Assignment 3 – Bioinformatics

A quick reminder…

To succeed in this assignment, you must be familiar with the following terms from basic genetics: DNA, allele, gene, genetic-linkage, and from the genome and bioinformatics: gene characteristics, polymorphic markers and databases.

The assignment

In the previous mission, you located a gene in a certain region in the genome, based on the connection between a particular phenotype and polymorphic markers in a family. In this assignment we shall locate the gene involved in hearing on a segment of chromosome 5.

How do we locate a gene in the genome?

Look at the diagram of human chromosome 5, which indicates the location of the DNA segment between the markers that we found in the genetic linkage test. Click on Play to view the diagram:

Markers and genes have been identified in the diagram of the DNA segment to form a map. You can see that this segment contains a great many genes. The segment is about 10 Mb long. The size of the gene we are looking for can be up to a few thousand nucleotides.

Although the use of polymorphic markers reduced the gene search area, these 10 million nucleotides contain dozens of genes. Some of the genes in the DNA segment have been identified and the protein they encode is known. Gene characteristics have been identified in some of the sequences in this segment, meaning that they are probably genes, although their function remains unknown.

Imagine that the genome map is a road map of a large city. The polymorphc markers are landmarks on the map, the various genes are addresses, and the "Wanted" gene is the address you want to reach. The road map can direct you to the right neighborhood, but when you arrive there, you realize that you have no idea what the exact address is – you know neither the name of the street you are looking for nor the number of the house you want. Any of the houses might be the right one. What do you do now – walk around the neighborhood and knock on every door to find the right house?

One way of finding the "Wanted" gene

You can go around the neighborhood and knock on every door. This is akin to scanning all the genes and sequences suspected to be genes in the DNA segment on chromosome 5, in an attempt to locate the allele with an identical DNA sequence in all the deaf adults in the family (that is different from the second allele and the alleles of adults in the family with normal hearing). Such an allele would indicate that the candidate gene has been found, but such a method of checking is obviously tedious and time-consuming.

Another way – using a model organism

To shorten the process, scientists look for creative solutions. One of the more elegant solutions that researchers have found is to work with a model organism, an animal used for research. The assumption is that the results and conclusions stemming from the study with the model organism can be applied to humans.

The DNA segment in chromosome 5 in humans has a homologous DNA segment in chromosome 18 in mice. In the homologous segment in mice, a gene involved in hearing called brn-3c has been identified. A mutation in this gene causes deafness in mice. Scientists hypothesize that there is a similarity between the gene sequence in mice and a homologous sequence on chromosome 5 in humans in the region identified through the genetic linkage tests.

In this assignment, you will compare the sequence of the gene involved in hearing, brn-3c (also known as sequence S69352) in mice with all the sequences in the Genome Project database, with the aim of finding, a possible similarity between the gene sequence in the mouse and DNA sequences in the database. The comparison will be made using BLAST.

Let's start

Enter basic BLAST

Copy the gene accession number S69352 to the "Query Sequence" box and click on the BLAST button.

Do you think you've found what you were looking for?

Clue: You can search "chromosome 5" in the results page.

What have you learned from this assignment?

It appears that the biological reasoning was sound: researchers have chosen an elegant way of identifying the candidate gene on the DNA segment bordered by the markers. Instead of checking all the genes – a process that could be long and difficult and that may not yield any results – they located a known gene involved in the hearing process in a segment of chromosome 18 in mice, which is homologous to a segment of chromosome 5 in man. Using BLAST to search the databases and the locate similar sequences, they identified the sequence of a homologous gene in man whose function was not previously known. There is no doubt that this gene makes for a very good candidate gene.