ZF_MrSol-sc-2010-12-03
ZF_MrSol
The Zebrafish is becoming a popular model organism for developmental biology and human disease. This increasing popularity has resulted in a demand for reverse genetics, which has traditionally been neglected in favour of forward genetic approaches because of the lack of an efficient gene knockout (KO) technology. Thousands of phenotypes have been identified using forward genetic approaches, but time consuming positional cloning has slowed the identification of the genes involved. Morpholino oligonucleotides have become the method of choice for gene knockdown in the Zebrafish, but are restricted to early processes, and insertional mutagenesis has also become a popular method for gene led investigations. However, this still does not allow the targeted knockdown of genes of choice. More recently, zinc finger nucleases have been shown to be effective for gene targeting, but this method can be expensive and labour intensive, and is not seen as practical for the KO of hundreds of genes. A project to sequence and finish (to 99.9% accuracy) the Zebrafish genome (one of only 3 vertebrate genomes to be completed to this accuracy, alongside human and mouse) has contributed to the effectiveness of a process termed TILLING, first described in arabadopsis and worm, to be used to create Zebrafish targeted alleles. This method traditionally uses cel-1 nuclease and fragment analysis to identify mutations, which is labour intensive and misses mutations, especially near SNPs, which are common. Here we show that by using re-sequencing, we are able to identify more mutations. Using this method we have screened 2 ENU mutagenised living libraries in 2 years, and identified ~200 KO. In total, the ZF Models Workpackage 4 collaboration has identified 243 Mutations in the Zebrafish, which will be publicly available via Ensembl, The Sanger Institute and ZIRC. In addition to identifying deleterious mutations in the Zebrafish, the Sanger Institiute has committed to describing the phenotype of all mutations created during this project. Both morphological and molecular (by microarray or transcript counting on the Illumina platform) phenotypes will be described and published via ensembl and Zfin. The advent of next generation sequencing technologies has significantly changed the amount of mutations that can be identified. We are now investigating the use of sequence capture (rather than PCR) for exon enrichment from mutagenised individuals. This will mean a further increase in throughput, and has opened up the possibility of identifying a non-sense allele in every protein coding gene within a reasonable time frame and budget.. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Target selected mutagenesis, or TILLING (for targeting induced local lesions in genomes), is a proven method that allows mutations to be identified in virtually any gene. We have previously shown that capillary-sequencing can be used to effectively identify mutations in a high throughput manner. A library of Zebrafish non-sense alleles is being created by the Zebrafish Mutation Resource, each with an associated morphological and molecular phenotype. Phenotypic data will be published via ZFIN (using an adapted version of the Phenote database). Information about the mutations identified by the project can be found on our website: http://www.sanger.ac.uk/Projects/D_rerio/mutres/. The advent of next generation sequencing technologies has significantly changed the amount of mutations that can be identified. We are now investigating the use of sequence capture (rather than PCR) for exon enrichment from mutagenised individuals. This will mean a further increase in throughput, and has opened up the possibility of identifying a non-sense allele in every protein coding gene within a reasonable time frame and budget.