyadenylated mRNAs from eukaryotes.
    • 10.1016/0014-5793(80)80515-1, 6997068
    • Katinakis PK, Slater A, Burdon RH. Non-polyadenylated mRNAs from eukaryotes. FEBS Lett 1980, 116:1-7. 10.1016/0014-5793(80)80515-1, 6997068.
    • (1980) FEBS Lett , vol.116 , pp. 1-7
    • Katinakis, P.K.1    Slater, A.2    Burdon, R.H.3
  • 13
    • 13044313468 scopus 로고    scopus 로고
    • The poly(A)-limiting element is a conserved cis-acting sequence that regulates poly(A) tail length on nuclear pre-mRNAs.
    • 10.1073/pnas.96.16.8943, 17712, 10430875
    • Gu H, Das Gupta J, Schoenberg DR. The poly(A)-limiting element is a conserved cis-acting sequence that regulates poly(A) tail length on nuclear pre-mRNAs. Proc Natl Acad Sci USA 1999, 96:8943-8948. 10.1073/pnas.96.16.8943, 17712, 10430875.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 8943-8948
    • Gu, H.1    Das Gupta, J.2    Schoenberg, D.R.3
  • 14
    • 36148973188 scopus 로고    scopus 로고
    • A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells.
    • 10.1093/nar/gkm830, 2095794, 17933768
    • Meijer HA, Bushell M, Hill K, Gant TW, Willis AE, Jones P, de Moor CH. A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells. Nucleic Acids Res 2007, 35:e132. 10.1093/nar/gkm830, 2095794, 17933768.
    • (2007) Nucleic Acids Res , vol.35
    • Meijer, H.A.1    Bushell, M.2    Hill, K.3    Gant, T.W.4    Willis, A.E.5    Jones, P.6    de Moor, C.H.7
  • 17
    • 78649449778 scopus 로고    scopus 로고
    • A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing.
    • 10.1016/j.ygeno.2010.07.010, 20688152
    • Cui P, Lin Q, Ding F, Xin C, Gong W, Zhang L, Geng J, Zhang B, Yu X, Yang J, Hu S, Yu J. A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing. Genomics 2010, 96:259-265. 10.1016/j.ygeno.2010.07.010, 20688152.
    • (2010) Genomics , vol.96 , pp. 259-265
    • Cui, P.1    Lin, Q.2    Ding, F.3    Xin, C.4    Gong, W.5    Zhang, L.6    Geng, J.7    Zhang, B.8    Yu, X.9    Yang, J.10    Hu, S.11    Yu, J.12
  • 18
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
    • 10.1186/gb-2009-10-3-r25, 2690996, 19261174
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 20
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq.
    • 10.1038/nmeth.1226, 18516045
    • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5:621-628. 10.1038/nmeth.1226, 18516045.
    • (2008) Nat Methods , vol.5 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 21
    • 33847185603 scopus 로고    scopus 로고
    • A screen for nuclear transcripts identifies two linked non-coding RNAs associated with SC35 splicing domains.
    • 10.1186/1471-2164-8-39, 1800850, 17270048
    • Hutchinson JN, Ensminger AW, Clemson CM, Lynch CR, Lawrence JB, Chess A. A screen for nuclear transcripts identifies two linked non-coding RNAs associated with SC35 splicing domains. BMC Genomics 2007, 8:39. 10.1186/1471-2164-8-39, 1800850, 17270048.
    • (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
  • 23
    • 45949090187 scopus 로고    scopus 로고
    • Multiple Em for Motif Elicitation.
    • Multiple Em for Motif Elicitation. , http://meme.nbcr.net/meme4_4_0/intro.html
  • 24
    • 47049122843 scopus 로고    scopus 로고
    • Alu element-mediated gene silencing.
    • 10.1038/emboj.2008.94, 2435129, 18497743
    • Chen LL, DeCerbo JN, Carmichael GG. Alu element-mediated gene silencing. EMBO J 2008, 27:1694-1705. 10.1038/emboj.2008.94, 2435129, 18497743.
    • (2008) EMBO J , vol.27 , pp. 1694-1705
    • Chen, L.L.1    DeCerbo, J.N.2    Carmichael, G.G.3
  • 25
    • 68949212914 scopus 로고    scopus 로고
    • Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: Functional role of a nuclear non-coding RNA.
    • 10.1016/j.molcel.2009.06.027, 2749223, 19716791
    • Chen LL, Carmichael GG. Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: Functional role of a nuclear non-coding RNA. Mol Cell 2009, 35:467-478. 10.1016/j.molcel.2009.06.027, 2749223, 19716791.
    • (2009) Mol Cell , vol.35 , pp. 467-478
    • Chen, L.L.1    Carmichael, G.G.2
  • 27
    • 33947524604 scopus 로고    scopus 로고
    • Histone variants - the structure behind the function.
    • 10.1093/bfgp/ell020, 16772274
    • Ausio J. Histone variants - the structure behind the function. Brief Funct Genomic Proteomic 2006, 5:228-243. 10.1093/bfgp/ell020, 16772274.
    • (2006) Brief Funct Genomic Proteomic , vol.5 , pp. 228-243
    • Ausio, J.1
  • 28
    • 44649186259 scopus 로고    scopus 로고
    • The histone H1 family: specific members, specific functions?
    • 10.1515/BC.2008.037, 18208346
    • Izzo A, Kamieniarz K, Schneider R. The histone H1 family: specific members, specific functions?. Biol Chem 2008, 389:333-343. 10.1515/BC.2008.037, 18208346.
    • (2008) Biol Chem , vol.389 , pp. 333-343
    • Izzo, A.1    Kamieniarz, K.2    Schneider, R.3
  • 29
    • 27144544622 scopus 로고    scopus 로고
    • Assembly of variant histones into chromatin.
    • 10.1146/annurev.cellbio.21.012704.133518, 16212490
    • Henikoff S, Ahmad K. Assembly of variant histones into chromatin. Annu Rev Cell Dev Biol 2005, 21:133-153. 10.1146/annurev.cellbio.21.012704.133518, 16212490.
    • (2005) Annu Rev Cell Dev Biol , vol.21 , pp. 133-153
    • Henikoff, S.1    Ahmad, K.2
  • 30
    • 29744447772 scopus 로고    scopus 로고
    • Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells.
    • 10.1016/j.devcel.2005.10.017, 1868458, 16399082
    • Meshorer E, Yellajoshula D, George E, Scambler PJ, Brown DT, Misteli T. Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. Dev Cell 2006, 10:105-116. 10.1016/j.devcel.2005.10.017, 1868458, 16399082.
    • (2006) Dev Cell , vol.10 , pp. 105-116
    • Meshorer, E.1    Yellajoshula, D.2    George, E.3    Scambler, P.J.4    Brown, D.T.5    Misteli, T.6
  • 32
    • 16844370131 scopus 로고    scopus 로고
    • Cell cycle and developmental regulations of replication factors in mouse embryonic stem cells.
    • 10.1074/jbc.M412224200, 15659392
    • Fujii-Yamamoto H, Kim JM, Arai K, Masai H. Cell cycle and developmental regulations of replication factors in mouse embryonic stem cells. J Biol Chem 2005, 280:12976-12987. 10.1074/jbc.M412224200, 15659392.
    • (2005) J Biol Chem , vol.280 , pp. 12976-12987
    • Fujii-Yamamoto, H.1    Kim, J.M.2    Arai, K.3    Masai, H.4
  • 33
    • 30444461346 scopus 로고    scopus 로고
    • Cell cycle control of embryonic stem cells.
    • 10.1385/SCR:1:2:131, 17142847
    • White J, Dalton S. Cell cycle control of embryonic stem cells. Stem Cell Rev 2005, 1:131-138. 10.1385/SCR:1:2:131, 17142847.
    • (2005) Stem Cell Rev , vol.1 , pp. 131-138
    • White, J.1    Dalton, S.2
  • 34
    • 33750524413 scopus 로고    scopus 로고
    • Self-renewal of human embryonic stem cells is supported by a shortened G1 cell cycle phase.
    • 10.1002/jcp.20776, 16972248
    • Becker KA, Ghule PN, Therrien JA, Lian JB, Stein JL, van Wijnen AJ, Stein GS. Self-renewal of human embryonic stem cells is supported by a shortened G1 cell cycle phase. J Cell Physiol 2006, 209:883-893. 10.1002/jcp.20776, 16972248.
    • (2006) J Cell Physiol , vol.209 , pp. 883-893
    • Becker, K.A.1    Ghule, P.N.2    Therrien, J.A.3    Lian, J.B.4    Stein, J.L.5    van Wijnen, A.J.6    Stein, G.S.7
  • 36
    • 18744375483 scopus 로고    scopus 로고
    • Basic FGF and suppression of BMP signaling sustain undifferentiated proliferation of human ES cells.
    • 10.1038/nmeth744, 15782187
    • Xu RH, Peck RM, Li DS, Feng X, Ludwig T, Thomson JA. Basic FGF and suppression of BMP signaling sustain undifferentiated proliferation of human ES cells. Nat Methods 2005, 2:185-190. 10.1038/nmeth744, 15782187.
    • (2005) Nat Methods , vol.2 , pp. 185-190
    • Xu, R.H.1    Peck, R.M.2    Li, D.S.3    Feng, X.4    Ludwig, T.5    Thomson, J.A.6
  • 37
    • 36248966518 scopus 로고    scopus 로고
    • Induction of pluripotent stem cells from adult human fibroblasts by defined factors.
    • 10.1016/j.cell.2007.11.019, 18035408
    • Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, Yamanaka S. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 2007, 131:861-872. 10.1016/j.cell.2007.11.019, 18035408.
    • (2007) Cell , vol.131 , pp. 861-872
    • Takahashi, K.1    Tanabe, K.2    Ohnuki, M.3    Narita, M.4    Ichisaka, T.5    Tomoda, K.6    Yamanaka, S.7
  • 38
    • 70350222219 scopus 로고    scopus 로고
    • Lack of ABCG2 expression and side population properties in human pluripotent stem cells.
    • 10.1002/stem.192, 19670287
    • Zeng H, Park JW, Guo M, Lin G, Crandall L, Compton T, Wang X, Li XJ, Chen FP, Xu R. Lack of ABCG2 expression and side population properties in human pluripotent stem cells. Stem Cells 2009, 27:2435-2445. 10.1002/stem.192, 19670287.
    • (2009) Stem Cells , vol.27 , pp. 2435-2445
    • Zeng, H.1    Park, J.W.2    Guo, M.3    Lin, G.4    Crandall, L.5    Compton, T.6    Wang, X.7    Li, X.J.8    Chen, F.P.9    Xu, R.10


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.