Genome mapping

BioCodeKb - Bioinformatics Knowledgebase

Genome mapping is assigning/locating of a specific gene to particular region of a chromosome and determining the location of and relative distances between genes on the chromosome. Genome mapping provided a typical starting point for the Human Genome Project.

To produce a genetic map, researchers collect blood or tissue samples from members of families in which a certain disease or trait is prevalent. Using certain laboratory techniques, the scientists isolate DNA from these samples and examine it for unique patterns that are seen only in family members who have the disease or trait.

A genome map highlights the key ‘landmarks’ in an organism’s genome. The landmarks on a genome map may include short DNA sequences, regulatory sites that turn genes on and off or the genes themselves.

Different types of genome mapping

Genetic/linkage mapping looks at how genetic information is shuffled between chromosomes or between different regions in the same chromosome during meiosis. Genes that are on the same chromosome are said to be ‘linked’ and the distance between these genes is called a ‘linkage distance’. The smaller the distance the more likely two genes will be inherited together.

Physical mapping looks at the physical distance between known DNA sequences (including genes) by working out the number of base pairs (A-T, C-G) between them.

Modern genetic maps

With more recent genetic mapping techniques, the position of genes is worked out from finding the exact frequency of genetic recombination that has occurred.

There are several different techniques used for physical mapping. These include:

Restriction mapping

This uses specific restriction enzymes to cut an unknown segment of DNA at short, known base sequences called restriction sites. Restriction enzymes always cut DNA at a specific sequence of DNA (restriction site). For example, the restriction enzyme EcoRI always cuts at the sequence GAATTC/CTTAAG.

A restriction map shows all the locations of that particular restriction site (GAATTC) throughout the genome.

There a two specific types of restriction mapping

  1. In fingerprint mapping the genome is broken into fragments which are then copied in bacteria cells. The DNA copies (clones) are then cut by restriction enzymes and the lengths of the resulting fragments are estimated using a lab method called electrophoresis. Electrophoresis separates the fragments of DNA according to size resulting in a distinct banding pattern. The fingerprint map is constructed by comparing the patterns from all the fragments of DNA to find areas of similarity.

  2. Optical mapping uses single molecules of DNA that are stretched and held in place on a slide. Restriction enzymes are added to cut the DNA at specific points leaving gaps behind. The fragments are then stained with dye and the gaps are visualized under a flourescence microscope. The intensity of the fluorescence is used to construct an optical map of single molecules.

Fluorescent in situ hybridisation (FISH) mapping

This uses fluorescent probes to detect the location of DNA sequences on chromosomes.

First, the probes are prepared. The probes are then labelled with fluorescent dye before being mixed with the chromosome DNA so that it can bind to a complementary strand of DNA on the chromosome.

The fluorescent tag allows the scientist to see the location of the DNA sequence on the chromosome.

Sequence-tagged site (STS) mapping

This technique maps the positions of short DNA sequences (between 200-500 base pairs in length) that are easily recognizable and only occur once in the genome. These short DNA sequences are called sequence-tagged sites (STSs).

To map a set of STSs a collection of overlapping DNA fragments from a single chromosome or the entire genome is required.

Special primers are designed to bind either side of the STS to ensure that only that part of the DNA is copied.

If two DNA fragments are found to contain the same STS then they must represent overlapping parts of the genome.

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