RNA-seq and microarray complement each other in transcriptome profiling

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Kogenaru, Sunitha ^a   Qing, Yan ^a   Guo, Yinping ^a   Wang, Nian ^a  

^a UNIVERSITY OF FLORIDA   (United States)

Author keywords

Citrus canker disease; Effectors; HrpX; Microarray; Pathogenic bacteria; RNA seq; Transcriptome profiling; Type 3 secretion system; Virulence; Xanthomonas

Indexed keywords

TRANSCRIPTOME;

ARTICLE; BACTERIAL GENE; COMPARATIVE STUDY; CONTROLLED STUDY; CORRELATION ANALYSIS; GAMMAPROTEOBACTERIA; GENE EXPRESSION; GENE MUTATION; GENE TARGETING; GENETIC PROCEDURES; HRPX GENE; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PERFORMANCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; TRANSCRIPTION REGULATION; TRANSCRIPTOME PROFILING; WILD TYPE; XANTHOMONAS CITRI;

BACTERIAL PROTEINS; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN BINDING; REAL-TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION FACTORS; TRANSCRIPTOME; XANTHOMONAS;

CITRUS; PROTEOBACTERIA; XANTHOMONAS; XANTHOMONAS CITRI;

EID: 84868676938     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-629     Document Type: Article

References (97)

1. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10:57-63.
2. Baginsky S, Hennig L, Zimmermann P, Gruissem W. Gene expression analysis, proteomics, and network discovery. Plant Physiol 2010, 152:402-410.
3. Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 2008, 5:613-619.
4. Costa V, Angelini C, De Feis I, Ciccodicola A. Uncovering the complexity of transcriptomes with RNA-Seq. J Biomed Biotechnol 2010, 2010:853916.
5. DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet 1996, 14:457-460.
6. Ekins R, Chu FW. Microarrays: their origins and applications. Trends Biotechnol 1999, 17:217-218.
7. Fodor SP, Rava RP, Huang XC, Pease AC, Holmes CP, Adams CL. Multiplexed biochemical assays with biological chips. Nature 1993, 364:555-556.
8. Hegde P, Qi R, Abernathy K, Gay C, Dharap S, Gaspard R, Hughes JE, Snesrud E, Lee N, Quackenbush J. A concise guide to cDNA microarray analysis. Biotechniques 2000, 29:548-4. 556..
9. Marguerat S, Bahler J. RNA-seq: from technology to biology. Cell Mol Life Sci 2010, 67:569-579.
10. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008, 320:1344-1349.
11. Nagalakshmi U, Waern K, Snyder M. RNA-Seq: a method for comprehensive transcriptome analysis. Curr Protoc Mol Biol 2010, Chapter 4: . Unit 4.11.1-13..
12. Ramsay G. DNA chips: state-of-the art. Nat Biotechnol 1998, 16:40-44.
13. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270:467-470.
14. Tan PK, Downey TJ, Spitznagel EL, Xu P, Fu D, Dimitrov DS, Lempicki RA, Raaka BM, Cam MC. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 2003, 31:5676-5684.
15. Toung JM, Morley M, Li M, Cheung VG. RNA-sequence analysis of human B-cells. Genome Res 2011, 21:991-998.
16. 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.
17. Xiang CC, Chen Y. cDNA microarray technology and its applications. Biotechnol Adv 2000, 18:35-46.
18. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5:621-628.
19. Pariset L, Chillemi G, Bongiorni S, Romano SV, Valentini A. Microarrays and high-throughput transcriptomic analysis in species with incomplete availability of genomic sequences. N Biotechnol 2009, 25:272-279.
20. Schena M, Heller RA, Theriault TP, Konrad K, Lachenmeier E, Davis RW. Microarrays: biotechnology's discovery platform for functional genomics. Trends Biotechnol 1998, 16:301-306.
21. Fu X, Fu N, Guo S, Yan Z, Xu Y, Hu H, Menzel C, Chen W, Li Y, Zeng R, et al. Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics 2009, 10:161.
22. Shendure J. The beginning of the end for microarrays?. Nat Methods 2008, 5:585-587.
23. van Vliet AH. Next generation sequencing of microbial transcriptomes: challenges and opportunities. FEMS Microbiol Lett 2010, 302:1-7.
24. Raz T, Kapranov P, Lipson D, Letovsky S, Milos PM, Thompson JF. Protocol dependence of sequencing-based gene expression measurements. PLoS One 2011, 6:e19287.
25. Martin JA, Wang Z. Next-generation transcriptome assembly. Nat Rev Genet 2011, 12:671-682.
26. Zhou X, Ren L, Meng Q, Li Y, Yu Y, Yu J. The next-generation sequencing technology and application. Protein Cell 2010, 1:520-536.
27. 't Hoen PA, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, de Menezes RX, Boer JM, van Ommen GJ, den Dunnen JT. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res 2008, 36:e141.
28. Leimena MM, Wels M, Bongers RS, Smid EJ, Zoetendal EG, Kleerebezem M. Comparative Analysis of Lactobacillus plantarum WCFS1 Transcriptomes by Using DNA Microarray and Next-Generation Sequencing Technologies. Appl Environ Microbiol 2012, 78:4141-4148.
29. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008, 18:1509-1517.
30. Su Z, Li Z, Chen T, Li QZ, Fang H, Ding D, Ge W, Ning B, Hong H, Perkins RG, et al. Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys. Chem Res Toxicol 2011, 24:1486-1493.
31. Wengelnik K, Bonas U. HrpXv, an AraC-type regulator, activates expression of five of the six loci in the hrp cluster of Xanthomonas campestris pv. vesicatoria. J Bacteriol 1996, 178:3462-3469.
32. da Silva AC, Ferro JA, Reinach FC, Farah CS, Furlan LR, Quaggio RB, Monteiro-Vitorello CB, Van Sluys MA, Almeida NF, Alves LM, et al. Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 2002, 417:459-463.
33. Guo Y, Figueiredo F, Jones J, Wang N. HrpG and HrpX play global roles in coordinating different virulence traits of Xanthomonas axonopodis pv. citri. Mol Plant Microbe Interact 2011, 24:649-661.
34. Civerolo E. Bacterial canker disease of citrus. J Rio Grande Vall Hortic Soc 1984, 37:127-145.
35. Astua-Monge G, Freitas-Astua J, Bacocina G, Roncoletta J, Carvalho SA, Mchado MA. Expression profiling of virulence and pathogenicity genes of Xanthomonas axonopodis pv. citri. J Bacteriol 2005, 187:1201-1205.
36. Fenselau S, Bonas U. Sequence and expression analysis of the hrpB pathogenicity operon of Xanthomonas campestris pv. vesicatoria which encodes eight proteins with similarity to components of the Hrp, Ysc, Spa, and Fli secretion systems. Mol Plant Microbe Interact 1995, 8:845-854.
37. Koebnik R, Kruger A, Thieme F, Urban A, Bonas U. Specific binding of the Xanthomonas campestris pv. vesicatoria AraC-type transcriptional activator HrpX to plant-inducible promoter boxes. J Bacteriol 2006, 188:7652-7660.
38. Noel L, Thieme F, Nennstiel D, Bonas U. Two novel type III-secreted proteins of Xanthomonas campestris pv. vesicatoria are encoded within the hrp pathogenicity island. J Bacteriol 2002, 184:1340-1348.
39. Alfano JR, Collmer A. The type III (Hrp) secretion pathway of plant pathogenic bacteria: trafficking harpins, Avr proteins, and death. J Bacteriol 1997, 179:5655-5662.
40. Bonas U. hrp genes of phytopathogenic bacteria. Curr Top Microbiol Immunol 1994, 192:79-98.
41. Buttner D, Bonas U. Regulation and secretion of Xanthomonas virulence factors. FEMS Microbiol Rev 2010, 34:107-133.
42. Iwamoto M, Oku T. Cloning and molecular characterization of hrpX from Xanthomonas axonopodis pv. citri. DNA Seq 2000, 11:167-173.
43. Gurlebeck D, Thieme F, Bonas U. Type III effector proteins from the plant pathogen Xanthomonas and their role in the interaction with the host plant. J Plant Physiol 2006, 163:233-255.
44. Oku T, Alvarez AM, Kado CI. Conservation of the hypersensitivity-pathogenicity regulatory gene hrpX of Xanthomonas campestris and X. oryzae. DNA Seq 1995, 5:245-249.
45. Lahaye T, Bonas U. Molecular secrets of bacterial type III effector proteins. Trends Plant Sci 2001, 6:479-485.
46. Kelley DR, Schatz MC, Salzberg SL. Quake: quality-aware detection and correction of sequencing errors. Genome Biol 2010, 11:R116.
47. Klebanov L, Yakovlev A. How high is the level of technical noise in microarray data?. Biol Direct 2007, 2:9.
48. Oshlack A, Wakefield MJ. Transcript length bias in RNA-seq data confounds systems biology. Biol Direct 2009, 4:14.
49. Sahl JW, Rasko DA. Analysis of global transcriptional profiles of enterotoxigenic Escherichia coli isolate E24377A. Infect Immun 2012, 80:1232-1242.
50. Alfano JR, Collmer A. Type III secretion system effector proteins: double agents in bacterial disease and plant defense. Annu Rev Phytopathol 2004, 42:385-414.
51. Collmer A, Bauer DW. Erwinia chrysanthemi and Pseudomonas syringae: plant pathogens trafficking in extracellular virulence proteins. Curr Top Microbiol Immunol 1994, 192:43-78.
52. Cornelis GR. The type III secretion injectisome. Nat Rev Microbiol 2006, 4:811-825.
53. Szczesny R, Jordan M, Schramm C, Schulz S, Cogez V, Bonas U, Buttner D. Functional characterization of the Xcs and Xps type II secretion systems from the plant pathogenic bacterium Xanthomonas campestris pv vesicatoria. New Phytol 2010, 187:983-1002.
54. Van GF, Genin S, Boucher C. Conservation of secretion pathways for pathogenicity determinants of plant and animal bacteria. Trends Microbiol 1993, 1:175-180.
55. White FF, Potnis N, Jones JB, Koebnik R. The type III effectors of Xanthomonas. Mol Plant Pathol 2009, 10:749-766.
56. Lindgren PB. The role of hrp genes during plant-bacterial interactions. Annu Rev Phytopathol 1997, 35:129-152.
57. Lipscomb L, Schell MA. Elucidation of the regulon and cis-acting regulatory element of HrpB, the AraC-type regulator of a plant pathogen-like type III secretion system in Burkholderia pseudomallei. J Bacteriol 2011, 193:1991-2001.
58. Kim JG, Park BK, Yoo CH, Jeon E, Oh J, Hwang I. Characterization of the Xanthomonas axonopodis pv. glycines Hrp pathogenicity island. J Bacteriol 2003, 185:3155-3166.
59. Hu GB, Rice WJ, Drose S, Altendorf K, Stokes DL. Three-dimensional structure of the KdpFABC complex of Escherichia coli by electron tomography of two-dimensional crystals. J Struct Biol 2008, 161:411-418.
60. Jehl MA, Arnold R, Rattei T. Effective-a database of predicted secreted bacterial proteins. Nucleic Acids Res 2011, 39:D591-D595.
61. Korotkov KV, Sandkvist M, Hol WG. The type II secretion system: biogenesis, molecular architecture and mechanism. Nat Rev Microbiol 2012, 10:336-351.
62. Furutani A, Takaoka M, Sanada H, Noguchi Y, Oku T, Tsuno K, Ochiai H, Tsuge S. Identification of novel type III secretion effectors in Xanthomonas oryzae pv. oryzae. Mol Plant Microbe Interact 2009, 22:96-106.
63. Wang L, Rong W, He C. Two Xanthomonas extracellular polygalacturonases, PghAxc and PghBxc, are regulated by type III secretion regulators HrpX and HrpG and are required for virulence. Mol Plant Microbe Interact 2008, 21:555-563.
64. Mukherjee K, Burglin TR. MEKHLA, a novel domain with similarity to PAS domains, is fused to plant homeodomain-leucine zipper III proteins. Plant Physiol 2006, 140:1142-1150.
65. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, et al. Gene ontology: tool for the unification of biology The Gene Ontology Consortium. Nat Genet 2000, 25:25-29.
66. Kanehisa M, Goto S, Kawashima S, Nakaya A. The KEGG databases at GenomeNet. Nucleic Acids Res 2002, 30:42-46.
67. Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 2012, 40:D742-D753.
68. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, et al. The transcriptional landscape of the mammalian genome. Science 2005, 309:1559-1563.
69. Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, et al. The developmental transcriptome of Drosophila melanogaster. Nature 2011, 471:473-479.
70. Mane SP, Evans C, Cooper KL, Crasta OR, Folkerts O, Hutchison SK, Harkins TT, Thierry-Mieg D, Thierry-Mieg J, Jensen RV. Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing. BMC Genomics 2009, 10:264.
71. 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.
72. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 2008, 321:956-960.
73. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 28:511-515.
74. Van BH, Nislow C, Blencowe BJ, Hughes TR. Most " dark matter" transcripts are associated with known genes. PLoS Biol 2010, 8:e1000371.
75. Bullard JH, Purdom E, Hansen KD, Dudoit S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinforma 2010, 11:94.
76. Labaj PP, Leparc GG, Linggi BE, Markillie LM, Wiley HS, Kreil DP. Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling. Bioinformatics 2011, 27:i383-i391.
77. Risso D, Schwartz K, Sherlock G, Dudoit S. GC-content normalization for RNA-Seq data. BMC Bioinforma 2011, 12:480.
78. Draghici S, Khatri P, Eklund AC, Szallasi Z. Reliability and reproducibility issues in DNA microarray measurements. Trends Genet 2006, 22:101-109.
79. Goryachev AB, Macgregor PF, Edwards AM. Unfolding of microarray data. J Comput Biol 2001, 8:443-461.
80. Kerr MK, Martin M, Churchill GA. Analysis of variance for gene expression microarray data. J Comput Biol 2000, 7:819-837.
81. Tseng GC, Oh MK, Rohlin L, Liao JC, Wong WH. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res 2001, 29:2549-2557.
82. Wang X, Wang D, Chen X, Hu M, Wang J, Li Y, Guo N, Shen B. cDNA cloning and function analysis of two novel erythroid differentiation related genes. Sci China C Life Sci 2001, 44:99-105.
83. Cleveland WS, Devlin SJ, Grosse E. Regression by Local Fitting: Methods, Properties, and Computational Algorithms. J Econ 1988, 37:87-114.
84. Engelen K, Coessens B, Marchal K, De MB. MARAN: normalizing micro-array data. Bioinformatics 2003, 19:893-894.
85. Ihaka R, Gentleman R. R: A language for data analysis and graphics. Journal of Computational and Graphical Statistics. Journal of Computational and Graphical Statistics 1996, 5:299-314.
86. Venet D. MatArray: a Matlab toolbox for microarray data. Bioinformatics 2003, 19:659-660.
87. Kumar R, Lawrence ML, Watt J, Cooksey AM, Burgess SC, Nanduri B. RNA-seq based transcriptional map of bovine respiratory disease pathogen " Histophilus somni 2336" . PLoS One 2012, 7:e29435.
88. Wurtzel O, Sapra R, Chen F, Zhu Y, Simmons BA, Sorek R. A single-base resolution map of an archaeal transcriptome. Genome Res 2010, 20:133-141.
89. Yoder-Himes DR, Chain PS, Zhu Y, Wurtzel O, Rubin EM, Tiedje JM, Sorek R. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci U S A 2009, 106:3976-3981.
90. Tarazona S, Garcia-Alcalde F, Dopazo J, Ferrer A, Conesa A. Differential expression in RNA-seq: a matter of depth. Genome Res 2011, 21:2213-2223.
91. Daniels MJ, Barber CE, Turner PC, Sawczyc MK, Byrde RJ, Fielding AH. Cloning of genes involved in pathogenicity of Xanthomonas campestris pv. campestris using the broad host range cosmid pLAFR1. EMBO J 1984, 3:3323-3328.
92. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol 2010, 11:R106.
93. Reimers M, Carey VJ. Bioconductor: an open source framework for bioinformatics and computational biology. Methods Enzymol 2006, 411:119-134.
94. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
95. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pagès F, Trajanoski Z, Galon J. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 2009, 25:1091-1093.
96. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504.
97. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001, 25:402-408.