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Transcriptional profiling by cDNA-AFLP and microarray analysis reveals novel insights into the early response to ethylene in Arabidopsis

(2004) PLANT JOURNAL. 39(4). p.537-559
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Abstract
A comprehensive transcriptome analysis by means of cDNA-amplified fragment length polymorphism (AFLP) and cDNA-microarray technology was performed in order to gain further understanding of the molecular mechanisms of immediate transcriptional response to ethylene. Col-0 plants were treated with exogenous ethylene and sampled at six different time-points ranging from 10 min until 6 h. In order to isolate truly ethylene-responsive genes, both the ethylene-insensitive mutant ein2-1 and the constitutive mutant (ctr1-1) were analysed in parallel by cDNA-AFLP while ein2-1 was included for the microarray experiment. Out of the cDNA-transcript profiling covering about 5% of the Arabidopsis transcriptome, 46 ethylene-responsive genes were isolated, falling in different classes of expression pattern and including a number of novel genes. Out of the 6008 genes present on the chip, 214 genes were significantly (alpha = 0.001) differentially expressed between Col-0 and ein2-1 over time. Cluster analysis and functional grouping of co-regulated genes allowed to determine the major ethylene-regulated classes of genes. In particular, a large number of genes involved in cell rescue, disease and defence mechanisms were identified as early ethylene-regulated genes. Furthermore, the data provide insight into the role of protein degradation in ethylene signalling and ethylene-regulated transcription and protein fate. Novel interactions between ethylene response and responses to several other signals have been identified by this study. Of particular interest is the overlap between ethylene response and responses to abscisic acid, sugar and auxin. In conclusion, the data provide unique insight into early regulatory steps of ethylene response.
Keywords
ethylene, Arabidopsis, cDNA-AFLP transcript profiling, microarray analysis, defence, protein degradation, REGULATED GENE-EXPRESSION, SIGNAL-TRANSDUCTION PATHWAY, ELEMENT-BINDING FACTORS, ABSCISIC-ACID, CELL-DEATH, SALICYLIC-ACID, 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID, DISEASE RESISTANCE, NEGATIVE REGULATOR, CONFERS RESISTANCE

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Citation

Please use this url to cite or link to this publication:

MLA
De Paepe, Annelies, Marnik Vuylsteke, Paul Van Hummelen, et al. “Transcriptional Profiling by cDNA-AFLP and Microarray Analysis Reveals Novel Insights into the Early Response to Ethylene in Arabidopsis.” PLANT JOURNAL 39.4 (2004): 537–559. Print.
APA
De Paepe, Annelies, Vuylsteke, M., Van Hummelen, P., Zabeau, M., & Van Der Straeten, D. (2004). Transcriptional profiling by cDNA-AFLP and microarray analysis reveals novel insights into the early response to ethylene in Arabidopsis. PLANT JOURNAL, 39(4), 537–559.
Chicago author-date
De Paepe, Annelies, Marnik Vuylsteke, Paul Van Hummelen, Marc Zabeau, and Dominique Van Der Straeten. 2004. “Transcriptional Profiling by cDNA-AFLP and Microarray Analysis Reveals Novel Insights into the Early Response to Ethylene in Arabidopsis.” Plant Journal 39 (4): 537–559.
Chicago author-date (all authors)
De Paepe, Annelies, Marnik Vuylsteke, Paul Van Hummelen, Marc Zabeau, and Dominique Van Der Straeten. 2004. “Transcriptional Profiling by cDNA-AFLP and Microarray Analysis Reveals Novel Insights into the Early Response to Ethylene in Arabidopsis.” Plant Journal 39 (4): 537–559.
Vancouver
1.
De Paepe A, Vuylsteke M, Van Hummelen P, Zabeau M, Van Der Straeten D. Transcriptional profiling by cDNA-AFLP and microarray analysis reveals novel insights into the early response to ethylene in Arabidopsis. PLANT JOURNAL. 2004;39(4):537–59.
IEEE
[1]
A. De Paepe, M. Vuylsteke, P. Van Hummelen, M. Zabeau, and D. Van Der Straeten, “Transcriptional profiling by cDNA-AFLP and microarray analysis reveals novel insights into the early response to ethylene in Arabidopsis,” PLANT JOURNAL, vol. 39, no. 4, pp. 537–559, 2004.
@article{301730,
  abstract     = {A comprehensive transcriptome analysis by means of cDNA-amplified fragment length polymorphism (AFLP) and cDNA-microarray technology was performed in order to gain further understanding of the molecular mechanisms of immediate transcriptional response to ethylene. Col-0 plants were treated with exogenous ethylene and sampled at six different time-points ranging from 10 min until 6 h. In order to isolate truly ethylene-responsive genes, both the ethylene-insensitive mutant ein2-1 and the constitutive mutant (ctr1-1) were analysed in parallel by cDNA-AFLP while ein2-1 was included for the microarray experiment. Out of the cDNA-transcript profiling covering about 5% of the Arabidopsis transcriptome, 46 ethylene-responsive genes were isolated, falling in different classes of expression pattern and including a number of novel genes. Out of the 6008 genes present on the chip, 214 genes were significantly (alpha = 0.001) differentially expressed between Col-0 and ein2-1 over time. Cluster analysis and functional grouping of co-regulated genes allowed to determine the major ethylene-regulated classes of genes. In particular, a large number of genes involved in cell rescue, disease and defence mechanisms were identified as early ethylene-regulated genes. Furthermore, the data provide insight into the role of protein degradation in ethylene signalling and ethylene-regulated transcription and protein fate. Novel interactions between ethylene response and responses to several other signals have been identified by this study. Of particular interest is the overlap between ethylene response and responses to abscisic acid, sugar and auxin. In conclusion, the data provide unique insight into early regulatory steps of ethylene response.},
  author       = {De Paepe, Annelies and Vuylsteke, Marnik and Van Hummelen, Paul and Zabeau, Marc and Van Der Straeten, Dominique},
  issn         = {0960-7412},
  journal      = {PLANT JOURNAL},
  keywords     = {ethylene,Arabidopsis,cDNA-AFLP transcript profiling,microarray analysis,defence,protein degradation,REGULATED GENE-EXPRESSION,SIGNAL-TRANSDUCTION PATHWAY,ELEMENT-BINDING FACTORS,ABSCISIC-ACID,CELL-DEATH,SALICYLIC-ACID,1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID,DISEASE RESISTANCE,NEGATIVE REGULATOR,CONFERS RESISTANCE},
  language     = {eng},
  number       = {4},
  pages        = {537--559},
  title        = {Transcriptional profiling by cDNA-AFLP and microarray analysis reveals novel insights into the early response to ethylene in Arabidopsis},
  url          = {http://dx.doi.org/10.1111/j.1365-313X.2004.02156.x},
  volume       = {39},
  year         = {2004},
}

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