In situ Hybridization

Human-Rodent Somatic Cell Hybrids

Recombination Mapping of Meiotic Chromosomes

Fine Structure Mapping of Chromosomes

Map-based or Positional Cloning of Genes

Study Questions

Genomic Analysis WWW Links

Genetic Topics

Fine Structure Mapping of Chromosomes

Molecular maps can be used to identify a marker for a specific gene. These markers are quite useful For a specific gene that is difficult to score or is expressed late in the life cycle. Maps can also be used as a starting point for cloning a gene. A fine structure map of the species is quite useful for this purpose. Yeast artifical chromosome (YAC) clones and recently, bacterial artificial chromosome (BAC) clones are key tools for developing a fine structure map.

In principle, a YAC or BAC clone library should contain a series of clones that overlap each other. The key is to order each of these clones. The ordering of the clones often relies upon sequencene tagged sites (STS). STS are short sequences of DNA that are sequenced. PCR primers are developed, and if the same PCR product can be amplified from any two YAC or BAC clones, the two clones must overlap. Unlike the molecular markers that we described previously, the STS does not have to be highly polymorphic because the clones are all from one original DNA source.

In practise, a large number of clones are scored for different STS sites, and the data is analyzed to order the different clones. The following table is an example of such data. "+" means the STS is product is obtained from that clone, and "-" means the product is not amplified from the clone.

STS Site
Clone A B C D E


+ + + - -


+ - + - +


+ + - + -


- + - + -

Can you determine that the order is E-C-A-B-D? Further, the relative order of the different clones can be established. The following is that order.

           STS Site

E     C     A     B     D

This stretch of four clones is called a contig map. The goal of fine structure mapping is to develop complete contig maps for each chromosome of the species. If these complete maps are available, it is a simple matter to take the molecular marker you have obtained and select a clone to which it hybridized. Then you are immediately working at the molecular level for that species and are on your way to cloning that species.

Copyright © 1997. Phillip McClean