75 Integrating Membrane Transport with Male Gametophyte ... - TAIR

375 Natural genetic and epigenetic effects on gene expression and splicing variation in
Arabidopsis thaliana using whole genome tiling arrays
Xu Zhang 1 , Shinhan Shiu 2 , Justin Borevitz 1
1
Ecology and Evolution, University of Chicago, Chicago, IL 60634, 2 Plant biology, Michigan State University,
East Lansing, MI 48824
Natural variation in gene expression has a heritable component and has been explored in model organisms in
inbred lines and controllable environments. Gene expression variation is composed of steady state transcript level
differences, alternative spliced transcripts and allele specific expression differences in F1 hybrids. This is the result of
cis and/or trans regulatory polymorphisms caused by underlying genetic and epigenetic variation. We have investigated
the causes and effects of this variation using whole genome oligonucleotide tiling arrays. Over 100,000 Single Feature
Polymorphisms (SFPs) between two wild Arabidopsis accessions, Van and Col , were revealed by genomic DNA
hybridization. Subsequently true natural variation in gene expression and alternative splicing was analyzed accounting
for SFP variation. A linear model was fit testing main effects of overall transcriptional differences and differences among
transcript fragments (exons) for each gene, revealing ~ 2,300 gene expression polymorphism and ~2,100 exon level
polymorphisms (FDR 5%). Comparison of the transcript abundance among parental lines and F1 hybrids allows the
detection of additive, dominance, and maternal gene effects to be jointly estimated. cis-regulatory polymorphisms and
imprinting effects were also analyzed at the genome wide level by testing for allele specific expression in reciprocal
F1 hybrids. SFPs within a transcribed fragment are used to distinguish which allele is expressed (Ronald et al 2005,
Borevitz et al 2005). Upstream SFPs linked to expression variation are candidates for causative cis regulatory elements
in intergenic regions. When variation in expression is not determined by genotype but rather the parental or maternal
direction of the cross this allelic expression suggests imprinting effects. Genome wide cytosine methylation patterns
were also profiled in parental and hybrid lines to suggesting abundant underlying epigenetic variation which may also
contribute to such allelic expressional difference. Current results and methods will be presented (see also http://natural.
uchicago.edu/~xuzhang/expression.html).
376 Strain Selective Drugs: Exploiting Natural Variation in Chemical Genomics
Yang Zhao, Freeman Chow, Rachel Puckrin, Karen Ng, Simon Alfred, Pauline Fung, Sean Cutler
Department of Botany, University of Toronto
Natural genetic variation within a species can be documented at many levels of analysis ranging from simple
“aphenotypic” molecular polymorphisms to large scale differences in development such as flowering time. One facet
of natural variation explored primarily in humans is pharmacogenetic variation, a clinically important from of interindividual
variation in drug sensitivity. We reasoned that if pharmacogenetic variation is biologically pervasive it could
be used to identify genetic factors that modulate drug sensitivity in model systems. To survey pharmacogenetic variation
in Arabidopsis, several geographically diverse ecotypes were subjected to the same chemical genetic screen of ~13,500
small molecules library to identify compounds that show differential effects on hypocotyl cell elongation. This screen
uncovered 5 loci that act as simple Mendelian traits to modify sensitivity to 5 structurally unrelated cell expansion
inhibitors.
To gain insight into the molecular mechanisms of pharmacogenetic variation in plants, we have begun mapping and
cloning the pharmacogenetic loci identified. We will describe our work on the HYR1 locus, which confers resistance to
hypostatin, a new small molecule inhibitor of cell expansion that ~25% of Arabidopsis isolates are naturally resistant
to. Genetic analysis, map based cloning and biochemical analyses have shown that most hypostatin resistant strains
carry recessive mutations in HYR1, a glycosyl-transferase that converts hypostatin from a pro-drug into an activated
form by glycosylation. Intriguingly, HYR1 is part of the large UGT-superfamily of enzymes that play important roles as
pharmacogenetic factors in humans. Thus, intraspecific variation in UGT function acts to modulate drug sensitivity across
biological kingdoms suggesting that Arabidopsis may be a good model for exploring the mechanisms of pharmacogenetic
variation. Additionally, our results demonstrate that small molecules are effective tools for exposing and characterizing
natural variation.