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Transcriptional regulatory codes underlying Arabidopsis stress responses
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Hickman, Richard J. (2012) Transcriptional regulatory codes underlying Arabidopsis stress responses. PhD thesis, University of Warwick.
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Official URL: http://webcat.warwick.ac.uk/record=b2581660~S1
Abstract
Plant adaptation to stress is dependent upon the initialisation of molecular signalling networks
that regulate the expression of stress-related genes. By examining high-resolution
microarray datasets it has been possible to track gene expression changes over time during
senescence and in response to infection by fungal pathogen Botrytis cineria in the
model organism Arabidopsis thaliana. Dramatic variations in gene expression are observed
at the onset of stress with different groups of genes showing different expression
time-courses. This observation must, for a large part, be down to the action of different
transcription factors (TFs) binding to the cis-regulatory DNA in the promoters of genes
in each group and it is this regulatory code that underpins the gene regulatory networks
that regulate stress responses. This thesis presents an interdisciplinary investigation of
the regulatory codes that are responsible for controlling plant stress responses.
Computational analysis of non-coding sequences provides a powerful approach to
identify patterns within DNA that may function to regulate gene expression. This thesis
covers the development of Analysis of Plant Promoter-Linked Elements (APPLES), an
object-orientated software framework for the analysis of non-coding DNA. Within this
environment, methods were developed to probe the regulatory codes that exist within
these non-coding sequences and identify regulatory motifs that may function to regulate
stress responses in Arabidopsis. APPLES methods were used to identify a novel motif
that is likely to play a role in regulating drought responses in Arabidopsis, with experimental
approaches providing support for this view. Using known motifs that describe
previously characterised TF binding sites, it was possible to identify motifs that are
associated with clusters of co-regulated genes identified from the senescence and Botrytis
microarray time-course datasets. This analysis revealed cis-regulatory elements that
may contribute to generating the observed expression patterns.
In a contrasting approach to in silico identification of regulatory elements, the
Yeast-1-Hybrid (Y1H) assay was used to experimentally identify interactions between
TFs and non-coding DNA. The use of a TF library allowed the ability of approximately
1400 Arabidopsis TFs to interact with a given DNA sequence in a single assay. Using
the stress-associated ANAC092 promoter as a test case, it was possible to use this highthroughput
procedure to identify TFs that can bind to the promoter of this gene. This
high-throughput Y1H system was then used to perform a detailed mapping of protein-
DNA interactions that can occur across the core promoters of three highly related stress
inducible TF-encoding genes, ANAC019, ANAC055 and ANAC072. Microarrays were
used to assess the regulatory consequence of a subset of these interactions by perturbing
the expression of interacting TFs and observing the effect on target gene expression
during multiple stresses. This approach confirmed predicted regulatory relationships and
therefore enhanced the current understanding of the transcriptional regulatory networks
that operate during stress responses in Arabidopsis.
Item Type: | Thesis (PhD) | ||||
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Subjects: | Q Science > QK Botany | ||||
Library of Congress Subject Headings (LCSH): | Arabidopsis thaliana -- Effect of stress on -- Genetic aspects, Plant gene expression, Plant genetic regulation -- Computer programs, Botrytis | ||||
Official Date: | May 2012 | ||||
Dates: |
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Institution: | University of Warwick | ||||
Theses Department: | Systems Biology Doctoral Training Centre | ||||
Thesis Type: | PhD | ||||
Publication Status: | Unpublished | ||||
Supervisor(s)/Advisor: | Buchanan-Wollaston, Vicky ; Ott, Sascha | ||||
Extent: | xv, 198 leaves : ill. | ||||
Language: | eng |
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