메뉴 건너뛰기




Volumn 27, Issue 2, 2010, Pages 162-170

Computational identification of Ciona intestinalis MicroRNAs

Author keywords

Ascidian; Ciona; Computational prediction; MicroRNA; MiRNA

Indexed keywords

MICRORNA;

EID: 76849089331     PISSN: 02890003     EISSN: 02890003     Source Type: Journal    
DOI: 10.2108/zsj.27.162     Document Type: Article
Times cited : (13)

References (56)
  • 2
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and function
    • Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 4
    • 13944260434 scopus 로고    scopus 로고
    • Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes
    • Baskerville S, Bartel DP (2005) Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11: 241-247
    • (2005) RNA , vol.11 , pp. 241-247
    • Baskerville, S.1    Bartel, D.P.2
  • 5
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: A program to analyze DNA sequences
    • Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27: 573-580
    • (1999) Nucleic Acids Res , vol.27 , pp. 573-580
    • Benson, G.1
  • 7
    • 19944376457 scopus 로고    scopus 로고
    • Global identification of human transcribed sequences with genome tiling arrays
    • Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, et al. (2004) Global identification of human transcribed sequences with genome tiling arrays. Science 306: 2242-2246
    • (2004) Science , vol.306 , pp. 2242-2246
    • Bertone, P.1    Stolc, V.2    Royce, T.E.3    Rozowsky, J.S.4    Urban, A.E.5
  • 8
    • 0037270315 scopus 로고    scopus 로고
    • AVID: A global alignment program
    • Bray N, Dubchak I, Pachter L (2003) AVID: a global alignment program. Genome Res 13: 97-102
    • (2003) Genome Res , vol.13 , pp. 97-102
    • Bray, N.1    Dubchak, I.2    Pachter, L.3
  • 11
    • 9344235449 scopus 로고    scopus 로고
    • Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs
    • Cai X, Hagedorn CH, Cullen BR (2004) Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 10: 1957-1966
    • (2004) RNA , vol.10 , pp. 1957-1966
    • Cai, X.1    Hagedorn, C.H.2    Cullen, B.R.3
  • 12
    • 22344449952 scopus 로고    scopus 로고
    • The developmental miRNA profiles of zebrafish as determined by small RNA cloning
    • Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, et al. (2005) The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev 19: 1288-1293
    • (2005) Genes Dev , vol.19 , pp. 1288-1293
    • Chen, P.Y.1    Manninga, H.2    Slanchev, K.3    Chien, M.4    Russo, J.J.5
  • 13
    • 74049164557 scopus 로고    scopus 로고
    • Identification and characterization of novel amphioxus microRNAs by Solexa sequencing
    • Chen X, Li Q, Wang J, Guo X, Jiang X, et al. (2009) Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol 10: R78
    • (2009) Genome Biol , vol.10
    • Chen, X.1    Li, Q.2    Wang, J.3    Guo, X.4    Jiang, X.5
  • 14
    • 33144481470 scopus 로고    scopus 로고
    • Reciprocal actions of REST and a microRNA promote neuronal identity
    • Conaco C, Otto S, Han JJ, Mandel G (2006) Reciprocal actions of REST and a microRNA promote neuronal identity. Proc Natl Acad Sci USA 103: 2422-2427
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 2422-2427
    • Conaco, C.1    Otto, S.2    Han, J.J.3    Mandel, G.4
  • 16
    • 33644536713 scopus 로고    scopus 로고
    • Tunicates and not cephalochordates are the closest living relatives of vertebrates
    • Delsuc F, Brinkmann H, Chourrout D, Philippe H (2006) Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439: 965-968
    • (2006) Nature , vol.439 , pp. 965-968
    • Delsuc, F.1    Brinkmann, H.2    Chourrout, D.3    Philippe, H.4
  • 17
    • 44649088993 scopus 로고    scopus 로고
    • Altered miRNA repertoire in the simplified chordate, Oikopleura dioica
    • Fu X, Adamski M, Thompson EM (2008) Altered miRNA repertoire in the simplified chordate, Oikopleura dioica. Mol Biol Evol 25: 1067-1080
    • (2008) Mol Biol Evol , vol.25 , pp. 1067-1080
    • Fu, X.1    Adamski, M.2    Thompson, E.M.3
  • 18
    • 0141742278 scopus 로고    scopus 로고
    • Transcript mapping and genome annotation of ascidian mtDNA using EST data
    • Gissi C, Pesole G (2003) Transcript mapping and genome annotation of ascidian mtDNA using EST data. Genome Res 13: 2203-2212
    • (2003) Genome Res , vol.13 , pp. 2203-2212
    • Gissi, C.1    Pesole, G.2
  • 20
    • 3042767202 scopus 로고    scopus 로고
    • MicroRNAs: Small RNAs with a big role in gene regulation
    • He L, Hannon GJ (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5: 522-531
    • (2004) Nat Rev Genet , vol.5 , pp. 522-531
    • He, L.1    Hannon, G.J.2
  • 21
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31: 3429-3431
    • (2003) Nucleic Acids Res , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 22
    • 33744458441 scopus 로고    scopus 로고
    • Regulatory blueprint for a chordate embryo
    • Imai KS, Levine M, Satoh N, Satou Y (2006) Regulatory blueprint for a chordate embryo. Science 312: 1183-1187
    • (2006) Science , vol.312 , pp. 1183-1187
    • Imai, K.S.1    Levine, M.2    Satoh, N.3    Satou, Y.4
  • 25
    • 20444440706 scopus 로고    scopus 로고
    • Depletion of human micro-RNA miR-125b reveals that it is critical for the proliferation of differentiated cells but not for the downregulation of putative targets during differentiation
    • Lee YS, Kim HK, Chung S, Kim KS, Dutta A (2005) Depletion of human micro-RNA miR-125b reveals that it is critical for the proliferation of differentiated cells but not for the downregulation of putative targets during differentiation. J Biol Chem 280: 16635-16641
    • (2005) J Biol Chem , vol.280 , pp. 16635-16641
    • Lee, Y.S.1    Kim, H.K.2    Chung, S.3    Kim, K.S.4    Dutta, A.5
  • 26
    • 16344366331 scopus 로고    scopus 로고
    • Profile-based detection of microRNA precursors in animal genomes
    • Legendre M, Lambert A, Gautheret D (2005) Profile-based detection of microRNA precursors in animal genomes. Bioinformatics 21: 841-845
    • (2005) Bioinformatics , vol.21 , pp. 841-845
    • Legendre, M.1    Lambert, A.2    Gautheret, D.3
  • 29
    • 3042752769 scopus 로고    scopus 로고
    • An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues
    • Liu CG, Calin GA, Meloon B, Gamliel N, Sevignani C, et al. (2004) An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc Natl Acad Sci USA 101: 9740-9744
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 9740-9744
    • Liu, C.G.1    Calin, G.A.2    Meloon, B.3    Gamliel, N.4    Sevignani, C.5
  • 30
    • 56949083333 scopus 로고    scopus 로고
    • Computational prediction of amphioxus microRNA genes and their targets
    • Luo Y, Zhang S (2009) Computational prediction of amphioxus microRNA genes and their targets. Gene 428: 41-46
    • (2009) Gene , vol.428 , pp. 41-46
    • Luo, Y.1    Zhang, S.2
  • 31
    • 27544495467 scopus 로고    scopus 로고
    • Non-coding RNAs in Ciona intestinalis
    • Missal K, Rose D, Stadler PF (2005) Non-coding RNAs in Ciona intestinalis. Bioinformatics 21 Suppl 2: ii77-78
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Missal, K.1    Rose, D.2    Stadler, P.F.3
  • 32
    • 39149087993 scopus 로고    scopus 로고
    • Computational prediction and experimental validation of Ciona intestinalis microRNA genes
    • Norden-Krichmar TM, Holtz J, Pasquinelli AE, Gaasterland T (2007) Computational prediction and experimental validation of Ciona intestinalis microRNA genes. BMC Genomics 8: 445
    • (2007) BMC Genomics , vol.8 , pp. 445
    • Norden-Krichmar, T.M.1    Holtz, J.2    Pasquinelli, A.E.3    Gaasterland, T.4
  • 33
    • 0036437372 scopus 로고    scopus 로고
    • Control of developmental timing by microRNAs and their targets
    • Pasquinelli AE, Ruvkun G (2002) Control of developmental timing by microRNAs and their targets. Annu Rev Cell Dev Biol 18: 495-513
    • (2002) Annu Rev Cell Dev Biol , vol.18 , pp. 495-513
    • Pasquinelli, A.E.1    Ruvkun, G.2
  • 34
    • 0034597777 scopus 로고    scopus 로고
    • Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA
    • Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, et al. (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408: 86-89
    • (2000) Nature , vol.408 , pp. 86-89
    • Pasquinelli, A.E.1    Reinhart, B.J.2    Slack, F.3    Martindale, M.Q.4    Kuroda, M.I.5
  • 39
    • 26944488352 scopus 로고    scopus 로고
    • Surfing with the tunicates into the postgenome era
    • Satoh N, Levine M (2005) Surfing with the tunicates into the postgenome era. Genes Dev 19: 2407-2411
    • (2005) Genes Dev , vol.19 , pp. 2407-2411
    • Satoh, N.1    Levine, M.2
  • 40
    • 0037677689 scopus 로고    scopus 로고
    • Ciona intestinalis: An emerging model for whole-genome analyses
    • Satoh N, Satou Y, Davidson B, Levine M (2003) Ciona intestinalis: an emerging model for whole-genome analyses. Trends Genet 19: 376-381
    • (2003) Trends Genet , vol.19 , pp. 376-381
    • Satoh, N.1    Satou, Y.2    Davidson, B.3    Levine, M.4
  • 41
    • 2342642197 scopus 로고    scopus 로고
    • A high-throughput method to monitor the expression of microRNA precursors
    • Schmittgen TD, Jiang J, Liu Q, Yang L (2004) A high-throughput method to monitor the expression of microRNA precursors. Nucleic Acids Res 32: e43
    • (2004) Nucleic Acids Res , vol.32
    • Schmittgen, T.D.1    Jiang, J.2    Liu, Q.3    Yang, L.4
  • 42
    • 0037790717 scopus 로고    scopus 로고
    • Temporal regulation of microRNA expression in Drosophila melanogaster mediated by hormonal signals and broadcomplex gene activity
    • Sempere LF, Sokol NS, Dubrovsky EB, Berger EM, Ambros V (2003) Temporal regulation of microRNA expression in Drosophila melanogaster mediated by hormonal signals and broadcomplex gene activity. Dev Biol 259: 9-18
    • (2003) Dev Biol , vol.259 , pp. 9-18
    • Sempere, L.F.1    Sokol, N.S.2    Dubrovsky, E.B.3    Berger, E.M.4    Ambros, V.5
  • 43
    • 59649103076 scopus 로고    scopus 로고
    • A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate
    • Shi W, Hendrix D, Levine M, Haley B (2009) A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate. Nat Struct Mol Biol 16: 183-189
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 183-189
    • Shi, W.1    Hendrix, D.2    Levine, M.3    Haley, B.4
  • 45
    • 28944439309 scopus 로고    scopus 로고
    • Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution
    • Stark A, Brennecke J, Bushati N, Russell RB, Cohen SM (2005) Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution. Cell 123: 1133-1146
    • (2005) Cell , vol.123 , pp. 1133-1146
    • Stark, A.1    Brennecke, J.2    Bushati, N.3    Russell, R.B.4    Cohen, S.M.5
  • 47
    • 13944262052 scopus 로고    scopus 로고
    • A custom microarray platform for analysis of microRNA gene expression
    • Thomson JM, Parker J, Perou CM, Hammond SM (2004) A custom microarray platform for analysis of microRNA gene expression. Nat Methods 1: 47-53
    • (2004) Nat Methods , vol.1 , pp. 47-53
    • Thomson, J.M.1    Parker, J.2    Perou, C.M.3    Hammond, S.M.4
  • 48
    • 23744446773 scopus 로고    scopus 로고
    • Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
    • Vinson JP, Jaffe DB, O'Neill K, Karlsson EK, Stange-Thomann N, et al. (2005) Assembly of polymorphic genomes: algorithms and application to Ciona savignyi. Genome Res 15: 1127-1135
    • (2005) Genome Res , vol.15 , pp. 1127-1135
    • Vinson, J.P.1    Jaffe, D.B.2    O'Neill, K.3    Karlsson, E.K.4    Stange-Thomann, N.5
  • 49
    • 34147157651 scopus 로고    scopus 로고
    • The microRNA miR-124 antagonizes the anti-neural REST/SCP1 pathway during embryonic CNS development
    • Visvanathan J, Lee S, Lee B, Lee JW, Lee SK (2007) The microRNA miR-124 antagonizes the anti-neural REST/SCP1 pathway during embryonic CNS development. Genes Dev 21: 744-749
    • (2007) Genes Dev , vol.21 , pp. 744-749
    • Visvanathan, J.1    Lee, S.2    Lee, B.3    Lee, J.W.4    Lee, S.K.5
  • 51
    • 24644476482 scopus 로고    scopus 로고
    • MicroRNA identification based on sequence and structure alignment
    • DOI 10.1093/bioinformatics/bti562
    • Wang X, Zhang J, Li F, Gu J, He T, Zhang X, Li Y (2005) MicroRNA identification based on sequence and structure alignment. Bioinformatics 21: 3610-3614 (Pubitemid 41264095)
    • (2005) Bioinformatics , vol.21 , Issue.18 , pp. 3610-3614
    • Wang, X.1    Zhang, J.2    Li, F.3    Gu, J.4    He, T.5    Zhang, X.6    Li, Y.7
  • 53
    • 26944495173 scopus 로고    scopus 로고
    • MicroRNA function in animal development
    • Wienholds E, Plasterk RH (2005) MicroRNA function in animal development. FEBS Lett 579: 5911-5922
    • (2005) FEBS Lett , vol.579 , pp. 5911-5922
    • Wienholds, E.1    Plasterk, R.H.2
  • 54
    • 15244358503 scopus 로고    scopus 로고
    • Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
    • Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M (2005) Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature 434: 338-345
    • (2005) Nature , vol.434 , pp. 338-345
    • Xie, X.1    Lu, J.2    Kulbokas, E.J.3    Golub, T.R.4    Mootha, V.5    Lindblad-Toh, K.6    Lander, E.S.7    Kellis, M.8
  • 55
    • 33751250183 scopus 로고    scopus 로고
    • Computational identification of microRNAs and their targets
    • DOI 10.1016/j.compbiolchem.2006.08.006, PII S1476927106000697
    • Zhang B, Pan X, Wang Q, Cobb GP, Anderson TA (2006) Computational identification of microRNAs and their targets. Comput Biol Chem 30: 395-407 (Pubitemid 44792553)
    • (2006) Computational Biology and Chemistry , vol.30 , Issue.6 , pp. 395-407
    • Zhang, B.1    Pan, X.2    Wang, Q.3    Cobb, G.P.4    Anderson, T.A.5
  • 56
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415
    • (2003) Nucleic Acids Res , vol.31 , pp. 3406-3415
    • Zuker, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.