Tandemly repeated trinucleotides - comparative analysis.
Characteristics of 64 possible tandem trinucleotide repeats (TSSR) from Homo sapiens (hs), Mus musculus (mm) and Rattus norvegicus (rn) genomes are presented. Comparative analysis of TSSR frequency depending on their repetitiveness and similarity of the TSSR length distributions is shown. Comparative analysis of TSSR sequence motifs and association between type of motif and its length (n) using rho-coefficient method (quantitatively measuring the association between variables in contingency tables) is presented. These analyses were carried out in the context of neurodegenerative diseases based on trinucleotide tandems. The length of these tandems and their relation to other TSSR is estimated. It was found that the higher repetitiveness (n) the lower frequency of trinucleotides tandems. Differences between genomes under consideration, especially in longer than n=9 TSSR were discussed. A significantly higher frequency off A- and T-rich tandems is observed in the human genome (as well as in human mRNA). This observation also applies to mm and rn, although lower abundant in proportion to human genomes was found. The origin of elongation (or shortening) of TSSR seems to be neither frequency nor length dependent. The results of TSSR analysis presented in this work suggest that neurodegenerative disease-related microsatellites do not differ versus the other except the lower frequency versus the other TSSR. CAG occurs with relatively high frequency in human mRNA, although there are other TSSR with higher frequency that do not cause comparable disease disorders. It suggests that the mechanism of TSSR instability is not the only origin of neurodegenerative diseases.
Piwowar
Monika
M
Department of Bioinformatics and Telemedicine, Collegium Medicum, Jagiellonian University, Kraków, Poland.
Meus
Jan
J
Piwowar
Piotr
P
Wiśniowski
Zdzisław
Z
Stefaniak
Justyna
J
Roterman
Irena
I
D000818:Animals; D019295:Computational Biology / Q000379:methods; D016678:Genome / Q000235:genetics; D006801:Humans; D051379:Mice; D019636:Neurodegenerative Diseases / Q000235:genetics; D051381:Rats; D017422:Sequence Analysis, DNA / Q000379:methods; D020080:Tandem Repeat Sequences / Q000235:genetics*; D019680:Trinucleotide Repeat Expansion / Q000235:genetics; D018911:Trinucleotide Repeats / Q000235:genetics*