Genome-Wide Characterization of Fennel (Anethum foeniculum) MiRNome and Identification of its Potential Targets in Homo sapiens and Arabidopsis thaliana: An Inter and Intra-species Computational Scrutiny

• Published in: Biochemical genetics 2024-08, Vol.62 (4), p.2766-2795
• Main Authors: Trivedi, Tithi S., Shaikh, Aafrinbanu M., Mankad, Archana U., Rawal, Rakesh M., Patel, Saumya K.
• Format: Article
• Language: English
• Subjects: Algorithms; Anethum; Arabidopsis - genetics; Arabidopsis thaliana; Biochemistry; Biological activity; Biological effects; Biomarkers; Biomedical and Life Sciences; Biomedicine; Cancer; Cdc42 protein; Chromosome 5; Computational Biology - methods; Computer applications; Enrichment; Foeniculum; Foeniculum - genetics; Gene Expression Regulation, Plant; Gene set enrichment analysis; Genes; Genome, Plant; Genomes; Genomic analysis; Homo sapiens; Homology; Human Genetics; Humans; Impact analysis; Medical Microbiology; Medicinal plants; Metabolic pathways; MicroRNAs; MicroRNAs - genetics; miRNA; Network analysis; Nodes; Original Article; Pancreatic cancer; Pharmaceutical industry; Protein Interaction Maps; Proteins; RNA, Plant - genetics; Simulation analysis; Smad4 protein; Stat3 protein; Transcriptomes; Zoology
• ISSN: 0006-2928; 1573-4927; 1573-4927
• DOI: 10.1007/s10528-023-10575-7

MicroRNAs could be promising biomarkers for various diseases, and small RNA drugs have already been FDA approved for clinical use. This area of research is rapidly expanding and has significant potential for the future. Fennel ( Anethum foeniculum ) is a highly esteemed spice plant with economic and medicinal benefits, making it an invaluable asset in the pharmaceutical industry. To characterize the fennel miRNAs and their Arabidopsis thaliana and Homo sapience targets with functional enrichment analysis and human disease association. A homology-based computational approach characterized the MiRnome of the Anethum foeniculum  genome and assessed its impact on Arabidopsis thaliana and  Homo sapience transcriptomes. In addition, functional enrichment analysis was evaluated for both species’ targets. Moreover, PPI network analysis, hub gene identification, and MD simulation analysis of the top hub node with fennel miRNA were incorporated. We have identified 100 miRNAs of fennel and their target genes, which include 2536 genes in Homo sapiens and 1314 genes in Arabidopsis thaliana . Functional enrichment analysis reveals 56 Arabidopsis thaliana targets of fennel miRNAs showed involvement in metabolic pathways. Highly enriched human KEGG pathways were associated with several diseases, especially cancer. The protein–protein interaction network of human targets determined the top ten nodes; from them, seven hub nodes, namely MAPK1 , PIK3R1, STAT3, EGFR, KRAS, CDC42, and SMAD4, have shown their involvement in the pancreatic cancer pathway. Based on the Blast algorithm, 21 fennel miRNAs are homologs to 16 human miRNAs were predicted; from them, the CSPP1 target was a common target for afo-miR11117a-3p and has-miR-6880-5p homologs miRNAs. Our results are the first to report the 100 fennel miRNAs, and predictions for their endogenous and human target genes provide a basis for further understanding of Anethum foeniculum miRNAs and the biological processes and diseases with which they are associated.