Allam Appa Rao ^*, G Venkata Swamy, B L V Vinay Kumar, Ch S U Ravi Kumar

Department of Computer Sciences and System Engineering, Andhra University, Visakhapatnam, India

Copyright: © 2008 Allam AR, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Bioinformatics is the field of science in which biology, computer science, and information technology merge to form a single discipline. The revolutionary growth in the computation speed and memory storage capability has fueled a new era in the analysis of biological data. The ultimate goal of the field is to enable the discovery of new biological insights as well as to create a global perspective from which unifying principles in biology can be discerned. Bioinformatics, also known as genomics, computational genomics, or computational molecular biology is a rate.We have used the analogy of genome analysis and VIRUS (vital information recourse under siege) and analyzed KCNQ1, KCNH2 and SCN5A genes, which are playing an important role in LQTS disease. We tried to find out whether the presence of microsatellites or simple sequence repeats in the KCNQ1, KCNH2 and SCN5A genes, are having any significance in the generation of these mutations and checked whether these mutations are fallen in the regions of those microsatillites and if so, is there any significance of these microsatillites in the functional omains of the each gene?.Our analysis revealed that 24 of the 26 mutations of the KCNQ1 gene, 19 of the 21 mutations of the KCNH2 gene and 3 of the 7 mutations of the SCN5A gene, which are existing in the microsatellite regions are fallen in the domain regions of the respective genes and thus indicating a positive role of microsatellites in mutagenesis.

Long QT syndrome (LQTS) is a congenital disorder characterized by a prolongation of the QT interval on ECG and a propensity to ventricular tachyarrhythmia, which may lead to syncope, cardiac arrest, or sudden death. Congenital LQTS is usually inherited. It is caused by an abnormality in the gene that forms the ion channels, slowing the recovery phase of the heartbeat. LQTS is caused by mutations of the genes for cardiac potassium and sodium or calcium ion channels; 8 genes have been identified. On the basis of this genetic background, 6 types of Romano- Ward syndrome, 1 type of Andersen syndrome and 1 type of Timothy syndrome those genes are KVLQT1, or KCNQ1, KCNH2, SCN5A, ANK2, KCNE1, KCNE2, KCNJ2, and CACNA1C.

Apart from genes, the human genome also consists of a large number of nucleotide repeat units of size 1-6 bp repeated tandemly called Micro satellites or Simple Sequence Repeats (SSRs) or Short Tandem Repeats (STRs) (Schlotterer, C, 2000) Micro satellites are found in all the known genomes, spanning from prokaryotes, eukaryotes and viruses and are widely distributed both in coding and non-coding regions (Toth, G et al, 2000; Sreenu et al, 2007). Mutations in these microsatellite regions occur at much higher rate when compared with those in the rest of the genome (Ellegren, H, 2000).

Micro satellites are known to be highly polymorphic due to the high rate of mutations in their tracts (Jarne, P. and Lagoda, P.J.L, 1996). These mutations can be either in the form of increase / decrease of repeat units or in the form of single nucleotide substitutions/ deletions/insertions and other events (Fan, H. and Chu, J.Y, 2007). Increase or decrease of repeat units of micro satellites in coding regions might lead to shift in reading frames there by causing changes in protein product (Li, Y.C et al, 2004) and in non-coding regions are known to effect the gene regulation (Martin P et al, 2005). Point mutations (Substitutions and Indels) are also found to occur at a higher rate in micro satellites than elsewhere (Sibly, R.M et al, 2003).

Sl.No  Microsatellits Microsatellite region Codon Change Aminoacid Codon number Domain 1 CGG 501-508 GGG-AGG            Gly-Arg 168 Pfam00520 2 CGG 501-508 GGG-CGG            Gly-Arg 168 Pfam00520 3 TGGTC 515-530            CGC-TGC Arg-Cys 174      Pfam00520 4 TGGTC 515-530            CGC-CAC Arg-His 174      Pfam00520 5 CCG 530-542 GCC-ACC Ala-Thr 178 Pfam00520 6 CCG 530-542 GCC-CCC Ala-Thr 178 Pfam00520 7 CCG 530-542 GGC-AGC Gly-Ser 179 Pfam00520 8 GGC 563-570 GGG-AGG Gly-Arg 189 Pfam00520 9 GC 567-576 CGG-CAG Arg-Gln            190 Pfam00520 10 GC 567-576 CTG-CCG Leu-Pro 191 Pfam00520      11 TCC 689-697 CGC-TGC Arg-Cys 231 Pfam00520 12 CCA 771-779 CGC-CTC Arg-Leu 259      Pfam00520 13 CCA 771-779 CGC-TGC Arg-Cys 259 Pfam00520 14 TCT 818-829 TTC-TCC Phe-Ser 275      Pfam00520 15 TG 908-916 TGG-TAG Trp-Term 305      Pfam00520,Pfam07885 16 G 914-922 GGG-GTG Gly-Val 306 Pfam00520,Pfam07885 17 G 914-922 GGG-AGG Gly-Arg 306 Pfam00520,Pfam07885 18 CAC 926-938 GTC-ATC Val-Ile 310 Pfam00520,Pfam07885 19 CAC 926-938 ACC-ATC Thr-Ile 311 Pfam00520,Pfam07885 20 CAC 926-938 ACC-ATC Thr-Ile             312 Pfam00520,Pfam07885 21 AGG 1681-1688 AGG-ATG Arg-Met 562 Pfam03520 22 GC 1765-1773 GGC- GAC            Gly-Asp 589 Pfam03520 23 GC 1765-1773 GCC-ACC Ala-Thr 590 Pfam03520

Table1: For the Gene KCNQ1

sl.no   Microsatellites Microsatellite Region Codon Change Aminoacid Codon number Domain 1 ACG 134-142 GGC-GTC Gly-Val 47 PAS 2 GCAGG 207-222 CAC-CGC His-Arg 70 PAS 3 GC 213-216 CCG-CAG Pro-Gln            72 PAS 4 CGC 226-241 GCT-CCT Ala-Pro 78 PAS 5 TCA 365-382 ATG-AGG Met-Arg 124 PAC            6 TCA 1403-1411 AAC-GAC Asn-Asp 470 Pfam: Ion trans 7 CAC 1416-1424 ACC-ATC            Thr-Ile 474 Pfam: Ion trans 8 ACT 1475-1483 TAC-TGC            Tyr-Cys 493 Pfam: Ion trans 9 GCT 1576-1601 CGG-CAG            Arg-Gln 531 Pfam: Ion trans 10 TGCT 1646-1658            TTG-TCG Leu-Ser 552 Pfam: Ion trans 11 GGCT 1750-1757 GGC-AGC            Gly-Ser 584 Pfam: Ion trans 12 GGC 1807-1815 GGC-AGC Gly-Ser 604 Pfam: Ion trans, Pfam: Ion trans2 13 GGC 1876-1884 GGC-GTC            Gly-Val            626 Pfam: Ion trans, Pfam: Ion trans2 14 GGC 1876-1884 GGC-AGC Gly-Ser 626 Pfam: Ion trans, Pfam: Ion trans2 15 GGC 1876-1884 TTC-TTG Phe-Leu 627 Pfam: Ion trans, Pfam: Ion trans2 16 GGC 1876-1884 GGC-AGC Gly-Ser 628 Pfam: Ion trans, Pfam: Ion trans2 17 CCA 1895-1903 AAC-AGC Asn-Ser 633 Pfam: Ion trans, Pfam: Ion trans2 18 TCT 1916-1927 TTC-TTA Phe-Leu 640 Pfam: Ion trans, Pfam: Ion trans2 19 TCA 1931-1939 ATG-GTG Met-Val 645 Pfam: Ion trans, Pfam: Ion trans2

Table2: For the Gene KCNQ1

Micro satellite mutations with in or near certain genes are known to be responsible for some human neurodegenerative diseases. So, we made a brief study to check whether the mutations in KCNQ1, KCNH2 and SCN5A genes, have any relation with these microsatellites repeats and the study revealed interesting results.

All the experimental proved mutations of the genes KCNQ1,KCNH2 and SCN5A that are falling inside the coding region and are eventually leading to phenotypic differences were collected from the Human Gene Mutation Database (HGMD) (Stenson, P.D et al, 2003). Micro satellites are obtained from the Imperfect Micro satellite Extract (IMEX) tool (Mudunuri, S.B et al, 2007) using intermediate mode with default values 6 for single, 5 for di, 3 for tri, 2 for tetra, 2 for penta and 2 for hexa and obtained 74,129,196 microsatellites in KCNQ1,KCNH2 and SCN5A respectively. Since micro satellites are drawn from the nucleotide sequence and HGMD mutations are given for protein sequence we have used DNA to Amino Acid translator. We compared the microsatellite regions with the mutations wheather they have mutations in those regions and found some of the microsatellites have occurred in those regions. Now we analyzed whether these mutations and microsatellites have fallen in the functional domains of those genes by using Simple Modular Architecture Research Tool (SMART) (Letunic, I et al, 2004) and the results are as follows.

sl.no        Microsatellites Microsatellite region Codon Change Aminoacid Codon number Domain 1 GGC 3333-3349 GAC-AAC Asp-Asn 1114 Pfam: Na trans assoc 2 CTGCG 3901-3914 ACG-ATG    Thr-Met 1304 Pfam: Ion trans 3 TCA 4997-5005 GTC-ATC Val-Ile 1667 Pfam: Ion trans

Table3: For the Gene SCN5A

Long QT Syndrome can be acquired or congenital disorder. Here we have discussed about congenital since it is a inherited disease.We have taken KCNQ1,KCNH2 and SCN5A out of eight disease causing genes since LQT1,LQT2 and LQT3 account for most cases of LQTS, with estimated prevalences of 45%,45%and 7% respectively.we have calculated the microsatellites for these three genes found 24, 19 and 3 mutations in those genes which falls in the microsatellite regions and also falls in the different domains. And thus, we can state that Concurrency of Mutations, Microsatellites and Predicted Domains in KCNQ1, KCNH2 and SCN5A genes may leads to Long QT Syndrome disease.

Microsatillites are known for their higher rate of mutations and are known to be associated with various diseases. So, we analyzed the KCNQ1,KCNH2 and SCN5A gene mutations and their possible association with the micro satellites. These mutations from HGMD database are mapped on to the micro satellite tracts and the results seem to indicate that micro satellites play an important role in mutagenesis and by mapping the same with the functional domains we can say that these can cause functionalitychanges of those genes. Extending this work on a large scale by analyzing large number of genes might give a better evidence of the role of micro satellites in generating mutations.

The authors are thankful for partial financial support from IIT up gradation grants of AUCE (A).

1. Ellegren, H (2000) Heterogeneous mutation processes in human microsatellite DNA sequences. Nat Genet 24:400-402.   » CrossRef   » PubMed  »  Google Scholar
   
   
2. Fan H, Chu JY (2007) A brief review of short tandem repeat mutation. Genomics Proteomics Bioinformatics 5: 7-14.   » CrossRef   »  Google Scholar
   
   
3. Jarne P, Lagoda PJL (1996) Microsatellites, from molecules to populations and back. Trends Ecol Evol 11: 424-429.   » CrossRef   »   Google Scholar
   
   
4. Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P (2004) SMART 4.0: towards genomic data integration. Nucleic Acids Res 32: D142-4.  » CrossRef   » PubMed  »  Google Scholar
   
   
5. Li YC, Korol AB, Fahima T, Nevo E (2004) Microsatellites within genes: structure, function, and evolution. Mol Biol Evol 21: 991-1007.  » CrossRef   » PubMed  »  Google Scholar
   
   
6. Martin P, Makepeace K, Hill SA, Hood DW, Moxon ER (2005) Microsatellite instability regulates transcription factor binding and gene expression. PNAS 102: 3800- 3804.  » CrossRef   » PubMed  »  Google Scholar
   
   
7. Schlotterer C, (2000) Evolutionary dynamics of microsatellite DNA. Chromosoma 109: 365-371.  » CrossRef   » PubMed  »  Google Scholar
   
   
8. Mudunuri SB, Nagarajaram HA (2007) IMEx: Imperfect Microsatellite Extractor. Bioinformatics 23: 1181- 1187.   » CrossRef   » PubMed  »  Google Scholar
   
   
9. Sibly RM, Meade A, Boxall N, Wilkinson MJ, Corne DW, Whittaker JC (2003) The structure of interrupted human AC microsatellites. Mol Biol Evol 20: 453-9.   » CrossRef   » PubMed  »  Google Scholar
   
   
10. Splawski I, Shen J, Timothy KW, Vincent GM, Lelumann MH, Keating MT (2005) Genomic Structure of three long QT syndrome genes:KVLQT1, HERG, and KCNE1.Cardiology Division University of Utah Salt Lake City Utah 84112 USA.  » CrossRef   » PubMed  
    
    
11. Sreenu VB, Kumar P, Nagarajaram HA (2007) Simple sequence repeats in mycobacterial genomes. J Biosci 32: 3-15.  » CrossRef   » PubMed  »  Google Scholar
    
    
12. Stenson PD, Ball EV, Mort M, Phillips AD, Shiel JA, Thomas NS, Abeysinghe S, Krawczak M, Cooper DN (2003) The Human Gene Mutation Database (HGMD®): 2003 Update. Hum Mutat 21: 577-581.  » CrossRef   » PubMed  »  Google Scholar
    
    
13. Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10: 967-981.   » CrossRef   » PubMed  »  Google Scholar
    
    

   

 

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