thesis
Using systems biology approaches to elucidate gene regulatory networks controlling the plant defence response
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Abstract
Transcriptional regulation controlling pathogen-responsive gene expression in Arabidopsis
is believed to underlie the plant defence response, which confers partial
immunity of Arabidopsis to infection by Botrytis cinerea. In this thesis networks
of transcriptional regulation mediating the defence response are studied in various
ways.
First transcriptional regulation was predicted for all genes differentially expressed
during B. cinerea infection by development of a novel clustering approach, Temporal
Clustering by Affinity Propagation (TCAP). This approach finds groups of
genes whose expression profile time series have strong time-delayed correlation, a
measure that is demonstrated to be more predictive of transcriptional regulation
than conventionally used similarity measures. TCAP predicts the known regulation
of GI by LHY, and co-clusters ORA59 and some of its downstream targets.
Predicted novel regulators of pathogen-responsive gene expression were then studied
in a reverse genetics screen, which discovered several novel but weakly altered
susceptibility phenotypes. Comparison of predicted targets to known targets was
complicated by the sparsity of mutant versus wildtype gene expression experiments
performed during B. cinerea infections in the literature.
To explore the context-dependence of transcriptional regulation, evidence of transcriptional
regulation in different contexts was collected. This was compiled to generate
a qualitative model of transcriptional regulation during the defence response.
This model was validated and extended by experimental analysis of transcription
factor-promoter binding in Yeast and transcriptional activation in planta. Comparative
transcriptomics showed that downstream genes of some of these regulators
| TGA3, ARF2, ERF1 and ANAC072 | are over-represented in the list of genes
differentially expressed during B. cinerea infection, which is consistent with these
targets being regulated by them during B. cinerea infection.
Finally this qualitative model was used as prior information and was used along
with gene expression time series to infer quantitative models of the gene regulatory
network mediating the defence response. Some known regulation was predicted,
and additionally ANAC055 was predicted to be a central regulator of pathogenresponsive
gene expression