Positional Cloning Assignment

Introduction

Positional cloning is a technique that has been widely used to identify the specific genes and mutations involved in genetic diseases. Over 90 human genes have been identified in this way. Identification and characterization of these genes is important because it can lead to the development of a presymptomatic test for the genetic disease and in the future may lead to improved therapies.

The procedure involves first bracketing the gene between two markers whose positions on a chromosome are known. The markers can be genes or other kinds of markers (e.g. RFLP's). The technique used is genetic linkage analysis. The position of the gene of interest is further refined by identifying other markers that are located even closer to the gene of interest. Next, all of the genes in the region between the marker are identified and characterized. Finally, the gene carrying a mutation linked to the genetic disease is identified.

Assignment

In this assignment we are going to simulate a positional cloning experiment. We will use the technique to identify and locate a protein phosphatase gene in Baker's yeast (Saccharomyces cerevisiae). This gene codes for an enzyme that removes phosphate groups from serine and threonine residues of proteins.

The entire Saccharomyces cerevisiaae genome has been sequenced and the locations of all of its genes are known. A detailed map of this genome is available in the Saccharomyces cerevisiaae Genome Database (http://genome-www.stanford.edu/Saccharomyces/MAP/GENOMICVIEW/GenomicView.html). In initial experiments you were able to bracket the protein phosphatase gene between two gene markers (CDC9 and CDC2). In subsequent experiments you were able to further refine the location by bracketing the gene between other gene markers, RGT2 and CDC53. Your job now is to use the Saccharomyces cerevisiaae Genome Database (http://genome-www.stanford.edu/Saccharomyces/MAP/GENOMICVIEW/GenomicView.html) to identify which gene in this region is the protein phosphatase and to answer the following questions about the gene:

• What is the name of the gene (20 points)?
• On which chromosome is the gene located (10 point)?
• What are the names of the two genes that are the nearest neighbors to the protein phosphatase gene on the chromosome (10 point)?
• What is the fifth amino acid in the amino acid sequence of the protein phosphatase (10 point)?

You should submit the answers to these questions in the "PosClone Quiz" which you will find under the "Assignments" menu on the ClassNet student menu.