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Volumn 4, Issue 5, 2014, Pages 871-883

Bioinformatics analysis of alternative polyadenylation in green alga Chlamydomonas reinhardtii using transcriptome sequences from three different sequencing platforms

Author keywords

Alternative polyadenylation; Alternative splicing; Chlamydomonas reinhardtii; Intron retention; Poly(A) signals; Sequencing platforms

Indexed keywords

HYDROLASE; LIGASE; POLYADENYLIC ACID; SPACER DNA; TRANSCRIPTOME;

EID: 84901379457     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.114.010249     Document Type: Article
Times cited : (23)

References (46)
  • 1
    • 33846573830 scopus 로고    scopus 로고
    • Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis
    • Campbell, M. A., B. J. Haas, J. P. Hamilton, S. M. Mount, and C. R. Buell, 2006 Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 7: 327.
    • (2006) BMC Genomics , vol.7 , pp. 327
    • Campbell, M.A.1    Haas, B.J.2    Hamilton, J.P.3    Mount, S.M.4    Buell, C.R.5
  • 2
    • 84879408529 scopus 로고    scopus 로고
    • Alternative cleavage and polyadenylation: extent, regulation and function
    • Elkon, R., A. P. Ugalde, and R. Agami, 2013 Alternative cleavage and polyadenylation: extent, regulation and function. Nat. Rev. Genet. 14: 496-506.
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 496-506
    • Elkon, R.1    Ugalde, A.P.2    Agami, R.3
  • 3
    • 80052979140 scopus 로고    scopus 로고
    • Mechanisms and consequences of alternative polyadenylation
    • Di Giammartino, D. C., K. Nishida, and J. L. Manley, 2011 Mechanisms and consequences of alternative polyadenylation. Mol. Cell 43: 853-866.
    • (2011) Mol. Cell , vol.43 , pp. 853-866
    • Di Giammartino, D.C.1    Nishida, K.2    Manley, J.L.3
  • 4
    • 0033598805 scopus 로고    scopus 로고
    • In silico detection of control signals: mRNA 39-end-processing sequences in diverse species
    • Graber, J. H., C. R. Cantor, S. C. Mohr, and T. F. Smith, 1999 In silico detection of control signals: mRNA 39-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
  • 5
    • 25844497003 scopus 로고    scopus 로고
    • Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation
    • Hu, J., C. S. Lutz, J. Wilusz, and B. Tian, 2005 Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation. RNA 11: 1485-1493.
    • (2005) RNA , vol.11 , pp. 1485-1493
    • Hu, J.1    Lutz, C.S.2    Wilusz, J.3    Tian, B.4
  • 6
    • 84869187282 scopus 로고    scopus 로고
    • Plant polyadenylation factors: conservation and variety in the polyadenylation complex in plants
    • Hunt, A. G., D. Xing, and Q. Q. Li, 2012 Plant polyadenylation factors: conservation and variety in the polyadenylation complex in plants. BMC Genomics 13: 641.
    • (2012) BMC Genomics , vol.13 , pp. 641
    • Hunt, A.G.1    Xing, D.2    Li, Q.Q.3
  • 7
    • 7044269115 scopus 로고    scopus 로고
    • Nontemplated nucleotide addition prior to polyadenylation: a comparison of Arabidopsis cDNA and genomic sequences
    • Jin, Y., and T. Bian, 2004 Nontemplated nucleotide addition prior to polyadenylation: a comparison of Arabidopsis cDNA and genomic sequences. RNA 10: 1695-1697.
    • (2004) RNA , vol.10 , pp. 1695-1697
    • Jin, Y.1    Bian, T.2
  • 8
    • 77649098171 scopus 로고    scopus 로고
    • Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii
    • Labadorf, A., A. Link, M. F. Rogers, J. Thomas, A. S. Reddy et al., 2010 Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii. BMC Genomics 11: 114.
    • (2010) BMC Genomics , vol.11 , pp. 114
    • Labadorf, A.1    Link, A.2    Rogers, M.F.3    Thomas, J.4    Reddy, A.S.5
  • 9
    • 52049117699 scopus 로고    scopus 로고
    • Expressed sequence tags with cDNA termini: previously overlooked resources for gene annotation and transcriptome exploration in Chlamydomonas reinhardtii
    • Liang, C., Y. Liu, L. Liu, A. C. Davis, Y. Shen et al., 2008 Expressed sequence tags with cDNA termini: previously overlooked resources for gene annotation and transcriptome exploration in Chlamydomonas reinhardtii. Genetics 179: 83-93.
    • (2008) Genetics , vol.179 , pp. 83-93
    • Liang, C.1    Liu, Y.2    Liu, L.3    Davis, A.C.4    Shen, Y.5
  • 10
    • 27244444905 scopus 로고    scopus 로고
    • Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures
    • Loke, J. C., E. A. Stahlberg, D. G. Strenski, B. J. Haas, P. C. Wood et al., 2005 Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures. Plant Physiol. 138: 1457-1468.
    • (2005) Plant Physiol. , vol.138 , pp. 1457-1468
    • Loke, J.C.1    Stahlberg, E.A.2    Strenski, D.G.3    Haas, B.J.4    Wood, P.C.5
  • 11
    • 33749257983 scopus 로고    scopus 로고
    • The disparate nature of "intergenic" polyadenylation sites
    • Lopez, F., S. Granjeaud, T. Ara, B. Ghattas, and D. Gautheret, 2006 The disparate nature of "intergenic" polyadenylation sites. RNA 12: 1794- 1801.
    • (2006) RNA , vol.12
    • Lopez, F.1    Granjeaud, S.2    Ara, T.3    Ghattas, B.4    Gautheret, D.5
  • 12
    • 84891917151 scopus 로고    scopus 로고
    • Role of alternative polyadenylation in epigenetic silencing and antisilencing
    • Ma, L., C. Guo, and Q. Q. Li, 2014 Role of alternative polyadenylation in epigenetic silencing and antisilencing. Proc. Natl. Acad. Sci. USA 111: 9-10.
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , pp. 9-10
    • Ma, L.1    Guo, C.2    Li, Q.Q.3
  • 13
    • 0028982058 scopus 로고
    • Volvox carteri alpha 2- and beta 2-tubulin-encoding genes: regulatory signals and transcription
    • Mages, W., B. Cresnar, J. F. Harper, M. Bruderlein, and R. Schmitt, 1995 Volvox carteri alpha 2- and beta 2-tubulin-encoding genes: regulatory signals and transcription. Gene 160: 47-54.
    • (1995) Gene , vol.160 , pp. 47-54
    • Mages, W.1    Cresnar, B.2    Harper, J.F.3    Bruderlein, M.4    Schmitt, R.5
  • 15
    • 39649117755 scopus 로고    scopus 로고
    • The impact of next-generation sequencing technology on genetics
    • Mardis, E. R., 2008 The impact of next-generation sequencing technology on genetics. Trends Genet. 24: 133-141.
    • (2008) Trends Genet. , vol.24 , pp. 133-141
    • Mardis, E.R.1
  • 16
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high-density picolitre reactors
    • Margulies, M., M. Egholm, W. E. Altman, S. Attiya, J. S. Bader et al., 2005 Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1    Egholm, M.2    Altman, W.E.3    Attiya, S.4    Bader, J.S.5
  • 17
    • 35348896591 scopus 로고    scopus 로고
    • The Chlamydomonas genome reveals the evolution of key animal and plant functions
    • Merchant, S. S., S. E. Prochnik, O. Vallon, E. H. Harris, S. J. Karpowicz et al., 2007 The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318: 245-250.
    • (2007) Science , vol.318 , pp. 245-250
    • Merchant, S.S.1    Prochnik, S.E.2    Vallon, O.3    Harris, E.H.4    Karpowicz, S.J.5
  • 18
    • 84877111454 scopus 로고    scopus 로고
    • Widespread and extensive lengthening of 39 UTRs in the mammalian brain
    • Miura, P., S. Shenker, C. Andreu-Agullo, J. O. Westholm, and E. C. Lai, 2013 Widespread and extensive lengthening of 39 UTRs in the mammalian brain. Genome Res. 23: 812-825.
    • (2013) Genome Res. , vol.23 , pp. 812-825
    • Miura, P.1    Shenker, S.2    Andreu-Agullo, C.3    Westholm, J.O.4    Lai, E.C.5
  • 19
    • 84855219212 scopus 로고    scopus 로고
    • Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes
    • Oyola, S. O., T. D. Otto, Y. Gu, G. Maslen, M. Manske et al., 2012 Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics 13: 1.
    • (2012) BMC Genomics , vol.13 , pp. 1
    • Oyola, S.O.1    Otto, T.D.2    Gu, Y.3    Maslen, G.4    Manske, M.5
  • 21
    • 78649910014 scopus 로고    scopus 로고
    • Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation
    • Ozsolak, F., P. Kapranov, S. Foissac, S. W. Kim, E. Fishilevich et al., 2010 Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell 143: 1018-1029.
    • (2010) Cell , vol.143 , pp. 1018-1029
    • Ozsolak, F.1    Kapranov, P.2    Foissac, S.3    Kim, S.W.4    Fishilevich, E.5
  • 22
    • 0030265996 scopus 로고    scopus 로고
    • Plant mRNA 39-end formation
    • Rothnie, H. M., 1996 Plant mRNA 39-end formation. Plant Mol. Biol. 32: 43-61.
    • (1996) Plant Mol. Biol. , vol.32 , pp. 43-61
    • Rothnie, H.M.1
  • 23
    • 0016800090 scopus 로고
    • A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase
    • Sanger, F., and A. R. Coulson, 1975 A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J. Mol. Biol. 94: 441-448.
    • (1975) J. Mol. Biol. , vol.94 , pp. 441-448
    • Sanger, F.1    Coulson, A.R.2
  • 25
    • 37749031255 scopus 로고    scopus 로고
    • Next-generation sequencing transforms today's biology
    • Schuster, S. C., 2008 Next-generation sequencing transforms today's biology. Nat. Methods 5: 16-18.
    • (2008) Nat. Methods , vol.5 , pp. 16-18
    • Schuster, S.C.1
  • 26
    • 52049086511 scopus 로고    scopus 로고
    • Unique features of nuclear mRNA poly(A) signals and alternative polyadenylation in Chlamydomonas reinhardtii
    • Shen, Y., Y. Liu, L. Liu, C. Liang, and Q. Q. Li, 2008a Unique features of nuclear mRNA poly(A) signals and alternative polyadenylation 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
  • 27
    • 44349130371 scopus 로고    scopus 로고
    • Genome level analysis of rice mRNA 39-end processing signals and alternative polyadenylation
    • Shen, Y., G. Ji, B. J. Haas, X. Wu, J. Zheng et al., 2008b Genome level analysis of rice mRNA 39-end processing signals and alternative polyadenylation. Nucleic Acids Res. 36: 3150-3161.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 3150-3161
    • Shen, Y.1    Ji, G.2    Haas, B.J.3    Wu, X.4    Zheng, J.5
  • 28
    • 80052519170 scopus 로고    scopus 로고
    • Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing
    • Shen, Y., R. C. Venu, K. Nobuta, X. Wu, V. Notibala et al., 2011 Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing. Genome Res. 21: 1478-1486.
    • (2011) Genome Res. , vol.21 , pp. 1478-1486
    • Shen, Y.1    Venu, R.C.2    Nobuta, K.3    Wu, X.4    Notibala, V.5
  • 29
    • 84864695758 scopus 로고    scopus 로고
    • Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation
    • Sherstnev, A., C. Duc, C. Cole, V. Zacharaki, C. Hornyik et al., 2012 Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation. Nat. Struct. Mol. Biol. 19: 845-852.
    • (2012) Nat. Struct. Mol. Biol. , vol.19 , pp. 845-852
    • Sherstnev, A.1    Duc, C.2    Cole, C.3    Zacharaki, V.4    Hornyik, C.5
  • 30
    • 73649139638 scopus 로고    scopus 로고
    • Global changes in processing of mRNA 39 untranslated regions characterize clinically distinct cancer subtypes
    • Singh, P., T. L. Alley, S. M. Wright, S. Kamdar, W. Schott et al., 2009 Global changes in processing of mRNA 39 untranslated regions characterize clinically distinct cancer subtypes. Cancer Res. 69: 9422-9430.
    • (2009) Cancer Res. , vol.69 , pp. 9422-9430
    • Singh, P.1    Alley, T.L.2    Wright, S.M.3    Kamdar, S.4    Schott, W.5
  • 31
    • 40049091292 scopus 로고    scopus 로고
    • Using native and syntenically mapped cDNA alignments to improve de novo gene finding
    • Stanke, M., M. Diekhans, R. Baertsch, and D. Haussler, 2008 Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24: 637-644.
    • (2008) Bioinformatics , vol.24 , pp. 637-644
    • Stanke, M.1    Diekhans, M.2    Baertsch, R.3    Haussler, D.4
  • 32
    • 33744761434 scopus 로고    scopus 로고
    • Hierarchical clustering via joint between- within distances: extending Ward's minimum variance method
    • Szekely, G. J., and M. L. Rizzo, 2005 Hierarchical clustering via joint between- within distances: extending Ward's minimum variance method. J. Classification 22: 151-183.
    • (2005) J. Classification , vol.22 , pp. 151-183
    • Szekely, G.J.1    Rizzo, M.L.2
  • 33
    • 36849024331 scopus 로고    scopus 로고
    • Intronic polyadenylation signal sequences and alternate splicing generate human soluble Flt1 variants and regulate the abundance of soluble Flt1 in the placenta
    • Thomas, C. P., J. I. Andrews, and K. Z. Liu, 2007 Intronic polyadenylation signal sequences and alternate splicing generate human soluble Flt1 variants and regulate the abundance of soluble Flt1 in the placenta. FASEB J. 21: 3885-3895.
    • (2007) FASEB J. , vol.21 , pp. 3885-3895
    • Thomas, C.P.1    Andrews, J.I.2    Liu, K.Z.3
  • 34
    • 77956096765 scopus 로고    scopus 로고
    • Alternate processing of Flt1 transcripts is directed by conserved cis-elements within an intronic region of FLT1 that reciprocally regulates splicing and polyadenylation
    • Thomas, C. P., N. S. Raikwar, E. A. Kelley, and K. Z. Liu, 2010 Alternate processing of Flt1 transcripts is directed by conserved cis-elements within an intronic region of FLT1 that reciprocally regulates splicing and polyadenylation. Nucleic Acids Res. 38: 5130-5140.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 5130-5140
    • Thomas, C.P.1    Raikwar, N.S.2    Kelley, E.A.3    Liu, K.Z.4
  • 35
    • 84871881698 scopus 로고    scopus 로고
    • Genome-wide control of polyadenylation site choice by CPSF30 in Arabidopsis
    • Thomas, P. E., X. Wu, M. Liu, B. Gaffney, G. Ji et al., 2012 Genome-wide control of polyadenylation site choice by CPSF30 in Arabidopsis. Plant Cell 24: 4376-4388.
    • (2012) Plant Cell , vol.24 , pp. 4376-4388
    • Thomas, P.E.1    Wu, X.2    Liu, M.3    Gaffney, B.4    Ji, G.5
  • 36
    • 13744254695 scopus 로고    scopus 로고
    • A large-scale analysis of mRNA polyadenylation of human and mouse genes
    • Tian, B., J. Hu, H. Zhang, and C. S. Lutz, 2005 A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res. 33: 201-212.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 201-212
    • Tian, B.1    Hu, J.2    Zhang, H.3    Lutz, C.S.4
  • 37
    • 33846870354 scopus 로고    scopus 로고
    • Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing
    • Tian, B., Z. Pan, and J. Y. Lee, 2007 Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing. Genome Res. 17: 156-165.
    • (2007) Genome Res. , vol.17 , pp. 156-165
    • Tian, B.1    Pan, Z.2    Lee, J.Y.3
  • 38
    • 0032483307 scopus 로고    scopus 로고
    • Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
    • van Helden, J., B. André, and J. Collado-Vides, 1998 Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol. 281: 827-42.
    • (1998) J Mol Biol. , vol.281 , pp. 827-842
    • van Helden, J.1    André, B.2    Collado-Vides, J.3
  • 39
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: a revolutionary tool for transcriptomics
    • Wang, Z., M. Gerstein, and M. Snyder, 2009 RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10: 57-63.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 40
    • 34248545149 scopus 로고    scopus 로고
    • Gain and loss of polyadenylation signals during evolution of green algae
    • Wodniok, S., A. Simon, G. Glockner, and B. Becker, 2007 Gain and loss of polyadenylation signals during evolution of green algae. BMC Evol. Biol. 7: 65.
    • (2007) BMC Evol. Biol. , vol.7 , pp. 65
    • Wodniok, S.1    Simon, A.2    Glockner, G.3    Becker, B.4
  • 41
    • 18744383071 scopus 로고    scopus 로고
    • GMAP: a genomic mapping and alignment program for mRNA and EST sequences
    • Wu, T. D., and C. K. Watanabe, 2005 GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21: 1859-1875.
    • (2005) Bioinformatics , vol.21 , pp. 1859-1875
    • Wu, T.D.1    Watanabe, C.K.2
  • 42
    • 79961084431 scopus 로고    scopus 로고
    • Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation
    • Wu, X., M. Liu, B. Downie, C. Liang, G. Ji et al., 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
  • 43
    • 80054004461 scopus 로고    scopus 로고
    • Translation initiation: a regulatory role for poly(A) tracts in front of the AUG codon in Saccharomyces cerevisiae
    • Xia, X., V. MacKay, X. Yao, J. Wu, F. Miura et al., 2011 Translation initiation: a regulatory role for poly(A) tracts in front of the AUG codon in Saccharomyces cerevisiae. Genetics 189: 469-478.
    • (2011) Genetics , vol.189 , pp. 469-478
    • Xia, X.1    MacKay, V.2    Yao, X.3    Wu, J.4    Miura, F.5
  • 44
    • 79961040833 scopus 로고    scopus 로고
    • Alternative polyadenylation and gene expression regulation in plants, Wiley interdisciplinary reviews
    • Xing, D., and Q. Q. Li, 2011 Alternative polyadenylation and gene expression regulation in plants. Wiley interdisciplinary reviews. RNA 2: 445-458.
    • (2011) RNA , vol.2 , pp. 445-458
    • Xing, D.1    Li, Q.Q.2
  • 45
    • 0033059981 scopus 로고    scopus 로고
    • Formation of mRNA 39 ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis, Microbiology and molecular biology reviews
    • Zhao, J., L. Hyman, and C. Moore, 1999 Formation of mRNA 39 ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiology and molecular biology reviews. Microbiol. Mol. Biol. Rev. 63: 405-445.
    • (1999) Microbiol. Mol. Biol. Rev. , vol.63 , pp. 405-445
    • Zhao, J.1    Hyman, L.2    Moore, C.3
  • 46
    • 48449104617 scopus 로고    scopus 로고
    • GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis
    • Zheng, Q., and X.-J. Wang, 2008 GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res. 36: W358- 363.
    • (2008) Nucleic Acids Res. , vol.36
    • Zheng, Q.1    Wang, X.-J.2


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