Comparison between SAGE and cDNA microarray for quantitative accuracy in transcript profiling analyses

Eom, Eun Mi; Lee, Ji Yeors; Park, Hye-Sang; Byun, Youn Jung; Ha-Lee, Young Mie; Lee, Dong Hee

doi:10.1007/bf03031132

Cited by 4 publications

(7 citation statements)

References 17 publications

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“…To determine if there were transcriptional differences between reacclimated plants with improved cold tolerances and plants cold‐treated for the first time, we analyzed gene expression profiles during cold acclimation (CT), deacclimation (PT) and reacclimation (SCT) using the Coldstresschip (Eom et al , Byun et al , Jeong et al ). Gene expression profiles during cold acclimation were determined at eight time points (0.25, 0.5, 1, 3, 8, 16, 24 and 72 h; 0.25–72CT).…”

Section: Resultsmentioning

confidence: 99%

“…A specialized cDNA microarray generated in this laboratory for cold stress research was used (Eom et al , Byun et al , Jeong et al ). The microarray contained 1482 cDNA probes selected on the basis of SAGE and SSH data, as well as additional reference genes.…”

Section: Methodsmentioning

confidence: 99%

“…The massive quantities of gene expression and other functional genomics data could also provide insights into gene interactions within and across metabolic pathways (DeRisi et al , Duggan et al , Jones et al ). To study the gene expression profiles during repeated stress, cold acclimation, deacclimation and reacclimation, we used a specialized cDNA microarray for cold research, named “Coldstresschip” (Eom et al , Byun et al , Jeong et al ), which was constructed with genes that are differentially expressed in leaves and pollens of plants after cold treatment based on serial analysis of gene expression (SAGE) and SSH (suppression subtractive hybridization) data (Lee and Lee , Eom et al , Byun et al ). This chip has been useful in analyzing gene expression profiles during cold stress and detecting new genes involved in cold tolerance.…”

Section: Introductionmentioning

confidence: 99%

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Comparative analysis of gene expression under cold acclimation, deacclimation and reacclimation in Arabidopsis

Byun

Koo

Joo

et al. 2014

Physiologia Plantarum

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Cold acclimated plants show an elevated tolerance against subsequent cold stress. Such adaptation requires alterations in gene expression as well as physiological changes. We were interested in gene expression changes at the transcriptional level during adaptation processes. The patterns of transcriptional changes associated with cold acclimation, deacclimation and reacclimation in Arabidopsis leaves were characterized using the Coldstresschip. Gene expression profiles were further analyzed by 'coexpressed gene sets' using gene set enrichment analysis (GSEA). Genes involved in signal transduction through calcium, and cascades of kinases and transcription factor genes, were distinctively induced in the early response of cold acclimation. On the other hand, genes involved in antioxidation, cell wall biogenesis and sterol synthesis were upregulated in the late response of cold acclimation. After the removal of cold, the expression patterns of most genes rapidly returned to the original states. However, photosynthetic light-harvesting complex genes and lipid metabolism-related genes stayed upregulated in cold deacclimated plants compared to non-treated plants. It is also notable that many well-known cold-inducible genes are slightly induced in reacclimation and their expression remains at relatively low levels in cold reacclimation compared to the expression during the first cold acclimation. The results in this study show the dynamic nature of gene expression occurring during cold acclimation, deacclimation and reacclimation. Our results suggest that there is a memory of cold stress and that the 'memory of cold stress' is possibly due to elevated photosynthetic efficiency, modified lipid metabolism, increased calcium signaling, pre-existing defense protein made during first cold acclimation and/or modified signal transduction from pre-existing defense protein.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparative analysis of gene expression under cold acclimation, deacclimation and reacclimation in Arabidopsis

Byun

Koo

Joo

et al. 2014

Physiologia Plantarum

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“…A specialized cDNA microarray generated in this laboratory for cold stress research was used (Eom et al 2006). This microarray contained 1,482 cDNA probes selected on the basis of SAGE and SSH (Suppression Subtractive Hybridization) data, as well as additional reference genes.…”

Section: Microarray Hybridizationmentioning

confidence: 99%

LongSAGE analysis of the early response to cold stress in Arabidopsis leaf

Byun

Kim

Lee

2009

Planta

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The initial events involved in signal transduction generated by cold exposure are poorly known in plants. We were interested in the characterization of early response to cold stress in Arabidopsis leaves. So we examined plants exposed to 0 degrees C for 1 h. Using LongSAGE at the level of transcription, a total of 27,612 tags, including 11,089 unique tags were sequenced and analyzed. By adopting LongSAGE methods, the ambiguity of tag identification was reduced by about 10%. Only 46% of identified tags in the 1-h cold-stressed plants matched existing Arabidopsis UniGene entries. A comparison of the tags derived from the cold-treated leaves with those identified in the non-treated leaves revealed 315 differentially expressed genes (P < 0.01). Functional classification of expressed genes during the early cold response indicated that genes were involved in light harvesting, the Calvin cycle, and photorespiration were expressed at relatively low levels compared to their presence in non-cold-stressed plants. On other hand, genes involved in mitochondrial electron transport and ATP synthesis showed an increased expression. Some orphan LongSAGE tags uniquely matched pri-miRNA, suggesting the existence of miRNA in our SAGE library. These findings suggest that diverse protection strategies appear in the early response of leaves exposed to cold stress. First of all, several genes included in signal transduction through calcium mediated signal sensing, and cascades of several kinases, and transcription factors, were distinguished in the early cold response. Furthermore, genes affecting the synthesis of salicylic acid, nitrate assimilation, ammonia assimilation, the gluconeogenesis pathway, and glucosinolate biosynthesis were newly detected in relationship with cold stress. Finally, our results in the present work provide new insights into the molecular mechanisms involved in transcriptional regulation in response to cold exposure in plants.

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“…The synthesized, tagged cDNAs were then fluorescently labeled with Cy3-or Cy5-3DNA based on the sequence complementary to the 3DNA capture reagent, which contained an average of 375 fluorescent dyes. The labeled cDNA was hybridized on a version-3-specialized cDNA microarray, which included additionally 110 flooding stress-related cDNA probes (Klok et al 2002) on 1,482 cDNA probes of a version-2-specialized cDNA microarray as described by Eom et al (2006). The hybridization and washing procedures were performed according to the Genisphere technical protocol.…”

Section: Microarray Hybridization and Image Acquisitionmentioning

confidence: 99%

Expression Profile Analysis of Hypoxia Responses in Arabidopsis Roots and Shoots

Hwang¹,

Lee

Choy³

et al. 2011

J. Plant Biol.

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Physiological and molecular adaptation mechanisms enable plants to improve their survival under harsh conditions, including low oxygen levels caused by flooding. When Arabidopsis was exposed to hypoxia, we observed hyponastic response, shoot elongation, leaf chlorosis, and inhibited growth. To understand this response, we used a specialized complementary DNA microarray from our laboratory to examine the time-dependent profiles of gene expression in Arabidopsis roots and shoots. From this, we identified 282 hypoxia-responsive genes. These included novel genes for a zinc finger protein, WRKY family transcription factor, and glycosyl hydrolase as well as those previously identified as hypoxia-related genes including alcohol dehydrogenase (ADH), pyruvate decarboxylase (PDC), and phosphofructokinase. Cluster analysis of these profiles suggested that the hypoxia response occurs in two distinctive phases: early and late. The early response to imposed stress (hours 1, 3, and 8) includes increased expression of fermentation-related genes and transcription factors, such as by members of the C 2 H 2 zinc finger family and WRKY family. The late response (hours 24 and 72) involves the down-regulation of genes that function in secondary metabolic pathways and up-regulation of transcription factors that are mostly related to the ethylene-responsive element binding protein family. Mutants of Arabidopsis defective in sucrose synthase1 (SUS1), the At1g05060 gene (with unknown function), ADH, and the WRKY33 were more sensitive to hypoxic stress, evidence of the importance of these genes in that response. The genes presented here allow us to deepen our understanding of the mechanism for this stress response and, eventually, will aid in the development of more flood-tolerant crops.

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Comparison between SAGE and cDNA microarray for quantitative accuracy in transcript profiling analyses

Cited by 4 publications

References 17 publications

Comparative analysis of gene expression under cold acclimation, deacclimation and reacclimation in Arabidopsis

Comparative analysis of gene expression under cold acclimation, deacclimation and reacclimation in Arabidopsis

LongSAGE analysis of the early response to cold stress in Arabidopsis leaf

Expression Profile Analysis of Hypoxia Responses in Arabidopsis Roots and Shoots

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