BC C. elegans Gene Expression Consortium

Funded by Genome Canada and Genome British Columbia.
Project Objectives and Summary

The objective of this project is to define the RNA expression profiles in specific tissues and cells, and developmental stages of C. elegans. Two complementary approaches are being applied: serial analysis of gene expression (SAGE), and the construction of promoter::GFP fusions for in vivo analysis of gene expression.

SAGE is a sensitive and specific method for obtaining qualitative and quantitative information on expressed RNAs. SAGE will also allow us to identify non-protein-coding genes, and provide insight into alternatively spliced mRNA isoforms and their relative abundance between tissues.

We are examining total mRNA populations in all developmental stages, both in whole worms and in specific cells and tissues. We have generated 17 SAGE libraries, which include all developmental stages, mutation-specific populations, and specific tissues and cells, totalling approximately 1.8 million observed tags. Tissue- and cell-specific libraries were generated from FACS-sorted cells marked by expression of specific promoter::GFP fusions. To date, we have SAGE libraries for purified embryonic muscle, gut, and a subset of neurons.

Promoter::GFP fusions
Monitoring in vivo expression of the fusion constucts in transgenic worms allows the determination of the developmental stage, tissue, and in some cases, the cells where a particular gene is expressed. Our goal is to build promoter::GFP fusion constructs for C. elegans genes that have human orthologues. Of the over 5000 genes that fall into this category, 2000 are being targeted by the C. elegans Gene Knockout Consortium. Fusion constructs are being created for the same set of genes, with a focus on genes expressed in muscle and nerve tissues. When coupled with SAGE and knockout data, this will provide valuable and more complete expression profiles for cells, tissues, and developmental stages.

Other objectives
  • Development of a protein expression baseline for specific tissues during development

  • This project includes research teams from Vancouver, Canada (listed below) and the Karolinska Institute in Sweden.

    Members of the The Genome BC C. elegans Gene Expression Consortium:

    PI: David Baillie
    Group Leader: Robert Johnsen
    Department of Molecular Biology and Biochemistry
    Simon Fraser University
    8888 University Drive
    Burnaby, BC Canada V5A 1S6
    Phone: (604) 268-6590

    PI: Don Moerman
    GFP expression contact: Rebecca Newbury
    C. elegans Genomics Facility
    University of British Columbia
    2140 - 2350 Health Sciences Mall
    Vancouver, BC Canada V6T 1Z3
    Phone: (604) 822-3365

    PIs: Marco Marra, Steven Jones
    Group Leader: Kim Wong
    C. elegans Research Group
    Genome Sciences Centre
    British Columbia Cancer Agency
    600 West 10th Ave.
    Vancouver, BC Canada V5Z 4E6
    Phone: (604) 707-5964