Microsatellite

Tandem repeats of DNA is useful topic for forensic specialists, clinical lab personnel, medical students.

1. Microsatellite Dr.S.Sethupathy . M.D.,Ph.D ., Professor of Biochemistry, Rajah Muthiah Medical College, Annamalai University

2. Genome

3. Interspersed and tandem repeats

4. Long interspersed Nuclear Elements (LINEs)

5. SINEs

6. Microsatellite A  microsatellite  is a tract of repetitive DNA   in which certain  DNA motifs (ranging in length from one to nine base pairs ) are repeated, typically 5–50 times. They occur at thousands of locations within an organism's genome. They have a higher   mutation  rate leading to high  genetic diversity .

7. A microsatellite are typically repeated 5–50 times. The sequence TATATATATA is a dinucleotide microsatellite, and GTCGTCGTCGTCGTC is a trinucleotide microsatellite Microsatellites are distributed throughout the genome. The human genome for example contains 50,000–100,000 dinucleotide microsatellites, and lesser numbers of tri-, tetra- and pentanucleotide microsatellites.  Many are in non-coding region Some can also be located in regulatory regions and coding regions.

8. The name " satellite " DNA refers to the early observation - on centrifugation of genomic DNA - a prominent layer of bulk DNA from accompanying "satellite" layers of repetitive DNA Microsatellites or short tandem repeats  ( STRs ) or   simple sequence repeats  ( SSRs ) Microsatellites and longer repeats -  minisatellites , - together called as VNTR ( variable number of tandem repeats) DNA.

9. Satellite bands – Mini and microsatellite

10. Inter sequence repeats analysis

11. Tandem repeats A repeated pattern can be between one base pair l ong (a mononucleotide repeat) to several thousand base pairs long , Total size of a satellite DNA block can be several megabases without interruption. Long repeat units have been described containing domains of shorter repeated segments and mononucleotides (1-5 bp ), arranged in clusters of microsatellites Most satellite DNA is localized to the telomeric or the centromeric region of the chromosome.

12. Tandem repeats The nucleotide sequence of the repeats is fairly well conserved across species. Variation in the length of the repeat is common. For example,  minisatellite  DNA is a short region (1-5kb) of repeating elements with length >9 nucleotides. microsatellites  in DNA sequences are considered to have a length of 1-9 nucleotides .  The difference in how many of the repeats is present in the region (length of the region) is the basis for  DNA fingerprinting

13. Minisatellite

14. Minisatellite Microsatellite variable number tandem repeats  (VNTR). short sequence repeats (SSR)  or  simple tandem repeats (STR) . Tandem repeats- monomer repeat lengh – 10-100 base pairs Tandem repeats- monomer repeat lengh – 1-9 base pairs Rich with G,C bases Rich with A,T bases Non coding regions , useful for Fingerprinting Non coding regions , useful for Fingerprinting

15. Microsatellites in non-coding regions allows them to accumulate mutations unhindered over the generations So it gives rise to variability that can be used for DNA fingerprinting and identification purposes. Some microsatellites are located in regulatory regions of genes- Mutations in such cases can lead to phenotypic changes and diseases, notably in  triplet expansion diseases such as fragile X syndrome and Huntington's disease . [9]

16. Cancer diagnosis A tumour cell line might show a different genetic fingerprint from that of the host tissue In colorectal cancer, present with  loss of heterozygosity Microsatellites routinely used in cancer diagnosis to assess tumour progression

17. Forensic and medical fingerprinting Forensic analysis are all tetra- or penta -nucleotide repeats , as these give a high degree of error-free data Another consideration is that the person's  medical privacy  must be respected STRs are chosen which are non-coding , do not influence gene regulation Not trinucleotide STRs which could be involved in triplet expansion diseases  Forensic STR profiles are stored in DNA databanks

18. Genome wide association studies Single-nucleotide polymorphism SNP Microsatellites remain highly informative microsatellites can differentiate alleles within a SNP-defined linkage disequilibrium block of interest. Microsatellites - led to discoveries of type 2 diabetes (TCF7L2) and prostate cancer genes (the 8q21 region)

19. Population genetics Designing primers and amplification of sets of microsatellites cost low Their uses are wide-ranging Useful for measuring or local adaptation,the allelic fixation index ,  population size, and gene flow They remain a crucial tool in the field .

20. Plant breeding Marker assisted selection or marker aided selection (MAS) is an indirect selection process where a trait of interest is selected Based on  marker  (morphological, biochemical or DNA/RNA variation) linked to a trait of interest

21. Intron microsatelite & diseases For example, a GAA triplet expansion in the first intron of the X25 gene appears to interfere with transcription, and causes  Friedreich Ataxia Tandem repeats in the first intron of the Asparagine synthetase gene are linked to acute lymphoblastic leukaemia  A repeat polymorphism in the fourth intron of the NOS3 gene is linked to hypertension in a Tunisian population Reduced repeat lengths in the EGFR gene are linked with osteosarcomas .

22. Analysis Microsatellites are normally analysed by conventional PCR amplification and amplicon size determination, sometimes followed by Sanger DNA sequencing Once these sequences have been amplified, they are resolved either through  agarose gel or PAGE electrophoresis or capillary electrophoresis

23. Applications Used for DNA profiling in  cancer diagnosis In  kinship analysis (especially paternity testing) In forensic identification . They are also used in  genetic linkage  analysis to locate a gene or a mutation responsible for a given trait or disease. also used in  population genetics  to measure levels of relatedness between subspecies, groups and individuals.

24. Microsatellite instability

25. Microsatellites and diseases Causative roles in as many as 40 neurological  diseases Triplet repeat expansion disorders Huntington's  Disease Friedreich's Ataxia (FRDA) Spinocelebellar Ataxias (SCA) Fragile X syndrome (FRAXA) Myotonic Dystrophy types 1 and 2

26. Thank you