Project
Many of the known cis-regulatory sequence elements are conserved among different
species of plants. The identification of novel cis-regulatory elements will
allow both the design of novel effective markers for crop breeding and an
improved control and specificity of transgene expression in plants. We will
deliver comprehensive cross-cutting data access and bioinformatics tools for the
genome-wide in silico identification of large numbers of putative endogenous
cis-regulatory elements by employing the large, mostly untapped, resource of
publicly available expression profiling data, open-access genome sequence data
and complementary datasets newly generated in this project.
Transcription factors act on sets of co-regulated genes, which are characterized
by common cis-regulatory sequence elements. The identification of endogenous
cis-regulatory elements will be based on a combination of co-regulation
analysis within large datasets of genome-wide expression data from several
developmental stages, plant cell types and response-inducing conditions,
motif discovery in promoter sequences of
co-regulated genes, integration of
transcript profiles and genomic sequence data from related plant species in a
cross-species microarray hybridization approach to enhance the precision and
reliability of predicted putative cis-regulatory elements
("phylogenetic
footprinting"). In a complementary approach, we will additionally develop
and use tools for the experimental selection and evolution of
synthetic
cis-regulatory elements. For experimental validation,
minimal promoters will be constructed using putative cis-regulatory elements to
verify their responsiveness in cell culture and in intact plants, thereby
generating proof-of-concept for the construction of synthetic specifically
inducible promoters and providing validated cis-regulatory elements
for testing in heterologous crop plant species. For implementation, we will
integrate our results into the PathoPlant database and an expanded version of
the AthaMap database.
The prerequisites for our combined approach are uniquely available in a set of
Brassicaceae species, including Arabidopsis thaliana, A. lyrata
and A. halleri.
When genome sequence data and expression profiling platforms are available for
additional sets of closely related plant species, it will be possible to also
transfer the approach and the tools developed in this project to other sets of
closely related model and agronomic plants, such as, possibly, cereals, Medicago
truncatula and alfalfa, or Solanaceae species. Novel cis-regulatory elements can
be claimed for the construction of highly specific synthetic promoters for the
generation of stress-tolerant and resistant crop plants.
Figure 1. Phylogenetic tree of the Arabidopsis genus and related Brassicaceae genera.
The position of the three species A. halleri, A. lyrata and A. thaliana within the tree is highlighted in orange.
Strict consensus tree based on Chalcone Synthase sequences (modified from Koch et al., 2000, Mol Biol Evol., 17(10): 1483-98).
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