Microgenomics: Gene expression analysis at the tissue-specific and single-cell levels

Journal of Experimental Botany

Volumn 56, Issue 412, 2005, Pages 495-505

  Brandt, Stephan P ^a  

^a DARMSTADT UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

Array hybridization; cDNA libraries; Gene expression pattern; Glass capillary; Homomeric tailing; Linear antisense amplification; Microdissection; RT PCR; Single cell analysis; Tissue specificity

Indexed keywords

CELLS; METABOLISM; PHYSIOLOGY; PLANTS (BOTANY); STRESSES; TISSUE;

CELL-SPECIFIC SAMPLES; GENE EXPRESSION; MICROGENOMICS; SECONDARY METABOLISM;

GENETIC ENGINEERING;

PLANT DNA;

CYTOLOGY; DNA MICROARRAY; GENE LIBRARY; GENETIC PROCEDURES; GENETICS; GENOME; NUCLEOTIDE SEQUENCE; PLANT; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW;

BASE SEQUENCE; DNA, PLANT; GENE LIBRARY; GENETIC TECHNIQUES; GENOME, PLANT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 14544297828     PISSN: 00220957     EISSN: None     Source Type: Journal    
DOI: 10.1093/jxb/eri066     Document Type: Review

References (76)

1. Asano T, Masumura T, Kusano H, Kikuchi S, Kurita A, Shimada H, Kadowaki K. 2002. Construction of a specialized cDNA library from plant cells isolated by laser capture microdissection: toward comprehensive analysis of the genes expressed in the rice phloem. The Plant Journal 32, 401-408.
2. Baldwin D, Crane V, Rice D. 1999. A comparison of gel-based, nylon filter and microarray techniques to detect differential RNA expression in plants. Current Opinion in Plant Biology 2, 96-103.
3. Bauer D, Müller H, Reich J, Riedel H, Ahrenkiel V, Warthoe P, Strauss M. 1993. Identification of differentially expressed mRNA species by an improved display technique (DDRTPCR). Nucleic Acids Research 21, 4272-4280.
4. 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, 1956-1960.
5. Bligny R, Douce R. 2001. NMR and plant metabolism. Current Opinion in Plant Biology 4, 191-196.
6. Brandt S, Kehr J, Walz C, Imlau A, Willmitzer L, Fisahn J. 1999. A rapid method for detection of plant gene transcripts from epidermal, mesophyll and companion cells of intact leaves. The Plant Journal 20, 245-250.
7. Brandt S, Kloska S, Altmann T, Kehr J. 2002. Using array hybridization to monitor gene expression at the single cell level. Journal of Experimental Botany 53, 2315-2323.
8. Brandt S, Walz C, Schad M, Pavlovic N, Kehr J. 2003. A simple, chisel assisted mechanical microdissection system for harvesting homogenous plant tissue suitable for the analysis of nucleic acids and proteins. Plant Molecular Biology Reporter 21, 417-427.
9. Cheung VG, Nelson SF. 1996. Whole genome amplification using a degenerate oligonucleotide primer allows hundreds of genotypes to be performed on less than one nanogram of genomic DNA. Proceedings of the National Academy of Sciences, USA 93, 14676-14679.
10. Cornea A, Mungenast A. 2002. Comparison of current equipment. Methods in Enzymology 356, 3-12.
11. Dean FB, Hosono S, Fang L, et al. 2002. Comprehensive human genome amplification using multiple displacement amplification. Proceedings of the National Academy of Sciences, USA 99, 5261-5266.
12. Deiman B, van Aarle P, Sillekens P. 2002. Characteristics and applications of nucleic acid sequence-based amplification (NASBA). Molecular Biotechnology 20, 163-179.
13. de Ruijter NCA, Verhees J, van Leeuwen W, van der Krol AR. 2003. Evaluation and comparison of the GUS, LUC and GFP reporter system for gene expression studies in plants. Plant Biology 5, 103-115.
14. Dixon AK, Richardson PJ, Lee K, Carter NP, Freeman TC. 1998. Expression profiling of single cells using 3 prime end amplification (TPEA) PCR. Nucleic Acids Research 26, 4426-4431.
15. Dresselhaus T, Lörz H, Kranz E. 1994. Representative cDNA libraries from few plant cells. The Plant Journal 5, 605-610.
16. Ehrhardt D. 2003. GFP technology for live cell imaging. Current Opinion in Plant Biology 6, 622-628.
17. Elnifro EM, Ashshi AM, Cooper RJ, Klapper PE. 2000. Multiplex PCR: optimization and application in diagnostic virology. Clinical Microbiology Reviews 13, 559-570.
18. Engler JD, De Groodt R, Van Montagu M, Engler G. 2001. In situ hybridization to mRNA of Arabidopsis tissue sections. Methods 23, 325-334.
19. Fellmann F, Pretet JL, Fellmann D. 1996. Simplified protocol of solid-phase cDNA libraries for multiple PCR amplification. BioTechniques 21, 766-770.
20. Fricke W, Hinde PS, Leigh RS, Tomos AD. 1995. Vacuolar solutes in the upper epidermis of barley leaves. Planta 196, 40-49.
21. Gaedeke N, Klein M, Kolukisaoglu U, et al. 2001. The Arabidopsis thaliana ABC transporter AtMRP5 controls root development and stomata movement. EMBO Journal 20, 1875-1887.
22. Gallagher JA, Koroleva OA, Tomos AD, Farrar JF, Pollock CJ. 2001. Single cell analysis technique for comparison of specific mRNA abundance in plant cells. Journal of Plant Physiology 158, 1089-1092.
23. Gehwolf R, Griessner M, Peril H, Obermeyer G. 2002. First patch, then catch: measuring the activity and the mRNA transcripts of a proton pump in individual Lilium pollen protoplasts. FEBS Letters 512, 152-156.
24. Ginsberg SD, Che SL. 2002. RNA amplification in brain tissues. Neurochemical Research 27, 981-992.
25. Gjerdrum LM, Sorensen BS, Kjeldsen E, Sorensen FB, Nexo E, Hamilton-Dutoit S. 2004. Real-time quantitative PCR of micro-dissected paraffin-embedded breast carcinoma: an alternative method for HER-2/neu analysis. Journal of Molecular Diagnostics 6, 42-51.
26. Grosset J, Marty I, Chartier Y, Meyer Y. 1990. Messenger RNAs newly synthesized by tobacco mesophyll protoplasts are wound inducible. Plant Molecular Biology 15, 485-496.
27. Harrison J, Gallagher JA, Pollock CJ. 1997. A simple and rapid method for the analysis of water-soluble carbohydrates from small segments of cereal leaf tissue. Journal of Plant Physiology 151, 654-659.
28. He LP, Chinnery PF, Durham SE, Blakely EL, Wardell TM, Borthwick GM, Taylor RW, Turnbull DM. 2002. Detection and quantification of mitochondrial DNA deletions in individual cells by real-time PCR. Nucleic Acids Research 30, e68.
29. Henegariu O, Heerema NA, Dlouhy SR, Vance GH, Vogt PH. 1997. Multiplex PCR: critical parameters and step-by-step protocol. Biotechniques 23, 504-511.
30. Hertzberg M, Sievertzon M, Aspeborg H, Nilsson P, Sandberg G, Lundeberg J. 2001. cDNA microarray analysis of small plant tissue samples using a cDNA tag target amplification protocol. The Plant Journal 25, 585-591.
31. Iscove NN, Barbara M, Gu M, Gibson M, Modi C, Winegarden N. 2002. Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA. Nature Biotechnology 20, 940-943.
32. Ivashikina N, Deeken R, Ache P, Kranz E, Pommerrenig B, Sauer N, Hedrich R. 2003. Isolation of AtSUC2 promoter-GFP-marked companion cells for patch-clamp studies and expression profiling. The Plant Journal 36, 931-945.
33. Jones MA, Grierson CS. 2003. A simple method for obtaining cell-specific cDNA from small numbers of growing root-hair cells in Arabidopsis thaliana. Journal of Experimental Botany 54, 1373-1378.
34. Karrer EE, Lincoln JE, Hogenhout S, Bennett AB, Bostock RM, Martineau B, Lucas WJ, Gilchrist DG, Alexander D. 1995. In situ isolation of mRNA from individual plant cells: creation of cell-specific cDNA libraries. Proceedings of the National Academy of Sciences, USA 92, 3814-3818.
35. Kehr J. 2001. High resolution spatial analysis of plant systems. Current Opinion in Plant Biology 4, 197-201.
36. Kehr J. 2003. Single cell technology. Current Opinion in Plant Biology 6, 1-5.
37. Kerk NM, Ceserani T, Tausta SL, Sussex IM, Nelson TM. 2003. Laser capture microdissection of cells from plant tissues. Plant Physiology 132, 27-35.
38. Klein CA, Seidl S, Petat-Dutter K, et al. 2002. Combined transcriptome and genome analysis of single micrometastatic cells. Nature Biotechnology 20, 387-392.
39. Koltai H, Bird DM. 2000. High throughput cellular localization of specific plant mRNAs by liquid-phase in situ reverse transcription-polymerase chain reaction of tissue sections. Plant Physiology 123, 1203-1212.
40. Kopka J, Provart NJ, Müller-Rober B. 1997. Potato guard cells respond to drying soil by a complex change in the expression of genes related to carbon metabolism and turgor regulation. The Plant Journal 11, 871-882.
41. Laval V, Koroleva OA, Murphy E, Lu CG, Milner JJ, Hooks MA, Tomos AD. 2002. Distribution of actin gene isoforms in the Arabidopsis leaf measured in microsamples from intact individual cells. Planta 215, 287-292.
42. Leonhardt N, Kwak JM, Robert N, Waner D, Leonhardt G, Schroeder JI. 2004. Microarray expression analyses of Arabidopsis guard cells and isolation of a recessive abscisic acid hypersensitive protein phosphatase 2C mutant. The Plant Cell 16, 596-615.
43. Levsky JM, Shenoy SM, Pezo RC, Singer RH. 2002. Single cell gene expression profiling. Science 297, 836-840.
44. Levsky JM, Singer RH. 2003. Gene expression and the myth of the average cell. Trends in Cell Biology 13, 4-6.
45. Li H, Yeung ES. 2002. Selective genotyping of individual cells by capillary polymerase chain reaction. Electrophoresis 23, 3372-3380.
46. Liang P, Pardee AB. 1992. Differential display of eucaryotic messenger RNA by means of the polymerase chain reaction. Science 257, 967-971.
47. Liu X, Ma L, Zhang JF, Lu YT. 2004. Determination of single-cell gene expression in Arabidopsis by capillary electrophoresis with laser induced fluorescence detection. Journal of Chromatography B 808, 241-247.
48. Lu CG, Koroleva OA, Farrar JF, Gallagher JA, Pollock CJ, Tomos AD. 2002. Rubisco small subunit, chlorophyll a/b-binding protein and sucrose:fructan-6- fructosyl transferase gene expression and sugar status in single barley leaf cells in situ. Cell type specificity and induction by light. Plant Physiology 130, 1335-1348.
49. Luo L, Salunga RC, Guo H, et al. 1999. Gene expression profiles of laser-captured adjacent neuronal subtypes. Nature Medicine 5, 117-122.
50. 4-AP currents and Kv3.1 potassium channel transcripts in cortical neurons that develop distinct firing phenotypes. Journal of Neuroscience 17, 3136-3147.
51. Menke U, Müller-Röber B. 2001. RNA fingerprinting of specific plant cell types: adaption to plants and organization of RNA arbitrarily primed PCR (RAP-PCR). Plant Molecular Biology Reporter 19, 33-48.
52. Meyers BC, Galbraith DW, Nelson T, Agrawal V. 2004. Methods for transcriptional profiling in plants. Be fruitful and replicate. Plant Physiology 135, 637-652.
53. Mirabella R, Franken C, van der Krogt GNM, Bisseling T, Geurts R. 2004. Use of the fluorescent timer DsRED-E5 as reporter to monitor dynamics of gene activity in plants. Plant Physiology 135, 1879-1887.
54. + channel in potato gurad cells. EMBO Journal 14, 2409-2416.
55. Nakazono M, Qiu F, Borsuk LA, Schnable PS. 2003. Laser-capture micro dissection, a tool for the global analysis of gene expression in specific plant cell types: identification of genes expressed differentially in epidermal cells or vascular tissue of maize. The Plant Cell 15, 583-596.
56. O'Dell DM, Raghupathi R, Crino PB, Morrison B, Eberwine JH, McIntosh TK. 1998. Amplification of mRNAs from single, fixed, TUNEL-positive cells. BioTechniques 25, 566-569.
57. Ohyama H, Zhang X, Kohno Y, Alevizos I, Posner M, Wong DT, Todd R. 2000. Laser capture micro dissection-generated target sample for high-density oligonucleotide array hybridization. BioTechniques 29, 530-536.
58. Outlaw WH, Zhang SQ. 2001. Single-cell dissection and microdroplet chemistry. Journal of Experimental Botany 52, 605-614.
59. Pesquet E, Barbier O, Ranocha P, Jauneau A, Goffner D. 2004. Multiple gene detection by in situ RT-PCR in isolated plant cells and tissues. The Plant Journal 39, 947-959.
60. Petalidis L, Bhattacharyya S, Morris GA, Collins VP, Freeman TC, Lyons PA. 2003. Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis. Nucleic Acids Research 31, e142.
61. Phillips J, Eberwine JH. 1996. Antisense RNA amplification: a linear amplification method for analyzing the mRNA population from single living cell. Methods 10, 283-288.
62. Ponce MR, Pérez-Pérez JM, Piqueras P, Micol JL. 2000. A multiplex reverse transcriptase-polymerase chain reaction method for fluorescence-based semiautomated detection of gene expression in Arabidopsis thaliana. Planta 211, 606-608.
63. Raps A, Kehr J, Gugerli P, Moar WJ, Bigler F, Hilbeck A. 2001. Immunological analysis of phloem sap of Bacillus thuringiensis corn and of the nontarget herbivore Rhopalosiphum padi (Homoptera: Aphidae) for the presence of Cry1Ab. Moecular Ecoogy 10, 525-533.
64. Rausch C, Zimmermann P, Amrhein N, Bucher M. 2004. Expression analysis suggests novel roles for the plastidic phosphate transporter Pht2;1 in auto- and heterotrophic tissues in potato and Arabidopsis. The Plant Journal 39, 13-28.
65. Recchi MA, Hebbar M, Hornez L, Harduin-Lepers A, Peyrat JP, Delannoy P. 1998. Multiplex reverse transcription polymerase chain reaction assessment of sialyltransferase expression in human breast cancer. Cancer Research 58, 4066-4070.
66. Kichert J, Kranz E, Lörz H, Dresselhaus T. 1996. A reverse transcriptase-polymerase chain reaction assay for gene expression studies at the single cell level. Plant Science 114, 93-99.
67. Seki M, Satou M, Sakurai T, et al. 2004. RIKEN Arabidopsis full-length (RAFL) cDNA and its applications for expression profiling under abiotic stress conditions. Journal of Experimental Botany 55, 213-223.
68. Shu GG, Baum DA, Mets LJ. 1999. Detection of gene expression patterns in various plant tissues using nonradioactive mRNA in situ hybridization. World Wide Web Journal of Biology 4, http://www.epress.com/w3jbio/vol4/shu.
69. Titarenko E, Rojo E, Leon J, Sanchez-Serrano JJ. 1997. Jasmonic acid-dependent and -independent signaling pathways control wound-induced gene activation in Arabidopsis thaliana. Plant Physiology 115, 817-826.
70. Tomos AD, Sharrock RA. 2001. Cell sampling and analysis (SiCSA): metabolites measured at single cell resolution. Journal of Experimental Botany 52, 623-630.
71. Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH. 1990. Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proceedings of the National Academy of Sciences, USA 87, 1663-1667.
72. Vaskova D, Spak J, Klerks MM, Schoen CD, Thompson JR, Jelkmann W. 2004. Real-time NASBA for detection of strawberry vein banding virus. European Journal of Plant Pathology 110, 213-221.
73. Voelckel C, Baldwin IT. 2003. Detecting herbivore-specific transcriptional responses in plants with multiple DDRT-PCR and subtractive library procedures. Physiologia Plantarum 118, 240-252.
74. Volkov RA, Panchuk II, Schoffl F. 2003. Heat-stress-dependency and developmental modulation of gene expression: the potential of house-keeping genes as internal standards in mRNA expression profiling using real-time RT-PCR. Journal of Experimental Botany 54, 2343-2349.
75. Welsh J, Chada K, Dalai SS, Cheng S, Ralph D, McClelland M. 1992. Arbitrarily primed PCR fingerprinting of RNA. Nucleic Acids Research 20, 4965-4970.
76. Zabzdyr JL, Lillard SJ. 2001. UV- and visible-excited fluorescence of nucleis acids separated by capillary electrophoresis. Journal of Chromatography A 911, 269-276.