Genomics Inform.  2016 Sep;14(3):112-124. 10.5808/GI.2016.14.3.112.

In Silico Study of miRNA Based Gene Regulation, Involved in Solid Cancer, by the Assistance of Argonaute Protein

• Rath SN
• Das D
• Konkimalla VB
• Pradhan SK

• KMID: 2353663
• DOI: http://doi.org/10.5808/GI.2016.14.3.112

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.

Keyword

Argonaute; in silico; microRNAs; mRNA; solid cancer

MeSH Terms

Breast
Computer Simulation*
Endothelial Cells
Gene Silencing
Humans
Hydrogen Bonding
Lung
MicroRNAs*
Pancreas
Prostate
RNA Interference
RNA, Messenger
Stomach
Urinary Bladder
Urinary Bladder Neoplasms
MicroRNAs
RNA, Messenger