0.2 Eukaryotic genetics  (Page 9/9)

Single-nucleotide polymorphisms may fall within coding sequences of genes , non-coding regions of genes , or in the intergenic regions between genes. SNPs within a coding sequence will not necessarily change the amino acid sequence of the protein that is produced, due to degeneracy of the genetic code . A SNP in which both forms lead to the same polypeptide sequence is termed synonymous (sometimes called a silent mutation ) — if a different polypeptide sequence is produced they are nonsynonymous . A nonsynonymous change may either be missense or nonsense , where a missense change results in a different amino acid, while a nonsense change results in a premature stop codon . SNPs that are not in protein-coding regions may still have consequences for gene splicing , transcription factor binding, or the sequence of non-coding RNA .

Variations in the DNA sequences of humans can affect how humans develop diseases and respond to pathogens , chemicals , drugs , vaccines , and other agents. SNPs are also thought to be key enablers in realizing the concept of personalized medicine . [3] However, their greatest importance in biomedical research is for comparing regions of the genome between cohorts (such as with matched cohorts with and without a disease).

The study of single-nucleotide polymorphisms is also important in crop and livestock breeding programs (see genotyping ). See SNP genotyping for details on the various methods used to identify SNPs.

Microsatellites

One rare example of a microsatellite is a (CA)n repeat, where n is variable between alleles . These markers often present high levels of inter- and intra-specific polymorphism, particularly when tandem repeats number one hundred or greater. [2] The repeated sequence is often simple, consisting of two, three or four nucleotides (di-, tri-, and tetranucleotide repeats respectively), and can be repeated 10 to 100 times. CA nucleotide repeats are very frequent in human and other genomes , and are present in every few thousand base pairs. As there are often many alleles present at a microsatellite locus, genotypes within pedigrees are often fully informative, in that the progenitor of a particular allele can often be identified. In this way, microsatellites are ideal for determining paternity, population genetic studies and recombination mapping . It is also the only molecular marker to provide clues about which alleles are more closely related. [3]

Microsatellites owe their variability to an increased rate of mutation compared to other neutral regions of DNA. These high rates of mutation can be explained most frequently by slipped strand mispairing (slippage) during DNA replication on a single DNA strand. Mutation may also occur during recombination during meiosis . [4] Some errors in slippage are rectified by proofreading mechanisms within the nucleus , but some mutations can escape repair. The size of the repeat unit, the number of repeats and the presence of variant repeats are all factors, as well as the frequency of transcription in the area of the DNA repeat. Interruption of microsatellites, perhaps due to mutation, can result in reduced polymorphism. However, this same mechanism can occasionally lead to incorrect amplification of microsatellites; if slippage occurs early on during PCR, microsatellites of incorrect lengths can be amplified.

Microsatellites can be amplified for identification by the polymerase chain reaction (PCR) process, using the unique sequences of flanking regions as primers . DNA is repeatedly denatured at a high temperature to separate the double strand, then cooled to allow annealing of primers and the extension of nucleotide sequences through the microsatellite. This process results in production of enough DNA to be visible on agarose or polyacrylamide gels; only small amounts of DNA are needed for amplification as thermocycling in this manner creates an exponential increase in the replicated segment [5] .

Vntr

VNTR have high levels of polymorphism, many alleles and usually can be visualized by Southern blotting or PCR as shown below. VNTR loci are applied in DNA fingerprinting, forensic paternity and linkage analysis.

One can see a good PowerPoint presentation describing STRs and SSRs and their applications in MITOPENCOURSEWARE ( PDF ).