Finding physical defects in the appearance or behavior of flies has excited many a fly researcher, but they have often been stymied by the lack of tools to connect this phenotype with a genotype, i.e. to identify the relevant gene and to map its position on a chromosome. Barry Dickens and colleagues provide improved tools towards this goal. They developed a high density map of single nucleotide polymorphisms, so called SNPs (pronounced Snips), which provide a unique mark at every 6 genes and could be considered a HapMap for flies. To fine map the location of a mutation, they combine this map with over 60 fly stocks with two closely spaced visible markers. A combination of these two tools will allow researchers to place a mutation within chromosomal regions that contains only a few genes.
The authors provide the experimental and computational resources to allow high-throughput mapping screens at low costs.
Finding allele-specific gene expression
Nature Methods
Scientists have developed a genome-wide technique to identify whether a person is expressing genetic information from their mother or father. The assay is published in the April issue of Nature Methods.
A mammalian genome contains two copies per gene, one allele from the father, the other from the mother. But often the organism does not need the products from both genes, especially during development and therefore one copy is silenced, a process known as imprinting.
Bing Ren and colleagues devised an assay that allows the genome-wide interrogation of gene expression to determine which of the two alleles is being expressed. The researchers start with a method called chromatin immunoprecipitation (ChIP), which fishes out areas of the genome that bind to proteins responsible for transcription and are therefore likely to be expressed. Then they determine which of the two alleles they isolated by interrogating the presence of single nucleotide polymorphisms (SNP) on microarrays.
This combination of ChIP and SNP will allow not only the discovery of new imprinted genes across the genome, but also permit a closer look at the mechanism of allele-specific expression.
Author contact:
Bing Ren (University of California, San Diego, USA)
Tel: +1 858 822 5766; E-mail: biren@ucsd.edu
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