Limits...
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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Frequency of genes distributed according to GO-slim functional categories. Genes identified under control (inner ring) and low temperature (outer ring) growth conditions and identified as either A) plant specific or those sharing a B) conserved evolution.
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Figure 5: Frequency of genes distributed according to GO-slim functional categories. Genes identified under control (inner ring) and low temperature (outer ring) growth conditions and identified as either A) plant specific or those sharing a B) conserved evolution.

Mentions: The evolutionary origin of the low temperature responsive genes was inferred based on the classifications described by Gutierrez et al. [37] who determined that at least 14% (3,848) of Arabidopsis proteins are plant specific and 9% (2,436) are evolutionarily conserved with the Eukaryota, Bacteria and Archea domains. The SAGE analysis identified 162 plant specific genes and 127 conserved genes that were differentially regulated by low temperature (p < 0.01). Functional characterisation of these subsets revealed that low temperature treatment induced changes in the frequency distribution among several Gene Ontology (GO) slim categories (Figure 5).


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

Robinson SJ, Parkin IA - BMC Genomics (2008)

Frequency of genes distributed according to GO-slim functional categories. Genes identified under control (inner ring) and low temperature (outer ring) growth conditions and identified as either A) plant specific or those sharing a B) conserved evolution.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Frequency of genes distributed according to GO-slim functional categories. Genes identified under control (inner ring) and low temperature (outer ring) growth conditions and identified as either A) plant specific or those sharing a B) conserved evolution.
Mentions: The evolutionary origin of the low temperature responsive genes was inferred based on the classifications described by Gutierrez et al. [37] who determined that at least 14% (3,848) of Arabidopsis proteins are plant specific and 9% (2,436) are evolutionarily conserved with the Eukaryota, Bacteria and Archea domains. The SAGE analysis identified 162 plant specific genes and 127 conserved genes that were differentially regulated by low temperature (p < 0.01). Functional characterisation of these subsets revealed that low temperature treatment induced changes in the frequency distribution among several Gene Ontology (GO) slim categories (Figure 5).

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