Advertisement

The Wonderland of Global Expression Profiling

  • David W. GalbraithEmail author
Part of the Biotechnology in Agriculture and Forestry book series (AGRICULTURE, volume 63)

‘When I use a word,’ Humpty Dumpty said in rather a scornful tone, ‘it means just what I choose it to mean — neither more nor less.’

One wonders what Humpty might have said about compound words, such as ‘expression profiling’, for example. Only a few years ago, life was simple: rapid progress was being made towards defining the identities of specific genes, and the development of high-throughput methods for simultaneously analyzing genes in parallel led to the development of the concept of expression profiles which could uniquely represent the individual cell types and cellular states found within tissues and organs (Hughes et al. 2000). However, more recently, the primary concepts underpinning our understanding of the meaning of gene expression have blurred somewhat. Defining the physical bounds for a gene, for example, is no longer a question simply of determining mileposts up and downstream from the point of initiation of transcription, since these may be modulated and influenced by chromosomal context and chromatin state. Again, defining expression no longer solely reflects the concept of translation of the encoded information content of an mRNA into its cognate protein; we must include in our understanding the concepts of RNA processing, transport, sequestration, and degradation, and the roles of genes producing transcripts that are non-coding. Finally, it is becoming clear that specific sequences of DNA can interact via a number of mechanisms that influence expression, including an-tisense transcription, the occurrence of alternative splicing, and the production of small RNA molecules. The complexities can be maddening, as Alice in Wonderland observed: ‘But I don't want to go among mad people!’ ‘Oh, you can't help that,’ said the cat. ‘We're all mad here!’

Keywords

Maize Genome Quiescent Center Massively Parallel Signature Sequencing Global Expression Walbot Versus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Allison DB, Cui XQ, Page GP, Sabripour M (2006) Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 7:55–65PubMedCrossRefGoogle Scholar
  2. Baskerville S, Bartell DP (2005) Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11:241–247PubMedCrossRefGoogle Scholar
  3. Beuvink I, Kolb FA, Budach W, Garnier A, Lange J, Natt F, Dengler U, Hall J, Filipowicz W, Weiler J (2007) A novel microarray approach reveals new tissue-specific signatures of known and predicted mammalian microRNAs. Nucl Acids Res 35(e52)PubMedCrossRefGoogle Scholar
  4. Bhattramakki D, Dolan M, Hanafey M, Wineland R, Vaske D, Register JC, Tingey SV, Rafalski A (2002) Insertion-deletion polymorphisms in 3' regions of maize genes occur frequently and can be used as highly informative genetic markers. Plant Mol Biol 48:539–547PubMedCrossRefGoogle Scholar
  5. Birnbaum K, Shasha DE, Wang JY, Jung JW, Lambert GM, Galbraith DW, Benfey PN (2003) A gene expression map of the Arabidopsis root. Science 302:1956–1960PubMedCrossRefGoogle Scholar
  6. Birnbaum K, Jung JW, Wang JY, Lambert GM, Hirst JA, Galbraith DW, Benfey PN (2005) Cell-type specific expression profiling in plants using fluorescent reporter lines, protoplasting, and cell sorting. Nat Meth 2:1–5CrossRefGoogle Scholar
  7. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M, Roth R, George D, Eletr S, Albrecht G, Vermaas E, Williams SR, Moon K, Burcham T, Pallas M, DuBridge RB, Kirchner J, Fearon K, Mao J-I, Corcoran K (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotech 18:630–634CrossRefGoogle Scholar
  8. Casati P, Walbot V (2003) Gene expression profiling in response to ultraviolet radiation in maize genotypes with varying flavonoid content. Plant Physiol 132:1739–1754PubMedCrossRefGoogle Scholar
  9. Casati P, Walbot V (2004) Rapid transcriptome responses of maize (Zea mays) to UV-B in irradiated and shielded tissues. Genome Biol 5(R16)PubMedCrossRefGoogle Scholar
  10. Castoldi M, Schmidt S, Benes V, Noerholm M, Kulozik AE, Hentze MW, Muckenthaler MU (2006) A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA). RNA 12:913–920PubMedCrossRefGoogle Scholar
  11. Ching A, Dhugga KS, Appenzeller L, Meeley R, Bourett TM, Howard RJ, Rafalski A (2006) Brittle stalk 2 encodes a putative glycosylphosphatidylinositol-anchored protein that affects mechanical strength of maize tissues by altering the composition and structure of secondary cell walls. Planta 224:1174–1184PubMedCrossRefGoogle Scholar
  12. Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G, Shinn P, Warthmann N, Hu TT, Fu G, Hinds DA, Chen H, Frazer KA, Huson DH, Scholkopf B, Nordborg M, Ratsch G, Ecker JR, Weigel D (2007) Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317:338–342PubMedCrossRefGoogle Scholar
  13. Czechowski T, Bari RP, Stitt M, Scheible WR, Udvardi MK (2004) Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. Plant J 38:366–379PubMedCrossRefGoogle Scholar
  14. Dalma-Weiszhausz DD, Warrington J, Tanimoto EY, Miyada G (2006) The Affymetrix GeneChip® platform: an overview. Methods Enzymol 410:3–28PubMedCrossRefGoogle Scholar
  15. Davison TS, Johnson CD, Andruss BF (2006) Analyzing micro-RNA expression using microarrays. Methods Enzymol 411:14–34PubMedCrossRefGoogle Scholar
  16. Day RC, McNoe LA, Macknight RC (2007) Transcript analysis of laser microdissected plant cells. Physiol Plant 129:267–282CrossRefGoogle Scholar
  17. Emrich SJ, Barbazuk WB, Li L, Schnable PS (2007) Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res 17:69–73PubMedCrossRefGoogle Scholar
  18. Fernandes J, Brendel V, Gai X, Lal S, Chandler VL, Elumalai R, Galbraith DW, Pierson E, Walbot V (2002) Comparison of RNA expression profiles based on maize EST frequency analysis and microarray hybridization. Plant Physiol 128:896–910PubMedCrossRefGoogle Scholar
  19. Galbraith DW (2006) Microarray analyses in higher plants. OMICS J Integr Biol 10:455– 473CrossRefGoogle Scholar
  20. Galbraith DW, Birnbaum K (2006) Global studies of cell type-specific gene expression in plants. Annu Rev Plant Biol 57:451–475PubMedCrossRefGoogle Scholar
  21. Gao HR, Gordon-Kamm WJ, Lyznik LA (2004) ASF/SF2-like maize pre-mRNA splicing factors affect splice site utilization and their transcripts are alternatively spliced. Gene 339: 25–37PubMedCrossRefGoogle Scholar
  22. Gardiner JM, Buell CR, Elumalai R, Galbraith DW, Henderson DA, Iniguez AL, Kaeppler SM, Kim JJ, Liu J, Zheng L, Chandler VL (2005) Design, production, and utilization of long oligonucleotide microarrays for expression analysis in maize. Maydica 50:425–435Google Scholar
  23. Gore M, Bradbury P, Hogers R, Kirst M, Verstege E, van Oeveren J, Peleman J, Buckler E, van Eijk M (2007) Evaluation of target preparation methods for single-feature polymorphism detection in large complex plant genomes. Crop Sci 47: S135–S148CrossRefGoogle Scholar
  24. Gowda M, Li HM, Alessi J, Chen F, Pratt R, Wang GL (2006) Robust analysis of 5'-transcript ends (5'-RATE): a novel technique for transcriptome analysis and genome annotation. Nucleic Acids Res 34. doi:10.1093/nar/gkl522Google Scholar
  25. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai HY, He YDD, Kidd MJ, King AM, Meyer MR, Slade D, Lum PY, Stepaniants SB, Shoemaker DD, Gachotte D, Chakraburtty K, Simon J, Bard M, Friend SH (2000) Functional discovery via a compendium of expression profiles. Cell 102:109–126PubMedCrossRefGoogle Scholar
  26. Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, Kobayashi S, Davis C, Dai HY, He YDD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 19:342–347PubMedCrossRefGoogle Scholar
  27. Hunter BG, Beatty MK, Singletary GW, Hamaker BR, Dilkes BP, Larkins BA, Jung R (2002) Maize opaque endosperm mutations create extensive changes in patterns of gene expression. Plant Cell 14:2591–2612PubMedCrossRefGoogle Scholar
  28. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31(e15)PubMedCrossRefGoogle Scholar
  29. Jander G, Barth C (2007) Tandem gene arrays: a challenge for functional genomics. Trends Plant Sci 12:203–210PubMedCrossRefGoogle Scholar
  30. Jansen RC, Nap JP (2001) Genetical genomics: the added value from segregation. Trends Genet 17:388–391PubMedCrossRefGoogle Scholar
  31. Jiang K, Zhang SB, Lee S, Tsai G, Kim K, Huang HY, Chilcott C, Zhu T, Feldman LJ (2006) Transcription profile analyses identify genes and pathways central to root cap functions in maize. Plant Mol Biol 60:343–363PubMedCrossRefGoogle Scholar
  32. Kerk NM, Ceserani T, Tausta SL, Sussex IM, Nelson TM (2003) Laser capture microdissection of cells from plant tissues. Plant Physiol 132:27–35PubMedCrossRefGoogle Scholar
  33. Kim JB, Porreca GJ, Song L, Greenway SC, Gorham JM, Church GM, Seidman CE, Seidman JG (2007) Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science 316:1481–1484PubMedCrossRefGoogle Scholar
  34. Kirst M, Caldo R, Casati P, Tanimoto G, Walbot V, Wise RP, Buckler ES (2006) Genetic diversity contribution to errors in short oligonucleotide microarray analysis. Plant Biotechnol J 4:489– 498PubMedGoogle Scholar
  35. Kris RM, Felder S, Deyholos M, Lambert GM, Botros I, Martel R, Seligmann B, Galbraith DW (2007) High-throughput, high-sensitivity analysis of gene expression in Arabidopsis thaliana. Plant Physiol 144:1256–1266PubMedCrossRefGoogle Scholar
  36. Liang RQ, Li W, Li Y, Tan CY, Li JX, Jin YX, Ruan KC (2005) An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe. Nucl Acids Res 33(e17). doi: 10.1093/nar/gni019PubMedCrossRefGoogle Scholar
  37. Lipshutz RJ, Fodor SPA, Gingeras TR, Lockhart DJ (1999) High density synthetic oligonucleotide arrays. Nat Genetics 21(Suppl S):20–24CrossRefGoogle Scholar
  38. Lu C, Tej SS, Luo SJ, Haudenschild CD, Meyers BC, Green PJ (2005) Elucidation of the small RNA component of the transcriptome. Science 309:1567–1569PubMedCrossRefGoogle Scholar
  39. Ma J, Morrow DJ, Fernandes J, Walbot V (2006) Comparative profiling of the sense and antisense transcriptome of maize lines. Genome Biol 7(R22)PubMedCrossRefGoogle Scholar
  40. Ma J, Duncan D, Morrow DJ, Fernandes J, Walbot V (2007) Transcriptome profiling of maize anthers using genetic ablation to analyze pre-meiotic and tapetal cell types. Plant J 50:637–648PubMedCrossRefGoogle Scholar
  41. Makarevitch I, Stupar RM, Iniguez AL, Haun WJ, Barbazuk WB, Kaeppler SM, Springer NM (2007) Natural variation for alleles under epigenetic control by the maize chromomethylase Zmet2. Genetics 177:749–760PubMedCrossRefGoogle Scholar
  42. Messing J, Bharti AK, Karlowski WM, Gundlach H, Kim HR, Yu Y, Wei FS, Fuks G, Soderlund CA, Mayer KFX, Wing RA (2004) Sequence composition and genome organization of maize. Proc Natl Acad Sci USA 101:14349–14354PubMedCrossRefGoogle Scholar
  43. Nakazono M, Qiu F, Borsuk LA, Schnable PS (2003) Laser-capture microdissection, a tool for the global analysis of gene expression in specific plant cell types: identification of genes expressed differentially in epidermal cells or vascular tissues of maize. Plant Cell 15:583–596PubMedCrossRefGoogle Scholar
  44. Nawy T, Lee JY, Colinas J, Wang JY, Thongrod SC, Malamy JE, Birnbaum K, Benfey PN (2005) Transcriptional profile of the Arabidopsis root quiescent center. Plant Cell 17:1908– 1925PubMedCrossRefGoogle Scholar
  45. Nelson PT, Baldwin DA, Scearce LM, Oberholtzer JC, Tobias JW, Mourelatos Z (2004) Microarray–based, high–throughput gene expression profiling of microRNAs. Nat Methods 1:155–161PubMedCrossRefGoogle Scholar
  46. Nelson T, Tausta SL, Gandotra N, Liu T (2006) Laser microdissection of plant tissue: what you see is what you get. Annu Rev Plant Biol 57:181–201PubMedCrossRefGoogle Scholar
  47. Nobuta K, Venu RC, Lu C, Belo A, Vemaraju K, Kulkarni K, Wang WZ, Pillay M, Green PJ, Wang GL, Meyers BC (2007) An expression atlas of rice mRNAs and small RNAs. Nat Biotech 25:473–477CrossRefGoogle Scholar
  48. Ohtsu K, Takahashi H, Schnable PS, Nakazono M (2007) Cell type-specific gene expression profiling in plants by using a combination of laser microdissection and high-throughput technologies. Plant Cell Physiol 48:3–7PubMedCrossRefGoogle Scholar
  49. Parker R, Sheth U (2007) P bodies and the control of mRNA translation and degradation. Mol Cell 25:635–646PubMedCrossRefGoogle Scholar
  50. Perocchi F, Xu Z, Clauder-Münster S, Steinmetz LM (2007) Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res doi: 10.1093/nar/gkm683Google Scholar
  51. Poroyko V, Hejlek LG, Spollen WG, Springer GK, Nguyen HT, Sharp RE, Bohnert HJ (2005) The maize root transcriptome by serial analysis of gene expression. Plant Physiol 138:1700– 1710PubMedCrossRefGoogle Scholar
  52. Poroyko V, Spollen WG, Hejlek LG, Hernandez AG, LeNoble ME, Davis G, Nguyen HT, Springer GK, Sharp RE, Bohnert HJ (2007) Comparing regional transcript profiles from maize primary roots under well—watered and low water potential conditions. J Exp Bot 58:279–289PubMedCrossRefGoogle Scholar
  53. Rana TM (2007) Illuminating the silence: understanding the structure and function of small RNAs. Nat Rev Mol Cell Biol 8:23–36PubMedCrossRefGoogle Scholar
  54. Sawers RJH, Liu P, Anufrikova K, Hwang JTG, Brutnell TP (2007) A multi-treatment experimental system to examine photosynthetic differentiation in the maize leaf. BMC Genomics 8(12)PubMedCrossRefGoogle Scholar
  55. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TG, Milligan SB, Lamb JR, Cavet G, Linsley PS, Mao M, Stoughton RB, Friend SH (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature 422:297–302PubMedCrossRefGoogle Scholar
  56. Shi C, Uzarowska A, Ouzunova M, Landbeck M, Wenzel G, Lubberstedt T (2007) Identification of candidate genes associated with cell wall digestibility and eQTL (expression quantitative trait loci) analysis in a Flint × Flint maize recombinant inbred line population. BMC Genomics 8(22)PubMedCrossRefGoogle Scholar
  57. Singh-Gasson S, Green RD, Yue YJ, Nelson C, Blattner F, Sussman MR, Cerrina F (1999) Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol 17:974–978PubMedCrossRefGoogle Scholar
  58. Stupar RM, Springer NM (2006) Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F-1 hybrid. Genetics 173:2199–2210PubMedCrossRefGoogle Scholar
  59. Swanson-Wagner RA, Jia Y, DeCook R, Borsuk LA, Nettleton D, Schnable PS (2006) All possible modes of gene action are observed in a global comparison of gene expression in a maize F-1 hybrid and its inbred parents. Proc Natl Acad Sci USA 103:6805–6810PubMedCrossRefGoogle Scholar
  60. Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci USA 98:9161–9166PubMedCrossRefGoogle Scholar
  61. Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH (1990) Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci USA 87:1663–1667PubMedCrossRefGoogle Scholar
  62. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science 270:484–487PubMedCrossRefGoogle Scholar
  63. Wang H, Kawai K, Deyholos M, Galbraith DW, Bohnert HJ (2003) Temporal progression of gene expression responses to salt shock in maize roots. Plant Mol Biol 52:873–891PubMedCrossRefGoogle Scholar
  64. Wei F, Coe E, Nelson W, Bharti AK, Engler F, Butler E, Kim H, Goicoechea JL, Chen M, Lee S, Fuks G, Sanchez-Villeda H, Schroeder S, Fang Z, McMullen M, Davis G, Bowers JE, Paterson AH, Schaeffer M, Gardiner J, Cone K, Messing J, Soderlund C, Wing RA (2007) Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLOS Genetics 3:1254–1263CrossRefGoogle Scholar
  65. Woll K, Borsuk LA, Stransky H, Nettleton D, Schnable PS, Hochholdinger F (2005) Isolation, characterization, and pericycle-specific transcriptome analyses of the novel maize lateral and seminal root initiation mutant rum1. Plant Physiol 139:1255–1267PubMedCrossRefGoogle Scholar
  66. Woll K, Dressel A, Sakai H, Piepho HP, Hochholdinger F (2006) ZmGrp3: identification of a novel marker for root initiation in maize and development of a robust assay to quantify allele-specific contribution to gene expression in hybrids. Theor Appl Genet 113:1305–1315PubMedCrossRefGoogle Scholar
  67. Xu W, Bak S, Decker A, Paquette SM, Feyereisen R, Galbraith DW (2001) Microarray-based analysis of gene expression in very large gene families: the cytochrome P450 gene superfamily of Arabidopsis thaliana. Gene 272:61–74PubMedCrossRefGoogle Scholar
  68. Yamada K, Lim J, Dale JM, Chen HM, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, Pham P, Cheuk R, Karlin-Newmann G, Liu SX, Lam B, Sakano H, Wu T, Yu GX, Miranda M, Quach HL, Tripp M, Chang CH, Lee JM, Toriumi M, Chan MMH, Tang CC, Onodera CS, Deng JM, Akiyama K, Ansari Y, Arakawa T, Banh J, Banno F, Bowser L, Brooks S, Carninci P, Chao QM, Choy N, Enju A, Goldsmith AD, Gurjal M, Hansen NF, Hayashizaki Y, Johnson-Hopson C, Hsuan VW, Iida K, Karnes M, Khan S, Koesema E, Ishida J, Jiang PX, Jones T, Kawai J, Kamiya A, Meyers C, Nakajima M, Narusaka M, Seki M, Sakurai T, Satou M, Tamse R, Vaysberg M, Wallender EK, Wong C, Yamamura Y, Yuan SL, Shinozaki K, Davis RW, Theologis A, Ecker JR (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302:842–846PubMedCrossRefGoogle Scholar
  69. Yu LX, Setter TL (2003) Comparative transcriptional profiling of placenta and endosperm in developing maize kernels in response to water deficit. Plant Physiol 131:568–582PubMedCrossRefGoogle Scholar
  70. Zanetti ME, Chang I-F, Gong FC, Galbraith DW, Bailey-Serres J (2005) Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression. Plant Physiol 138:624–635PubMedCrossRefGoogle Scholar
  71. Zhang JL, Simmons C, Yalpani N, Crane V, Wilkinson H, Kolomiets M (2005) Genomic analysis of the 12-oxo-phytodienoic acid reductase gene family of Zea mays. Plant Mol Biol 59:323–343PubMedCrossRefGoogle Scholar
  72. Zhu T, Budworth P, Chen WQ, Provart N, Chang HS, Guimil S, Su WP, Estes B, Zou GZ, Wang X (2003) Transcriptional control of nutrient partitioning during rice grain filling. Plant Biotech J 1:59–70CrossRefGoogle Scholar
  73. Zinselmeier C, Sun YJ, Helentjaris T, Beatty M, Yang S, Smith H, Habben J (2002) The use of gene expression profiling to dissect the stress sensitivity of reproductive development in maize. Field Crops Res 75:111–121CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, B.V 2009

Authors and Affiliations

  1. 1.BIO5 Institute for Collaborative Bioresearch and Department of Plant SciencesUniversity of Arizona, Thomas W. Keating Bioresearch BuildingTucsonUSA

Personalised recommendations