Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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In Silico Study of miRNA Based Gene Regulation, Involved in Solid Cancer, by the Assistance of Argonaute Protein

  • Rath, Surya Narayan (BIF Centre, Department of Bioinformatics, Orissa University of Agriculture & Technology) ;
  • Das, Debasrita (BIF Centre, Department of Bioinformatics, Orissa University of Agriculture & Technology) ;
  • Konkimalla, V Badireenath (School of Biological Sciences, National Institute of Science Education and Research) ;
  • Pradhan, Sukanta Kumar (BIF Centre, Department of Bioinformatics, Orissa University of Agriculture & Technology)
  • Received : 2016.06.13
  • Accepted : 2016.08.09
  • Published : 2016.09.30
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Abstract

Solid tumor is generally observed in tissues of epithelial or endothelial cells of lung, breast, prostate, pancreases, colorectal, stomach, and bladder, where several genes transcription is regulated by the microRNAs (miRNAs). Argonaute (AGO) protein is a family of protein which assists in miRNAs to bind with mRNAs of the target genes. Hence, study of the binding mechanism between AGO protein and miRNAs, and also with miRNAs-mRNAs duplex is crucial for understanding the RNA silencing mechanism. In the current work, 64 genes and 23 miRNAs have been selected from literatures, whose deregulation is well established in seven types of solid cancer like lung, breast, prostate, pancreases, colorectal, stomach, and bladder cancer. In silico study reveals, miRNAs namely, miR-106a, miR-21, and miR-29b-2 have a strong binding affinity towards PTEN, TGFBR2, and VEGFA genes, respectively, suggested as important factors in RNA silencing mechanism. Furthermore, interaction between AGO protein (PDB ID-3F73, chain A) with selected miRNAs and with miRNAs-mRNAs duplex were studied computationally to understand their binding at molecular level. The residual interaction and hydrogen bonding are inspected in Discovery Studio 3.5 suites. The current investigation throws light on understanding miRNAs based gene silencing mechanism in solid cancer.

Keywords

References

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