24 avril 2014: Dr Derek Stemple

Thursday, April 24th 2014, 12h30

Head of Mouse & Zebrafish Genetics
Wellcome Trust Sanger Institute
Genome Campus, Hinxton, UK


«Transcript Counting as a Molecular Phenotyping Tool»

In the Zebrafish Mutation Project (www.sanger.ac.uk/Projects/D_rerio/zmp/) we are generating and phenotyping disruptive mutations in protein-coding genes on a genome-wide scale. We screen for mutant phenotypes arising within the first five days post-fertilisation. For any specific mutation, by comparing morphologically abnormal mutants with wild-type siblings using our differential expression transcript counting technique (DeTCT), we find a wealth of genes displaying alterations in transcript levels broadly reflecting the observed morphological changes. Ontology term enrichment analysis using the gene ontology (GO) annotations combined with the zebrafish anatomical and development (ZFA) ontology has led to surprisingly detailed insights into phenotypes. Thus far two general trends have emerged. Firstly, transcript profiles for previously uncharacterised mutants confirm predicted cellular function and show tissue specific effects on transcript abundance, thus providing mechanistic evidence. Secondly, we are beginning to build pathway specific gene networks. Transcript counting analysis of mutants has revealed novel candidate genes, which lead to a phenotype affecting the same developmental pathway when mutated. Our approach and the results will be discussed.

Dr Derek Stemple has worked in zebrafish genetics for over 20 years. Starting as a postdoctoral fellow with Wolfgang Driever at Massachusetts General Hospital, he participated in a large-scale systematic screen for mutations affecting embryogenesis. As a principal investigator first at the National Institute for Medical Research, now at the Wellcome Trust Sanger Institute, his research has lead to the identification of several genes involved in zebrafish notochord and muscle development. His most recent studies have been centred around completion of the Zebrafish Genome Sequencing Project (Howe, et al., 2013, Nature 496, 498–503) (www.ensembl.org/Danio_rerio/) and the Zebrafish Mutation Project (Kettleborough et al., 2013, Nature 496, 494-497) (www.sanger.ac.uk/Projects/D_rerio/zmp/), which aims to identify disruptive mutations in each of the 26,000 zebrafish protein-coding genes. Mutations have been identified in more than 45% of protein-coding genes so far and the phenotypic consequences of disruptive mutations have been analysed for over 1,000 genes.