miRNA-omics

Besides having relevance in the wider research community, the chicken is also an end-point organism for CSIRO as a significant livestock production animal. Tizard says that it is also likely to become even more important in the future because it is a source of high-quality protein/meat, but has a vastly reduced impact in terms of environmental footprint for production compared to some other production animals.

"Even at the free-range end of things, chickens take up less space and need less food and water per kilogram of meat generated and everything is quicker as well with an average production lifespan of 35-45 days," he says.

In terms of the global animal biotechnology market, the chicken is also valuable. The rate of stock turnover means that delivery of high-quality genetics to the marketplace is relatively easy.

The reported miRNAs in Tizard's Genome Research paper brings the number of miRNAs for the chicken in the Sanger miRBAse from 149 to 445 (including 19 new homologues and 277 novel sequences), with an additional 138 miRNA candidates to be validated.

Not unexpectedly, the highest number of annotated miRNAs in the Sanger database is in humans, at 678, with the actual number predicted to be much higher. For the mouse, the number is 472, and for zebrafish, 337 sequences. So, the chicken is right up there.

This miRNA catalogue gives Tizard's group an idea of exactly what they are dealing with miRNA-wise, or more precisely what the chicken is dealing with. The next step is to work out what all these miRNAs are doing in the cells.

Tizard's team is now characterising tissue-specific expression patterns using microarrays and in situ hybridisation to assemble a map of normal miRNA expression in different cells and tissues at different developmental stages.

"We've also got some leads on interesting differential processing of miRNAs, which is an emerging area in terms of understanding the mechanisms: that is, controlling the controller."

The plan then is to apply their findings to a range of areas. In the health arena, Tizard is interested in development of the immune system and in particular cells of lymphocytic lineages. "We would like to know which miRNAs are involved in determining the fate of the CD4 and CD8-type T cells because in the modern production environment for chicken, viral diseases are the greatest threat and of course the greatest of these in terms of public awareness is that of avian influenza."

Tizard's studies of miRNAs will also fit in with wider studies of gene expression going on in other parts of CSIRO. "In any study of transcriptomics, I think you have to now consider the miRNAomics, so that you can get a handle on which messenger RNAs are going to be affected by miRNA expression."