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Binding sites of miRNA on the overexpressed genes of oral cancer using 7mer-seed match

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Abstract

The microRNAs having a length of ~ 19–22 nucleotides are the small, non-coding RNAs. The evolution of microRNAs in many disorders may hold the key to tackle complex challenges. Oral cancer belongs to the group of head and neck cancer. It occurs in the mouth region that appears as an ulcer. In this study, we collected information on the overexpressed genes of oral cancer. The coding sequences of the genes were derived from NCBI and the entire set of human microRNAs present in miRBASE 21 was retrieved. The human microRNAs that can target the overexpressed genes of oral cancer were determined with the aid of our in-house software. The interaction between microRNAs and the overexpressed genes was evaluated with 7mer-m8 model of microRNA targeting. The genes DKK1 and APLN paired with only one miRNA i.e., miR-447 and miR-6087, respectively. But the genes INHBA and MMP1 were found to be targeted by 2 miRNAs, while the genes FN1, FAP, TGFPI, COL4A1, COL4A2, and LOXL2 were found to be targeted by 16, 5, 9, 18, 29, and 11 miRNAs. Subsequently, several measures such as free energy, translation efficiency, and cosine similarity metric were used to estimate the binding process. It was found that the target region’s stability was higher than the upstream and downstream zones. The overexpressed genes’ GC contents were calculated, revealing that the codons in target miRNA region were overall GC rich as well as GC3 rich. Lastly, gene ontology was performed to better understand each gene’s involvement in biological processes, molecular function, and cellular component. Our study showed the role of microRNAs in gene repression, which could possibly aid in the prognosis and diagnosis of oral cancer.

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The data that support the findings of this study are available in the supplementary material of this article.

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Acknowledgements

The authors are grateful to Assam University, Silchar-788011, Assam, India for providing the necessary research facility.

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The work was not funded.

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Authors and Affiliations

  1. Department of Bioinformatics, Christ College, Rajkot (Affiliated to Saurashtra University), Rajkot, Gujarat, India

    Manal A. A. Moustafa & John J. Georrge

  2. Department of Biotechnology, Assam University, Silchar, Assam, 788150, India

    Durbba Nath & Supriyo Chakraborty

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  1. Manal A. A. Moustafa
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  2. Durbba Nath
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  3. John J. Georrge
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  4. Supriyo Chakraborty
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Contributions

MM—Conceptualization, Formal analysis, Methodology, and Writing—original draft. DN—Formal analysis, Methodology, and Writing—review & editing. JJG—Review and editing. SC—Conceptualization, Methodology, Validation, Formal data analysis, Investigation, Writing—original draft, Data curation, and Supervision, review & final editing.

Corresponding author

Correspondence to Supriyo Chakraborty.

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Not applicable, the analysis is solely based on nucleic acid sequence data publicly available in databases.

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Moustafa, M.A.A., Nath, D., Georrge, J.J. et al. Binding sites of miRNA on the overexpressed genes of oral cancer using 7mer-seed match. Mol Cell Biochem 477, 1507–1526 (2022). https://doi.org/10.1007/s11010-022-04375-7

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  • DOI: https://doi.org/10.1007/s11010-022-04375-7

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