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Differential SAGE analysis in Arabidopsis uncovers increased transcriptome complexity in response to low temperature.

Robinson SJ, Parkin IA - BMC Genomics (2008)

Bottom Line: Abiotic stress, including low temperature, limits the productivity and geographical distribution of plants, which has led to significant interest in understanding the complex processes that allow plants to adapt to such stresses.Novel genes and cis-acting sequences have been identified as compelling targets to allow manipulation of the plant's ability to protect against low temperature stress.The analyses performed provide a contextual framework for the interpretation of quantitative sequence tag based transcriptome analysis which will prevail with the application of next generation sequencing technology.

View Article: PubMed Central - HTML - PubMed

Affiliation: Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada. robinsons@agr.gc.ca

ABSTRACT

Background: Abiotic stress, including low temperature, limits the productivity and geographical distribution of plants, which has led to significant interest in understanding the complex processes that allow plants to adapt to such stresses. The wide range of physiological, biochemical and molecular changes that occur in plants exposed to low temperature require a robust global approach to studying the response. We have employed Serial Analysis of Gene Expression (SAGE) to uncover changes in the transcriptome of Arabidopsis thaliana over a time course of low temperature stress.

Results: Five SAGE libraries were generated from A. thaliana leaf tissue collected at time points ranging from 30 minutes to one week of low temperature treatment (4 degrees C). Over 240,000 high quality SAGE tags, corresponding to 16,629 annotated genes, provided a comprehensive survey of changes in the transcriptome in response to low temperature, from perception of the stress to acquisition of freezing tolerance. Interpretation of these data was facilitated by representing the SAGE data by gene identifier, allowing more robust statistical analysis, cross-platform comparisons and the identification of genes sharing common expression profiles. Simultaneous statistical calculations across all five libraries identified 920 low temperature responsive genes, only 24% of which overlapped with previous global expression analysis performed using microarrays, although similar functional categories were affected. Clustering of the differentially regulated genes facilitated the identification of novel loci correlated with the development of freezing tolerance. Analysis of their promoter sequences revealed subsets of genes that were independent of CBF and ABA regulation and could provide a mechanism for elucidating complementary signalling pathways. The SAGE data emphasised the complexity of the plant response, with alternate pre-mRNA processing events increasing at low temperatures and antisense transcription being repressed.

Conclusion: Alternate transcript processing appears to play an important role in enhancing the plasticity of the stress induced transcriptome. Novel genes and cis-acting sequences have been identified as compelling targets to allow manipulation of the plant's ability to protect against low temperature stress. The analyses performed provide a contextual framework for the interpretation of quantitative sequence tag based transcriptome analysis which will prevail with the application of next generation sequencing technology.

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Freezing tolerance(LT50)of Arabidopsis plants exposed to cold acclimating conditions for various lengths of time.
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Figure 1: Freezing tolerance(LT50)of Arabidopsis plants exposed to cold acclimating conditions for various lengths of time.

Mentions: The degree of freezing tolerance in Arabidopsis was assayed at five time points, 0 minutes, 30 minutes, 2 hours, 2 days and 1 week of exposure to 4°C. As anticipated, the level of freezing tolerance was positively correlated with the period of time under acclimating conditions. Freezing tolerance was measured to be -4.2°C with non-acclimated material under these growth conditions. There was no detectable increase in freezing tolerance prior to 48 hours exposure to low temperature and after 1 week the freezing tolerance increased to -8.3°C (Figure 1). These results are in agreement with previous assessments of freezing tolerance for Arabidopsis [6,10].


Differential SAGE analysis in Arabidopsis uncovers increased transcriptome complexity in response to low temperature.

Robinson SJ, Parkin IA - BMC Genomics (2008)

Freezing tolerance(LT50)of Arabidopsis plants exposed to cold acclimating conditions for various lengths of time.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2568001&req=5

Figure 1: Freezing tolerance(LT50)of Arabidopsis plants exposed to cold acclimating conditions for various lengths of time.
Mentions: The degree of freezing tolerance in Arabidopsis was assayed at five time points, 0 minutes, 30 minutes, 2 hours, 2 days and 1 week of exposure to 4°C. As anticipated, the level of freezing tolerance was positively correlated with the period of time under acclimating conditions. Freezing tolerance was measured to be -4.2°C with non-acclimated material under these growth conditions. There was no detectable increase in freezing tolerance prior to 48 hours exposure to low temperature and after 1 week the freezing tolerance increased to -8.3°C (Figure 1). These results are in agreement with previous assessments of freezing tolerance for Arabidopsis [6,10].

Bottom Line: Abiotic stress, including low temperature, limits the productivity and geographical distribution of plants, which has led to significant interest in understanding the complex processes that allow plants to adapt to such stresses.Novel genes and cis-acting sequences have been identified as compelling targets to allow manipulation of the plant's ability to protect against low temperature stress.The analyses performed provide a contextual framework for the interpretation of quantitative sequence tag based transcriptome analysis which will prevail with the application of next generation sequencing technology.

View Article: PubMed Central - HTML - PubMed

Affiliation: Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada. robinsons@agr.gc.ca

ABSTRACT

Background: Abiotic stress, including low temperature, limits the productivity and geographical distribution of plants, which has led to significant interest in understanding the complex processes that allow plants to adapt to such stresses. The wide range of physiological, biochemical and molecular changes that occur in plants exposed to low temperature require a robust global approach to studying the response. We have employed Serial Analysis of Gene Expression (SAGE) to uncover changes in the transcriptome of Arabidopsis thaliana over a time course of low temperature stress.

Results: Five SAGE libraries were generated from A. thaliana leaf tissue collected at time points ranging from 30 minutes to one week of low temperature treatment (4 degrees C). Over 240,000 high quality SAGE tags, corresponding to 16,629 annotated genes, provided a comprehensive survey of changes in the transcriptome in response to low temperature, from perception of the stress to acquisition of freezing tolerance. Interpretation of these data was facilitated by representing the SAGE data by gene identifier, allowing more robust statistical analysis, cross-platform comparisons and the identification of genes sharing common expression profiles. Simultaneous statistical calculations across all five libraries identified 920 low temperature responsive genes, only 24% of which overlapped with previous global expression analysis performed using microarrays, although similar functional categories were affected. Clustering of the differentially regulated genes facilitated the identification of novel loci correlated with the development of freezing tolerance. Analysis of their promoter sequences revealed subsets of genes that were independent of CBF and ABA regulation and could provide a mechanism for elucidating complementary signalling pathways. The SAGE data emphasised the complexity of the plant response, with alternate pre-mRNA processing events increasing at low temperatures and antisense transcription being repressed.

Conclusion: Alternate transcript processing appears to play an important role in enhancing the plasticity of the stress induced transcriptome. Novel genes and cis-acting sequences have been identified as compelling targets to allow manipulation of the plant's ability to protect against low temperature stress. The analyses performed provide a contextual framework for the interpretation of quantitative sequence tag based transcriptome analysis which will prevail with the application of next generation sequencing technology.

Show MeSH
Related in: MedlinePlus