Edinburgh, Scotland, United Kingdom - TAIR

Sequencing across the genome-phenome
divide
The development of DNA sequencing technologies producing vast amounts of
sequence information has triggered a paradigm shift in biology, enabling
massively parallel surveying of complex nucleic acid populations. The diversity
of applications to which these technologies have already been applied
demonstrates the immense range of cellular processes and properties that can
now be studied at the single-base resolution. As part of the Arabidopsis 1001
genomes project (http://1001genome.org project), we have carried out both
resequencing and de novo sequencing and assembly of several accessions. In
parallel, we developed RNA-Seq and MethylC-Seq methods which now allow
sequence-level maps of the transcriptome and cytosine DNA methylome,
respectively. When combined with the genome sequences, an in depth view of
the relationship between genetic and epigenetic variation and their effects on
gene expression can be obtained. In addition, we have applied now-generation
DNA sequencing approaches to identify the sites of insertion of T-DNA in large
populations of arrayed plants. This approach should enable completion of the
Arabidopsis Unimutant Project, which aims to identify sequence-indexed
homozygous insertion mutations for all genes in the Col-0 genome (see
http://signal.salk.edu). Finally, a major deficiency in the repertoire of plant
genomic resources is the paucity of large-scale protein-protein and protein-DNA
information for Arabidopsis or any plant system. Genome-wide molecular
interaction maps (interactomes) are an indispensible tool for systems biology,
aid focused biological studies, provide network information for topological
analysis and aid the development of large-scale dynamic models. We have
created a first generation plant interactome map in a collaboration led by the
Center for Cancer Systems Biology. Utilizing both high throughput, high-quality
yeast-2-hybrid and improved protein array technologies, a 9k by 9k binary
interaction map has been developed using a recombination-vector based
ORFeome collection of sequence-validated Arabidopsis open reading frame
(ORF) clones. Properties of this first generation plant protein-protein interactome
map, examples of its utility and examples of novel biological insights derived
from it will be described.
63
C12
Wednesday 16:00 - 16:30
Tools and Resources
Joseph Ecker
The Salk Institute
La Jolla
CA
USA