From: Wootton, John (NIH/NLM/NCBI) [E]
Sent: Monday, March 24, 2008 10:19 AM
To: NLM/NCBI List ncbi-seminar
Subject: CBB Seminar, Tuesday, March 25, 2008, 11:00 AM

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CBB Seminar, Tuesday, March 25, 2008, 11:00 AM
Location: NCBI Seminar Room/Library, B2 Floor, Building 38A

Genome-wide quantitative genetics of transcription in Toxoplasma parasites 
during growth and intracellular development in human fibroblasts.

John Wootton, CBB, NCBI

I will introduce our analysis of genetic and developmental variation in 
the transcript levels from 7652 genes across the 62 Mb nuclear genome of the 
highly-successful Apicomplexan parasite, Toxoplasma gondii.  The analysis has 
an eQTL design ('expression Quantitative Trait Loci') based on sexual crosses 
between established laboratory isolates of Toxoplasma and high throughput 
expression data from these parents and their recombinant progeny.  The 
parental parasite genomes have been sequenced to high coverage across the 
14 chromsomes, defining very high SNP haplotype density informative for 
both evolutionary studies and experimental forward genetics.  The parents 
and progeny differ dramatically in recently-evolved pathogenesis-related 
phenotypes such as virulence, intracellular replication, developmental 
stage conversion, and transmission, which previously enabled us to use 
quantitative genetics to characterize a potent secreted protein kinase 
virulence factor[1].

The quantitative traits from the 'ToxoGeneChip' microarray hybridization 
traits show clear genetic variation for c 5 percent of genes.  This 
relatively low proportion reflects the notable developmental and 
mutational robustness of the Toxoplasma transcriptional program within the
protected intracellular vacuole environment.  As with eQTL studies in 
yeast and human cell lines, the genetic associations and segregation 
statistics of these traits can be clearly classified into 'local' 
(commonly called 'cis') and 'distant' ('trans') effects, with epistasis 
and transgressive inheritance in many cases.  We have found a few hotspots 
of pleitropic non-local eQTLs, some suggesting crucial indirect influences 
acting through physiological networks.  In a few favorable cases, these 
are starting to provide leads for experimental verification of specific 
candidate transcription factors and cis-acting sites - a long standing 
problem for Apicomplexa in general.  Equally interesting is the overall 
architecture of the robust Toxoplasma gene expression program, 
characterized by large eQTL effect sizes and a predominance of invariant 
and promoter-autonomous modes of transcriptional control. This contrasts 
markedly with the established paradigms from studies of the more 
environmentally adaptable yeast and mammalian cell lines.

[1] Taylor S, Barragan A, Su C, Fux B, Fentress SJ, Tang K, Beatty WL, 
Hajj HE, Jerome M, Behnke MS, White M, Wootton JC, Sibley LD. Science. 
2006 Dec 15;314(5806):1776-1780.  PMID: 17170305

Principal collaborators: Michael Behnke, Michael White (Montana State 
University, Veterinary Molecular Biology); David Roos, Amit Bahl 
(University of Pennsylvania, Genomics Institute); David Sibley (Washington 
University Medical School, Molecular Microbiology).