Ustilago maydis transcript features identified through full-length cDNA analysis

Molecular Genetics and Genomics

Volumn 286, Issue 2, 2011, Pages 143-159

  Doyle, Colleen E ^a   Donaldson, Michael E ^a   Morrison, Erin N ^a   Saville, Barry J ^a  

^a TRENT UNIVERSITY   (Canada)

Author keywords

Full length cDNA sequencing; Gene model annotation; Poly(A) addition signals; Promoter regions; Transcript structure; Untranslated regions; UORFs; Ustilago maydis

Indexed keywords

COMPLEMENTARY DNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CONTIG MAPPING; CONTROLLED STUDY; DNA DETERMINATION; DNA LIBRARY; DNA REPLICATION; DNA SEQUENCE; GENE FUNCTION; GENE IDENTIFICATION; GENE SYNTHESIS; GENETIC MODEL; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; POLYADENYLATION; PRIORITY JOURNAL; PROMOTER REGION; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION INITIATION SITE; USTILAGO MAYDIS; EXPRESSED SEQUENCE TAG; FUNGAL GENE; FUNGAL GENOME; GENETIC DATABASE; GENETICS; INTRON; MOLECULAR GENETICS; USTILAGO;

SACCHAROMYCES CEREVISIAE; USTILAGO MAYDIS;

BASE SEQUENCE; DATABASES, GENETIC; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENES, FUNGAL; GENOME, FUNGAL; INTRONS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; USTILAGO;

EID: 80053095672     PISSN: 16174615     EISSN: 16174623     Source Type: Journal    
DOI: 10.1007/s00438-011-0634-z     Document Type: Article

References (63)

1. Alexandrov NN, Brover VV, Freidin S, Troukhan ME, Tatarinova TV, Zhang H, Swaller TJ, Lu YP, Bouck J, Flavell RB, Feldmann KA (2009) Insights into corn genes derived from large-scale cDNA sequencing. Plant Mol Biol 69(1-2): 179-194
2. Allison LA (2007) Fundamental molecular biology. Blackwell, Malden
3. Aravind L, Watanabe H, Lipman DJ, Koonin EV (2000) Lineagespecific loss and divergence of functionally linked genes in eukaryotes. Proc Natl Acad Sci USA 97(21): 11319-11324
4. Banuett F (1995) Genetics of Ustilago maydis, a fungal pathogen that induces tumors in maize. Annu Rev Genet 29: 179-208 (Pubitemid 26005341)
5. Basehoar AD, Zanton SJ, Pugh BF (2004) Identification and distinct regulation of yeast tata box-containing genes. Cell 116: 699-709 (Pubitemid 38326728)
6. Bell SP, Kobayashi R, Stillman B (1993) Yeast origin recognition complex functions in transcription silencing and DNA replication. Science (New York, NY) 262(5141): 1844-1849 (Pubitemid 24041854)
7. Borevitz JO, Ecker JR (2004) Plant genomics: the third wave. Annu Rev Genomics Hum Genet 5: 443-477 (Pubitemid 39362753)
8. Burge CB, Karlin S (1998) Finding the genes in genomic DNA. Curr Opin Struct Biol 8(3): 346-354 (Pubitemid 28321363)
9. Carninci P, Kvam C, Kitamura A, Ohsumi T, Okazaki Y, Itoh M, Kamiya A, Shibata K, Sasaki M, Izawa M, Muramatsu M, Hayashizaki Y, Schneider C (1996) High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Genomics 37: 327-336 (Pubitemid 26386957)
10. Cenik C, Derti A, Mellor JC, Berriz GF, Roth FP (2010) Genomewide functional analysis of human 50 untranslated region introns. Genome Biol 11(3): R29
11. Chung BY, Simons C, Firth AE, Brown CM, Hellens RP (2006) Effect of 50UTR introns on gene expression in Arabidopsis thaliana. BMC Genomics 7: 120
12. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14(6): 1188-1190 (Pubitemid 38811555)
13. David L, Huber W, Granovskaia M, Toedling J, Palm CJ, Bofkin L, Jones T, Davis RW, Steinmetz LM (2006) A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci USA 103(14): 5320-5325
14. Dobson MJ, Tuite MF, Roberts NA, Kingsman AJ, Kingsman SM, Perkins RE, Conroy SC, Fothergill LA (1982) Conservation of high efficiency promoter sequences in Saccharomyces cerevisiae. Nucleic Acids Res 10(8): 2625-2637
15. Gomez SM, Eiglmeier K, Segurens B, Dehoux P, Couloux A, Scarpelli C, Wincker P, Weissenbach J, Brey PT, Roth CW (2005) Pilot Anopheles gambiae full-length cDNA study: sequencing and initial characterization of 35, 575 clones. Genome Biol 6(4): R39
16. Graber J.H. (2003) Variations in yeast 30-processing cis-elements correlate with transcript stability. Trends Genet TIG 19(9): 473-476 (Pubitemid 37101083)
17. Graber J.H., Cantor CR, Mohr SC, Smith TF (1999a) Genomic detection of new yeast pre-mRNA 30-end-processing signals. Nucleic Acids Res 27(3): 888-894 (Pubitemid 29209379)
18. Graber J.H., 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(24): 14055-14060
19. Haas BJ, Volfovsky N, Town CD, Troukhan M, Alexandrov N, Feldmann KA, Flavell RB, White O, Salzberg SL (2002) Fulllength messenger RNA sequences greatly improve genome annotation. Genome Biol 3(6): research0029.0021-0029.0012
20. Hayashizaki Y (2003) The Riken mouse genome encyclopedia project. Comptes Rendus Biol 326(10-11): 923-929 (Pubitemid 38016447)
21. Ho EC, Cahill MJ, Saville BJ (2007) Gene discovery and transcript analyses in the corn smut pathogen Ustilago maydis: expressed sequence tag and genome sequence comparison. BMC Genomics [computer file] 8(1): 334
22. Hogg JR, Goff SP (2010) Upf1 senses 30UTR length to potentiate mRNA decay. Cell 143(3): 379-389
23. Hu J, Lutz CS, Wilusz J, Tian B (2005) Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation. RNA (New York, NY) 11(10): 1485-1493 (Pubitemid 41396918)
24. Hughes JD, Estep PW, Tavazoie S, Church GM (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 296(5): 1205-1214
25. Hurowitz EH, Brown PO (2003) Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae. Genome Biol 5(1): R2
26. Kahmann R, Kämper J (2004) Ustilago maydis: how its biology relates to pathogenic development. New Phytol 164: 31-42 (Pubitemid 39260327)
27. Kämper J, Kahmann R, Bölker M, Ma LJ, Brefort T, Saville BJ, Banuett F, Kronstad JW, Gold SE, Mü ller O, Perlin MH, Wösten HA, de Vries R, Ruiz-Herrera J, Reynaga-Peña CG, Snetselaar K, McCann M, Pérez-Mart?́n J, Feldbrügge M, Basse CW, Steinberg G, Ibeas JI, Holloman W, Guzman P, Farman M, Stajich JE, Sentandreu R, González-Prieto JM, Kennell JC, Molina L, Schirawski J, Mendoza-Mendoza A, Greilinger D, Münch K, Rössel N, Scherer M, Vraneš M, Ladendorf O, Vincon V, Fuchs U, Sandrock B, Meng S, Ho EC, Cahill MJ, Boyce KJ, Klose J, Klosterman SJ, Deelstra HJ, Ortiz-Castellanos L, Li W, Sanchez-Alonso P, Schreier PH, Häuser-Hahn I, Vaupel M, Koopmann E, Friedrich G, Voss H, Schlüter T, Margolis J, Platt D, Swimmer C, Gnirke A, Chen F, Vysotskaia V, Mannhaupt G, Güldener U, Münsterkötter M, Haase D, Oesterheld M, Mewes HW, Mauceli EW, DeCaprio D, Wade CM, Butler J, Young S, Jaffe DB, Calvo S, Nusbaum C, Galagan J, Birren BW (2006) Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 444(7115): 97-101 (Pubitemid 44684763)
28. Kuersten S, Goodwin EB (2003) The power of the 30 UTR: translational control and development. Nat Rev Genet 4(8): 626-637 (Pubitemid 36917504)
29. Laurie JD, Linning R, Bakkeren G (2008) Hallmarks of RNA silencing are found in the smut fungus Ustilago hordei but not in its close relative Ustilago maydis. Curr Genet 53(1): 49-58 (Pubitemid 50006392)
30. Mandel CR, Bai Y, Tong L (2008) Protein factors in pre-mRNA 30- end processing. Cell Mol Life Sci CMLS 65(7-8): 1099-1122
31. Manley JL, Proudfoot NJ (1994) RNA 30 ends: formation and function-meeting review. Genes Dev 8: 259-264 (Pubitemid 24065968)
32. Mathé C, Sagot MF, Schiex T, Rouzé P (2002) Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res 30(19): 4103-4117 (Pubitemid 35175179)
33. Mewes HW, Dietmann S, Frishman D, Gregory R, Mannhaupt G, Mayer KF, Münsterkötter M, Ruepp A, Spannagl M, Stümpflen V, Rattei T (2008) MIPS: analysis and annotation of genome information in 2007. Nucleic Acids Res 36(database issue): D196-D201 (Pubitemid 351149721)
34. Miura F, Kawaguchi N, Sese J, Toyoda A, Hattori M, Morishita S, Ito T (2006) A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci USA 103(47): 17846-17851 (Pubitemid 44852248)
35. 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 (New York, NY) 320(5881): 1344-1349 (Pubitemid 351929471)
36. Neveu B, Belzile F, Belanger RR (2007) Cloning of the glyceraldehyde- 3-phosphate dehydrogenase gene from Pseudozyma flocculosa and functionality of its promoter in two Pseudozyma species. Antonie van Leeuwenhoek 92(2): 245-255 (Pubitemid 47062603)
37. Newlon CS (1988) Yeast chromosome replication and segregation. Microbiol Rev 52(4): 568-601 (Pubitemid 19003321)
38. Nugent KG, Choffe K, Saville BJ (2004) Gene expression during Ustilago maydis diploid filamentous growth: EST library creation and analyses. Fungal Genet Biol 41(3): 349-360 (Pubitemid 38169454)
39. Ogihara Y, Mochida K, Kawaura K, Murai K, Seki M, Kamiya A, Shinozaki K, Carninci P, Hayashizaki Y, Shin-I T, Kohara Y, Yamazaki Y (2004) Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags. Genes Genet Syst 79(4): 227-232 (Pubitemid 39469694)
40. Pavy N, Rombauts S, Déhais P, Mathé C, Ramana DV, Leroy P, Rouzé P (1999) Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences. Bioinformatics (Oxford, England) 15(11): 887-899 (Pubitemid 30103159)
41. Ringnér M, Krogh M (2005) Folding free energies of 50-UTRs impact post-transcriptional regulation on a genomic scale in yeast. PLoS Comput Biol 1(7): e72
42. Roth FP, Hughes JD, Estep PW, Church GM (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol 16(10): 939-945 (Pubitemid 28483622)
43. Rothnie HM, Reid J, Hohn T (1994) The contribution of AAUAAA and the upstream element UUUGUA to the efficiency of mRNA 30-end formation in plants. EMBO J 13(9): 2200-2210
44. Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Güldener U, Mannhaupt G, Münsterkötter M, Mewes HW (2004) The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res 32(18): 5539-5545 (Pubitemid 39545671)
45. Russo P, Li WZ, Hampsey DM, Zaret KS, Sherman F (1991) Distinct cis-acting signals enhance 30 endpoint formation of CYC1 mRNA in the yeast Saccharomyces cerevisiae. EMBO J 10(3): 563-571 (Pubitemid 21905509)
46. Sacadura NT, Saville BJ (2003) Gene expression and EST analyses of Ustilago maydis germinating teliospores. Fungal Genet Biol 40(1): 47-64 (Pubitemid 37013497)
47. Sasaki T, Gilbert DM (2007) The many faces of the origin recognition complex. Curr Opin Cell Biol 19(3): 337-343 (Pubitemid 46899509)
48. Schneider TD, Stephens RM (1990) Sequence logos: a new way to display consensus sequences.NucleicAcids Res 18(20): 6097-6100
49. Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, Sakurai T, Nakajima M, Enju A, Akiyama K, Oono Y, Muramatsu M, Hayashizaki Y, Kawai J, Carninci P, Itoh M, Ishii Y, Arakawa T, Shibata K, Shinagawa A, Shinozaki K (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science (New York, NY) 296(5565): 141-145 (Pubitemid 34280073)
50. Snetselaar KM, Mims CW (1992) Sporidial fusion and infection of maize seedlings by the smut fungus Ustilago maydis. Mycologia 84: 193-203
51. Stein L (2001) Genome annotation: from sequence to biology. Nat Rev Genet 2(7): 493-503 (Pubitemid 33674023)
52. Stothard P (2000) The sequence manipulation suite: JavaScript programs for analyzing and formating protein and DNA sequences. Biotechniques 28: 1102-1104
53. Tuller T, Ruppin E, Kupiec M (2009) Properties of untranslated regions of the S. cerevisiae genome. BMC Genomics 10: 391
54. Venkataraman K, Brown KM, Gilmartin GM (2005) Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition. Genes Dev 19(11): 1315-1327 (Pubitemid 41003021)
55. Vilela C, McCarthy JE (2003) Regulation of fungal gene expression via short open reading frames in the mRNA 50 untranslated region. Mol Microbiol 49: 859-867 (Pubitemid 36981334)
56. Wahle E (1995) 30-end cleavage and polyadenylation of mRNA precursors. Biochim Biophys Acta 1261(2): 183-194
57. Wahle E, Rüegsegger U (1999) 30-End processing of pre-mRNA in eukaryotes. FEMS Microbiol Rev 23(3): 277-295
58. Wang B, Guo G, Wang C, Lin Y, Wang X, Zhao M, Guo Y, He M, Zhang Y, Pan L (2010) Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucleic Acids Res 38(15): 5075-5087
59. Wang J, Holden DW, Leong SA (1988). Gene transfer system for the phytopathogenic fungus Ustilago maydis. Proc Natl Acad Sci USA 85(3): 865-869
60. Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bähler J (2008) Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453(7199): 1239-1243 (Pubitemid 351913597)
61. Win J, Kanneganti TD, Torto-Alalibo T, Kamoun S (2006) Computational and comparative analyses of 150 full-length cDNA sequences from the oomycete plant pathogen Phytophthora infestans. Fungal Genet Biol 43(1): 20-33 (Pubitemid 43038751)
62. Yassour M, Pfiffner J, Levin JZ, Adiconis X, Gnirke A, Nusbaum C, Thompson D.A., Friedman N, Regev A (2010) Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biol 11(8): R87
63. Zhang L, Kasif S, Cantor CR, Broude NE (2004) GC/AT-content spikes as genomic punctuation marks. Proc Natl Acad Sci USA 101(48): 16855-16860 (Pubitemid 39601328)