Work Package 3: Characterisation of enhancer elements of human disease genes

We will perform a systematic characterisation of enhancer elements of potential disease genes. This characterisation will build on the concept of genomic regulatory blocks (GRBs) which contain highly conserved non-coding elements (HCNEs) acting as long-range enhancers of developmental genes (recently discovered by T. Becker in the ZF-MODELS project). We will:

  • Identify and characterise computationally the regulatory regions of potential disease genes, by characterising haplotype blocks harboring risk alleles of human disorders, defining their GRBs, GRB target genes, and extracting all HCNEs.
  • Characterise the regulatory activity of these HCNEs in a high-throughput transgenic zebrafish assay, by creating transgenic lines containing specific HCNEs.
  • Perform imaging on HCNE-driven transgenic zebrafish to determine cellular specificity and expression levels.
  • Order HCNEs relevant for disease into signaling pathways to understand the underlying regulatory defects.

This approach will allow us to test a large number of regulatory elements of any given disease relevant gene and to elucidate where and when human sequence variants predispose towards disease. We will target especially brain diseases known to affect glia (such as autism, epilepsy, spastic paraplegia) as well as type 2 diabetes (a disease affecting a large part of the European population) and focus on gene expression in glia and the pancreas, respectively. However, the approach can be used for any disease with genetic risk factors. In total we expect to study a minimum of 30 target genes. Project partners involved in enhancer analysis will be mainly USYD (Australia), UNIPD (Italy) and UiB (Norway).

We will additionally sequence several sister species of the zebrafish at a moderate coverage, which will help to define conservation of synteny in the zebrafish (mainly ALU-FR, Germany, and GRL, UK).

Eventually we aim to extend our bioinformatic analysis to the entire genome, generating a unique resource for the discovery of novel disease regions of interest which will be available through Ensembl. This genome-wide analysis will also build on experience gathered in the NeuroXsys project, a pilot study focusing on GRBs on the human X chromosome coordinated by T. Becker.

(Work Package Leader: USYD)

Dissemination of results

Enhancers identified in these studies may be further characterised by ChIP-Seq (for which facilities will be available at ALU-FR, Germany, and BHAM, UK), and candidate genes by targeted mutagenesis, phenotyping and small-molecule screening (see WP1, WP2 and WP5), involving additional project partners. The transgenic zebrafish lines will be submitted to the European Zebrafish Resource Center (see WP1), and the images of expression patterns will be available through the ZFIN model organism database after an initial scientific publication.