Studying whole genomes

DNA profiling:

Also known as genetic fingerprinting.

• Used in forensic crime scene analysis and paternity and maternity testing.

Genomic sequencing and comparative genome mapping:

• Used in research into the function of genes and regulatory DNA sequences.

Genetic engineering:

• Used in the production of pharmaceutical chemicals, genetically modified organisms and xenotransplantation.

Gene therapy:

• Used to treat conditions such as cystic fibrosis.

• DNA strands can be cut into smaller fragments using restriction endonuclease enzymes.
• The fragments can then be separated by size using electrophoresis and replicated many times to produce multiple copies using a process called the polymerase chain reaction. 
• DNA fragments can be analysed to give their specific base sequence.
• DNA fragments can be sealed together using ligase enzyme.
• DNA probes can be used to locate specific sequences on DNA fragments. 

These techniques mean that sections of DNA, including whole genes can be identified and manipulated.

Genomic age:

Genes - Code for the production of polypeptides and proteins.

• This coding DNA forms only a small part of the DNA found in an organism.
• Much DNA is non-coding DNA.
• Genomics = The study of genomes and genes. 
• Comparing genes and regulatory sequences of different organisms hekps us to understand the role of genetic information in organisms. 

Sequencing can only operate on a length of DNA of about 750 base pairs. This means the genome must be broken up and sequenced in sections.

Stages:

Genome is first mapped to identify which part of the genome they have come from. Information that is already known is used e.e. using the location of microsatellites.

Samples of the genome are sheared into smaller sections of around 100,000 base pairs (shotgun approach). 

These sections are placed into separate bacterial artificial chromosomes (BAC's) and transferred to E.coli cells. As the cells grow in culture, many clones of the sections are produced. These cells are known as clone libraries. 

Sequencing a BAC section:

1. Cells containing specific BACs are taken and cultured. The DNA is extracted from the cells and restriction enzymes are used to cut it into smaller fragments. The use of different restriction enzymes on a number of samples gives different fragment types. 

2. The fragments are separated using a process known as electrophoresis.

3. Each fragment is sequencing using an automated process.

4. Computer programmes then compare overlapping regions from the cuts made by different restriction enzymes in order to reassemble the whole BAC segment sequence.

Comparing genomes:

Comparative gene mapping: Comparing genes for the same proteins across a range of organisms.

Wide range of applications:

• Identification of genes for proteins found in all/many living organisms gives clues to relative importance of these genes to life. 
• Comparing genes/DNA of different species shows evolutionary relationships.  The more DNA sequences organisms share, more closely related they are likely to be. 
• Modelling effects of changes to DNA/genes can be carried out. 

• Comparing genomes from pathogenic and similar but non-pathogenic organisms can be used to identify the genes or base pair sequences that are most important in causing the disease. This can lead to identification of targets for developing more effective drug treatments and vaccines. 
• DNA of individuals can be analysed. Ths analysis can reveal mutant alleles, or the presence of alleles associated with increased risk of particular diseases e.g. heart disease or cancer.