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Volumn 287, Issue 11-12, 2012, Pages 895-907

In silico prediction of mRNA poly(A) sites in Chlamydomonas reinhardtii

Author keywords

Alternative polyadenylation; Chlamydomonas; Combined classifier; Pattern assembly; Polyadenylation

Indexed keywords

MESSENGER RNA; POLYADENYLIC ACID;

EID: 84870439173     PISSN: 16174615     EISSN: 16174623     Source Type: Journal    
DOI: 10.1007/s00438-012-0725-5     Document Type: Article
Times cited : (9)

References (37)
  • 1
    • 78349239707 scopus 로고    scopus 로고
    • POLYAR, a new computer program for prediction of poly(A) sites in human sequences
    • Akhtar MN, Bukhari SA, Fazal Z, Qamar R, Shahmuradov I (2010) POLYAR, a new computer program for prediction of poly(A) sites in human sequences. BMC Genomics 11:646
    • (2010) BMC Genomics , vol.11 , pp. 646
    • Akhtar, M.N.1    Bukhari, S.A.2    Fazal, Z.3    Qamar, R.4    Shahmuradov, I.5
  • 2
    • 0033858202 scopus 로고    scopus 로고
    • Patterns of variant polyadenylation signal usage in human genes
    • DOI 10.1101/gr.10.7.1001
    • Beaudoing E, Freier S, Wyatt JR, Claverie JM, Gautheret D (2000) Patterns of variant polyadenylation signal usage in human genes. Genome Res 10:1001-1010 (Pubitemid 30608635)
    • (2000) Genome Research , vol.10 , Issue.7 , pp. 1001-1010
    • Beaudoing, E.1    Freier, S.2    Wyatt, J.R.3    Claverie, J.-M.4    Gautheret, D.5
  • 4
    • 33749997848 scopus 로고    scopus 로고
    • Prediction of mRNA polyadenylation sites by support vector machine
    • DOI 10.1093/bioinformatics/btl394
    • Cheng Y, Miura RM, Tian B (2006) Prediction of mRNA polyadenylation sites by support vector machine. Bioinformatics 22:2320-2325 (Pubitemid 44566959)
    • (2006) Bioinformatics , vol.22 , Issue.19 , pp. 2320-2325
    • Cheng, Y.1    Miura, R.M.2    Tian, B.3
  • 6
    • 0033081347 scopus 로고    scopus 로고
    • Genomic detection of new yeast pre-mRNA 3'-end-processing signals
    • DOI 10.1093/nar/27.3.888
    • Graber JH, Cantor CR, Mohr SC, Smith TF (1999a) Genomic detection of new yeast pre-mRNA 30-end-processing signals. Nucleic Acids Res 27:888-894 (Pubitemid 29209379)
    • (1999) Nucleic Acids Research , vol.27 , Issue.3 , pp. 888-894
    • Graber, J.H.1    Cantor, C.R.2    Mohr, S.C.3    Smith, T.F.4
  • 7
    • 0033598805 scopus 로고    scopus 로고
    • In silico detection of control signals: MRNA 30 end-processing sequences in diverse species
    • Graber JH, Cantor CR, Mohr SC, Smith TF (1999b) In silico detection of control signals: mRNA 30 end-processing sequences in diverse species. Proc Natl Acad Sci USA 96:14055-14060
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 14055-14060
    • Graber, J.H.1    Cantor, C.R.2    Mohr, S.C.3    Smith, T.F.4
  • 8
    • 3242672609 scopus 로고    scopus 로고
    • A probabilistic model of 3' end formation in Caenorhabditis elegans
    • DOI 10.1093/nar/gkh656
    • Hajarnavis A, Korf I, Durbin R (2004) A probabilistic model of 30 end formation in Caenorhabditis elegans. Nucleic Acids Res 32:3392-3399 (Pubitemid 39117455)
    • (2004) Nucleic Acids Research , vol.32 , Issue.11 , pp. 3392-3399
    • Hajarnavis, A.1    Korf, I.2    Durbin, R.3
  • 10
    • 25844497003 scopus 로고    scopus 로고
    • Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation
    • DOI 10.1261/rna.2107305
    • Hu J, Lutz CS, Wilusz J, Tian B (2005) Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation. RNA 11:1485-1493 (Pubitemid 41396918)
    • (2005) RNA , vol.11 , Issue.10 , pp. 1485-1493
    • Hu, J.1    Lutz, C.S.2    Wilusz, J.3    Tian, B.4
  • 11
    • 77949538391 scopus 로고    scopus 로고
    • Reprogramming of 3' untranslated regions of mRNAs by alternative polyadenylation in generation of pluripotent stem cells from different cell types
    • Ji Z, Tian B (2009) Reprogramming of 3' untranslated regions of mRNAs by alternative polyadenylation in generation of pluripotent stem cells from different cell types. PLoS ONE 4:e8419
    • (2009) PLoS ONE , vol.4
    • Ji, Z.1    Tian, B.2
  • 13
    • 66049104920 scopus 로고    scopus 로고
    • Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development
    • Ji Z, Lee JY, Pan Z, Jiang B, Tian B (2009) Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc Natl Acad Sci USA 106:7028-7033
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 7028-7033
    • Ji, Z.1    Lee, J.Y.2    Pan, Z.3    Jiang, B.4    Tian, B.5
  • 14
    • 77954447517 scopus 로고    scopus 로고
    • Messenger RNA polyadenylation site recognition in green alga Chlamydomonas Reinhardtii
    • Ji G, Wu X, Li Q, Zheng J (2010a) Messenger RNA polyadenylation site recognition in green alga Chlamydomonas Reinhardtii. Lect Notes Comput Sci 6063:17-26
    • (2010) Lect Notes Comput Sci , vol.6063 , pp. 17-26
    • Ji, G.1    Wu, X.2    Li, Q.3    Zheng, J.4
  • 15
    • 77954620520 scopus 로고    scopus 로고
    • A classification-based prediction model of messenger RNA polyadenylation sites
    • Ji G, Wu X, Shen Y, Huang J, Li QQ (2010b) A classification-based prediction model of messenger RNA polyadenylation sites. J Theor Biol 265:287-296
    • (2010) J Theor Biol , vol.265 , pp. 287-296
    • Ji, G.1    Wu, X.2    Shen, Y.3    Huang, J.4    Li, Q.Q.5
  • 16
    • 0035036534 scopus 로고    scopus 로고
    • Gene structure prediction and alternative splicing analysis using genomically aligned ESTs
    • DOI 10.1101/gr.155001
    • Kan ZY, Rouchka EC, Gish WR, States DJ (2001) Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res 11:889-900 (Pubitemid 32447871)
    • (2001) Genome Research , vol.11 , Issue.5 , pp. 889-900
    • Kan, Z.1    Rouchka, E.C.2    Gish, W.R.3    States, D.J.4
  • 17
    • 46749108874 scopus 로고    scopus 로고
    • Recognition of polyadenylation sites from Arabidopsis genomic sequences
    • Koh CH, Wong L (2007) Recognition of polyadenylation sites from Arabidopsis genomic sequences. Genome Inform 19:73-82
    • (2007) Genome Inform , vol.19 , pp. 73-82
    • Koh, C.H.1    Wong, L.2
  • 18
    • 37849040553 scopus 로고    scopus 로고
    • Combining classifiers to predict gene function in Arabidopsis thaliana using largescale gene expression measurements
    • Lan H, Carson R, Provart NJ, Bonner AJ (2007) Combining classifiers to predict gene function in Arabidopsis thaliana using largescale gene expression measurements. BMC Bioinform 8:358
    • (2007) BMC Bioinform , vol.8 , pp. 358
    • Lan, H.1    Carson, R.2    Provart, N.J.3    Bonner, A.J.4
  • 19
    • 10044280127 scopus 로고    scopus 로고
    • An in silico method for prediction of polyadenylation signals in human sequences
    • Liu H, Han H, Li J, Wong L (2003) An in silico method for prediction of polyadenylation signals in human sequences. Genome Inform 14:84-93
    • (2003) Genome Inform , vol.14 , pp. 84-93
    • Liu, H.1    Han, H.2    Li, J.3    Wong, L.4
  • 20
    • 74849099777 scopus 로고    scopus 로고
    • Targeted 30 processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing
    • Liu F, Marquardt S, Lister C, Swiezewski S, Dean C (2010) Targeted 30 processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing. Science 327:94-97
    • (2010) Science , vol.327 , pp. 94-97
    • Liu, F.1    Marquardt, S.2    Lister, C.3    Swiezewski, S.4    Dean, C.5
  • 21
    • 27244444905 scopus 로고    scopus 로고
    • Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures
    • DOI 10.1104/pp.105.060541
    • Loke JC, Stahlberg EA, Strenski DG, Haas BJ, Wood PC, Li QQ (2005) Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures. Plant Physiol 138:1457-1468 (Pubitemid 43142092)
    • (2005) Plant Physiology , vol.138 , Issue.3 , pp. 1457-1468
    • Loke, J.C.1    Stahlberg, E.A.2    Strenski, D.G.3    Haas, B.J.4    Wood, P.C.5    Qingshun, Q.L.6
  • 23
    • 68749113985 scopus 로고    scopus 로고
    • Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells
    • Mayr C, Bartel DP (2009) Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138:673-684
    • (2009) Cell , vol.138 , pp. 673-684
    • Mayr, C.1    Bartel, D.P.2
  • 24
    • 3543007130 scopus 로고    scopus 로고
    • Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing
    • DOI 10.1038/nbt992
    • Meyers BC, Vu TH, Tej SS, Ghazal H, Matvienko M, Agrawal V, Ning JC, Haudenschild CD (2004) Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing. Nat Biotechnol 22:1006-1011 (Pubitemid 39014478)
    • (2004) Nature Biotechnology , vol.22 , Issue.8 , pp. 1006-1011
    • Meyers, B.C.1    Vu, T.H.2    Tej, S.S.3    Ghazal, H.4    Matvienko, M.5    Agrawal, V.6    Ning, J.7    Haudenschild, C.D.8
  • 25
    • 67349093990 scopus 로고    scopus 로고
    • From systems biology to fuel - Chlamydomonas reinhardtii as a model for a systems biology approach to improve biohydrogen production
    • Rupprecht J (2009) From systems biology to fuel - Chlamydomonas reinhardtii as a model for a systems biology approach to improve biohydrogen production. J Biotechnol 142:10-20
    • (2009) J Biotechnol , vol.142 , pp. 10-20
    • Rupprecht, J.1
  • 26
    • 44349130371 scopus 로고    scopus 로고
    • Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation
    • DOI 10.1093/nar/gkn158
    • Shen Y, Ji G, Haas BJ, Wu X, Zheng J, Reese GJ, Li QQ (2008a) Genome level analysis of rice mRNA 30-end processing signals and alternative polyadenylation. Nucleic Acids Res 36:3150-3161 (Pubitemid 351737206)
    • (2008) Nucleic Acids Research , vol.36 , Issue.9 , pp. 3150-3161
    • Shen, Y.1    Ji, G.2    Haas, B.J.3    Wu, X.4    Zheng, J.5    Reese, G.J.6    Li, Q.Q.7
  • 27
    • 52049086511 scopus 로고    scopus 로고
    • Unique features of nuclear mRNA poly(A) signals and alternative polvadenylation in Chlamydomonas reinhardtii
    • Shen Y, Liu Y, Liu L, Liang C, Li QQ (2008b) Unique features of nuclear mRNA poly(A) signals and alternative polvadenylation in Chlamydomonas reinhardtii. Genetics 179:167-176
    • (2008) Genetics , vol.179 , pp. 167-176
    • Shen, Y.1    Liu, Y.2    Liu, L.3    Liang, C.4    Li, Q.Q.5
  • 28
    • 84862526272 scopus 로고    scopus 로고
    • Signals for pre-mRNA cleavage and polyadenylation
    • Tian B, Graber JH (2012) Signals for pre-mRNA cleavage and polyadenylation. Wiley Interdiscip Rev RNA 3:385-396
    • (2012) Wiley Interdiscip Rev RNA , vol.3 , pp. 385-396
    • Tian, B.1    Graber, J.H.2
  • 29
    • 13744254695 scopus 로고    scopus 로고
    • A large-scale analysis of mRNA polyadenylation of human and mouse genes
    • DOI 10.1093/nar/gki158
    • Tian B, Hu J, Zhang HB, Lutz CS (2005) A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res 33:201-212 (Pubitemid 40276942)
    • (2005) Nucleic Acids Research , vol.33 , Issue.1 , pp. 201-212
    • Tian, B.1    Hu, J.2    Zhang, H.3    Lutz, C.S.4
  • 30
    • 79957972503 scopus 로고    scopus 로고
    • PolyA-iEP: A data mining method for the effective prediction of polyadenylation sites
    • Tzanis G, Kavakiotis I, Vlahavas I (2011) PolyA-iEP: a data mining method for the effective prediction of polyadenylation sites. Expert Syst Appl 38:12398-12408
    • (2011) Expert Syst Appl , vol.38 , pp. 12398-12408
    • Tzanis, G.1    Kavakiotis, I.2    Vlahavas, I.3
  • 31
    • 0034651804 scopus 로고    scopus 로고
    • Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals
    • Van Helden J, Del Olmo M, Perez-Ortin JE (2000) Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals. Nucleic Acids Res 28:1000-1010 (Pubitemid 30085328)
    • (2000) Nucleic Acids Research , vol.28 , Issue.4 , pp. 1000-1010
    • Van Helden, J.1    Del Olmo, M.2    Perez-Ortin, J.E.3
  • 32
    • 33751018002 scopus 로고    scopus 로고
    • Rnall: An efficient algorithm for predicting RNA local secondary structural landscape in genomes
    • Wan X, Lin G, Xu D (2006) Rnall: an efficient algorithm for predicting RNA local secondary structural landscape in genomes. J Bioinform Comput Biol 4:1015-1032
    • (2006) J Bioinform Comput Biol , vol.4 , pp. 1015-1032
    • Wan, X.1    Lin, G.2    Xu, D.3
  • 36
    • 79961084431 scopus 로고    scopus 로고
    • Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation
    • Wu X, Liu M, Downie B, Liang C, Ji G, Li QQ, Hunt AG (2011) Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc Natl Acad Sci USA 108:12533-12538
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 12533-12538
    • Wu, X.1    Liu, M.2    Downie, B.3    Liang, C.4    Ji, G.5    Li, Q.Q.6    Hunt, A.G.7
  • 37
    • 79961040833 scopus 로고    scopus 로고
    • Alternative polyadenylation and gene expression regulation in plants
    • Xing D, Li QQ (2010) Alternative polyadenylation and gene expression regulation in plants. Wiley Interdiscip Rev RNA 2:445-458
    • (2010) Wiley Interdiscip Rev RNA , vol.2 , pp. 445-458
    • Xing, D.1    Li, Q.Q.2


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