Research Information

Investigation of animal development in the nematode, Caenorhabditis elegans, through gene expression

C. elegansAnimal development is the process by which a single cell, the fertilised egg, becomes a mature adult organism. Differential gene expression from cell to cell is a major factor in the generation of cellular diversity during development. Since the advent of molecular genetic techniques, we have begun to understand how gene expression is co-ordinated throughout a developing animal.

In this laboratory, we study the nematode worm Caenorhabditis elegans (C. elegans). C. elegans has many characteristics which make this species a particularly important model for studies of animal development (see WormClassroom for more background).

We have used five approaches, with progressive improvements in efficiency and quality, for determination of the expression patterns for a large number of genes within C. elegans. In each approach regulatory regions of C. elegans genes have been fused to a reporter gene and transgenic C. elegans lines, transformed with these constructs, were examined to reveal gene expression patterns in situ.

  1. The first approach utilised random C.elegans genomic DNA fragments and so involved examining large numbers of fusions to detect the low proportion that were active (Hope, I.A. ('91) Development 113, 399-408).
  2. In the second approach, regulatory regions of potential genes, as predicted from the data that were being amassed in the international project to sequence the entire C. elegans genome, were fused specifically to the reporter gene (Lynch, A.S., Briggs, D. & Hope, I.A. ('95) Nature Genetics 11, 309-13). This approach became possible and was initiated as the C. elegans genome sequencing project started. C. elegans was the first multicellular organism to have its genome sequenced.
  3. In the third approach, the reporter fusions were made at random as in the first approach but sequencing of the fusion junctions, with comparison to the C. elegans genome sequence data, identified those recombinant plasmids that contained appropriate gene fusions (Mounsey, A., Bauer, P. & Hope, I.A. ('02) Genome Research, 12, 770-5). The third approach had only become possible as the sequencing project neared completion.
  4. In the fourth approach, in a collaboration led by Marc Vidal (DFCI, Harvard), and including Marian Walhout (UMass Med School), promoter::gfp fusions were made in a directed yet genomic scale, using MultiSite Gateway recombination technology (Hope, I.A. et al. ('04) Genome Research. 14, 2070-5; Dupuy, D. et al. ('04) Genome Research. 14, 2169-75). Transgenic C. elegans lines containing these reporter gene fusions were made by microprojectile bombardment rather than the microinjection procedures used previously (Reece-Hoyes, J.S. et al. ('07) BMC Genomics, 8, 27., Dupuy, D., et al. ('07) Nature Biotechnology, 25, 663-8.).
  5. In the fifth and current approach we are using recombineering of fosmids to introduce reporter genes into precise positions within genes within large genomic DNA fragments to maximize the likelihood that all regulatory elements acting on the target gene have been retained (Dolphin, C.T. and Hope, I.A. ('06) Nucleic Acids Research, 34, e72.) in a collaboration with Colin Dolphin (King's College, London)

Results of these studies are contributing to our understanding of how gene expression is organised during development. A few genes, identified on the basis of their interesting expression patterns, are being characterised further in this laboratory to determine the molecular details of the mechanisms by which these expression patterns are generated. Recently, collaborations with Elwyn Isaac (also in SBIO, Leeds) and Netta Cohen (School of Computing, Leeds) have led into Systems Biology and Computer Modelling concerning the C. elegans nervous system and behaviour.

The expression pattern data we have generated are available in our database. Our data may also be found in the C. elegans database ACeDB/WormBase, where it is integrated with the genetic and sequence data for this organism.

Another major project to determine gene expression patterns in C. elegans using reporter gene fusions, but constructed using an alternative strategy, is underway at UBC. The data generated by the BC C. elegans Gene Expression Consortium can be found on their web site at The BC database also includes expression pattern data generated by SAGE.