15th International Conference on Arabidopsis Research - TAIR

T11-009
Non-Random Distribution of Transcription Factor
Binding Sites in the Arabidopsis thaliana Genome
Claudia Galuschka(1), Nils Ole Steffens(1), Lorenz Bülow(1), Reinhard Hehl(1)
1-Institute for Genetics, Technical University Braunschweig,Spielmannstrasse 7, D-38106 Braunschweig,
Germany
Transcription factors (TFs) are essential for regulation of gene expression
by controlling transcription through binding to specific regulatory DNA sequences
and interaction with other TFs. Specific target sequences of a TF can
be determined experimentally and are generally described using a positional
weight matrix.
In this study, 31 plant matrices were employed in screenings for putative
transcription factor binding sites (TFBSs) with PATSER using the Arabidopsis
thaliana genome as target sequence. A software tool was developed
to calculate the occurrence of neighbouring TFBSs and to determine the
preferred distance between them. Low distances between TFBS were found
to be overrepresented indicating a clustering of matches. A distance of up
to 50bp was discovered as the most preferred space with a 30 fold higher
frequency than expected. Colocalization frequencies remain elevated in distance
windows ranging up to 1000 bp. A positional analysis was performed
for each matrix in order to consider the genomic context of the TFBSs relative
to the neighbouring translational initiation ATG. Several matrices showed a
preference for binding to the region located upstream of the next ATG. Others
exhibited an indifferent distribution or an accumulation downstream of the
next ATG. This study shows that TFBSs are not randomly distributed in the
Arabidopsis thaliana genome.
15 th <strong>International</strong> <strong>Conference</strong> on Arabidopsis Research 2004 · Berlin
T11-010
New tools for computer visualisation and modeling of
cell interactions.
Tim Rudge(1), Sarah Hodge(1), Smita Kurup(1), Jean-Maurice Assie(1), Lilian
Ricaud(1), Jennifer Clark(1), Jim Haseloff(1)
1-Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge. CB2 3EA.
UK.
The genetic control of plant development is mediated by cellular interactions,
and an exchange of positional information contributes to the self-organisation
and coordination of cells during development. The Arabidopsis root meristem
provides an ideal test-bed for probing these interactions. The root meristem
grows indeterminately, is genetically amenable, has a simple and transparent
architecture, and can be induced to form de novo in adult tissues. We have
developed new genetic and optical techniques for following organisation of
cells within living meristems, using modified green fluorescent proteins, and
have generated a two large libraries of Arabidopsis lines that can be used
for targeted gene expression in the root meristem. Confocal fluorescence
microscopy techniques allow high resolution imaging, and 3D reconstruction
of Arabidopsis root cells during initiation and growth of the meristem.
We have adapted computer segmentation methods for the description of 3D
cell arrangements in plant tissue, and in our first steps towards developing a
system for dynamic modelling of plant cell interactions, we have generated
a 2D description of the physical properties of cells, using a novel double
spring model to describe cell wall properties. This physical model provides an
engine for the production of cells through enlargement and division. Fields
of proliferating cells can then be programmed via a genetic script to produce
and respond to different morphogens. We are using this 2D system as a pilot
study for modelling cell dynamics and interactions in 3D.
web site: http://www.plantsci.cam.ac.uk/Haseloff
T11 Modeling the Virtual Plant / Bioinformatics