Tithi S. Trivedi, Aafrinbanu M. Shaikh, Archana U. Mankad, Rakesh M. Rawal, Saumya K. Patel
{"title":"小茴香(Anethum foeniculum) MiRNome的全基因组特征及其在智人和拟南芥中的潜在靶点鉴定:种间和种内计算审查。","authors":"Tithi S. Trivedi, Aafrinbanu M. Shaikh, Archana U. Mankad, Rakesh M. Rawal, Saumya K. Patel","doi":"10.1007/s10528-023-10575-7","DOIUrl":null,"url":null,"abstract":"<div><p>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 (<i>Anethum foeniculum</i>) 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 <i>Arabidopsis thaliana</i> and <i>Homo sapience</i> targets with functional enrichment analysis and human disease association. A homology-based computational approach characterized the MiRnome of the <i>Anethum foeniculum </i>genome and assessed its impact on <i>Arabidopsis thaliana</i> and <i>Homo sapience</i> 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 <i>Homo sapiens</i> and 1314 genes in <i>Arabidopsis thaliana</i>. Functional enrichment analysis reveals 56 <i>Arabidopsis thaliana</i> 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 <i>MAPK1</i><i>, PIK3R1, STAT3, EGFR, KRAS, CDC42, and SMAD4,</i> 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 <i>CSPP1</i> 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 <i>Anethum foeniculum</i> miRNAs and the biological processes and diseases with which they are associated.</p></div>","PeriodicalId":482,"journal":{"name":"Biochemical Genetics","volume":null,"pages":null},"PeriodicalIF":2.1000,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"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\",\"authors\":\"Tithi S. Trivedi, Aafrinbanu M. Shaikh, Archana U. Mankad, Rakesh M. Rawal, Saumya K. Patel\",\"doi\":\"10.1007/s10528-023-10575-7\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>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 (<i>Anethum foeniculum</i>) 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 <i>Arabidopsis thaliana</i> and <i>Homo sapience</i> targets with functional enrichment analysis and human disease association. A homology-based computational approach characterized the MiRnome of the <i>Anethum foeniculum </i>genome and assessed its impact on <i>Arabidopsis thaliana</i> and <i>Homo sapience</i> 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 <i>Homo sapiens</i> and 1314 genes in <i>Arabidopsis thaliana</i>. Functional enrichment analysis reveals 56 <i>Arabidopsis thaliana</i> 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 <i>MAPK1</i><i>, PIK3R1, STAT3, EGFR, KRAS, CDC42, and SMAD4,</i> 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 <i>CSPP1</i> 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 <i>Anethum foeniculum</i> miRNAs and the biological processes and diseases with which they are associated.</p></div>\",\"PeriodicalId\":482,\"journal\":{\"name\":\"Biochemical Genetics\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":2.1000,\"publicationDate\":\"2023-11-28\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Biochemical Genetics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://link.springer.com/article/10.1007/s10528-023-10575-7\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Biochemical Genetics","FirstCategoryId":"99","ListUrlMain":"https://link.springer.com/article/10.1007/s10528-023-10575-7","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
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
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.
期刊介绍:
Biochemical Genetics welcomes original manuscripts that address and test clear scientific hypotheses, are directed to a broad scientific audience, and clearly contribute to the advancement of the field through the use of sound sampling or experimental design, reliable analytical methodologies and robust statistical analyses.
Although studies focusing on particular regions and target organisms are welcome, it is not the journal’s goal to publish essentially descriptive studies that provide results with narrow applicability, or are based on very small samples or pseudoreplication.
Rather, Biochemical Genetics welcomes review articles that go beyond summarizing previous publications and create added value through the systematic analysis and critique of the current state of knowledge or by conducting meta-analyses.
Methodological articles are also within the scope of Biological Genetics, particularly when new laboratory techniques or computational approaches are fully described and thoroughly compared with the existing benchmark methods.
Biochemical Genetics welcomes articles on the following topics: Genomics; Proteomics; Population genetics; Phylogenetics; Metagenomics; Microbial genetics; Genetics and evolution of wild and cultivated plants; Animal genetics and evolution; Human genetics and evolution; Genetic disorders; Genetic markers of diseases; Gene technology and therapy; Experimental and analytical methods; Statistical and computational methods.