Regulatory Genetics Project

High-throughput screening of gene targets
related to common genetic diseases.

Susceptibility to common diseases as well as both the physiological response to therapeutics and the efficacy of any treatment vary from individual to individual. These differences arise from the complex interplay between genetic and environmental factors. Functional single nucleotide polymorphisms in regulatory sequences (rSNPs) cause variation in gene expression, which may in part be responsible for observed phenotypic differences1. Studying the effect of SNPs and/or haplotypes on gene expression variation and their association with diseases will deepen our insight into the mechanisms of gene regulation and the genetic factors underlying disease susceptibility. These discoveries will form a solid basis for the development of new diagnostic and therapeutic targets.

High throughput pipelines (Drs. Hudson and Pastinen, Innovation Centre) have been set up for gene expression screening to reveal those genes in specific tissues (Dr. Vohl, Laval University) that show allelic imbalance i.e. regulatory irregularities 2. Follow-up studies will distinguish between the different mechanisms causing the allelic imbalance (such as rSNPs; imprinting; stability of the different mRNAs; splicing differences). Regulatory regions of these genes are surveyed for SNPs by automated dHPLC (Drs. Sinnett and Labuda, Ste-Justine Hospital) and putative rSNPs identified in silico are validated in vitro by electrophoretic mobility shift assays (EMSA) and gene reporter assays. Regulatory sites are selected on the basis of evolutionary conservation by comparison of sequences from up to eight species (Dr. Dewar, Innovation Centre). Selected candidate genes will be further validated and their functions will be studied through the production of transgenic mice 3 (Dr. Peterson, Royal Victoria Hospital). The data is then integrated into a relational database (THOR; THousands Of Regulations).

Population frequencies, haplotypes (Drs. Labuda, Morgan and Hudson), and association with expression assays in several tissues will identify potential rSNPs to form a basis for further association studies in various disease cohorts. For more details, please visit the website www.regulatorygenetics.org

References

• Hudson, T. J. Wanted: regulatory SNPs. Nat.Genet. 33, 439-440 (2003).
• Pastinen, T. et al. A survey of genetic and epigenetic variation affecting human gene expression. Physiol Genomics (2003).
• Farhadi, H. F. et al. A combinatorial network of evolutionarily conserved myelin basic protein regulatory sequences confers distinct glial-specific phenotypes. J.Neurosci. 23, 10214-10223 (2003).