In silico prediction of human genes as potential targets for rice miRNAs

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.

Dietary Epigenetic Modulators: Unravelling the Still-Controversial Benefits of miRNAs in Nutrition and Disease

In the context of nutrient-driven epigenetic alterations, food-derived miRNAs can be absorbed into the circulatory system and organs of recipients, especially humans, and potentially contribute to modulating health and diseases. Evidence suggests that food uptake, by carrying exogenous miRNAs (xenomiRNAs), regulates the individual miRNA profile, modifying the redox homeostasis and inflammatory conditions underlying pathological processes, such as type 2 diabetes mellitus, insulin resistance, metabolic syndrome, and cancer. The capacity of diet to control miRNA levels and the comprehension of the unique characteristics of dietary miRNAs in terms of gene expression regulation show important perspectives as a strategy to control disease susceptibility via epigenetic modifications and refine the clinical outcomes. However, the absorption, stability, availability, and epigenetic roles of dietary miRNAs are intriguing and currently the subject of intense debate; additionally, there is restricted knowledge of their physiological and potential side effects. Within this framework, we provided up-to-date and comprehensive knowledge on dietary miRNAs' potential, discussing the latest advances and controversial issues related to the role of miRNAs in human health and disease as modulators of chronic syndromes.

Genome-wide identification and analysis of the PAL genes from the orchids Apostasia shenzhenica, Dendrobium catenatum and Phalaenopsis equestris

Phenylalanine ammonia-lyase (PAL) is a key gateway enzyme that connects the phenylpropanoid pathway to primary metabolism. The phenylpropanoid pathway plays a vital role in the growth and environmental adaptation of many plants leading to the production of valuable bioactive compounds with industrial and medical applications. In the present study, nine putative PAL genes from three orchids were identified; five in Apostasia shenzhenica and two each in Dendrobium catenatum and Phalaenopsis equestris. Eighteen motifs and four major conserved functional domains were identified as reported in PAL proteins of other species. All the nine PALs were stable based on their computed physicochemical properties and localized in the cytoplasm. The three-dimensional structures of PALs revealed a homo-tetrameric structure consisting of four identical subunits. A total of 21 cis-regulatory elements with known functions were identified from the promoter regions of all PALs which are responsible for various plant responses to light, stress and growth regulators like auxins, gibberellins and abscisic acid. Phylogenetic analysis showed that the studied PAL proteins clustered in two major clades (clade I and II), placing dicot and monocot PALs in two separate monophyletic clades. In silico gene expression of the identified PALs in different vegetative and reproductive tissues revealed the differential expressions based on tissue type and disclosed that the expression of PAL genes was upregulated in all the tissues examined with an exception of PePAL leaf samples where no expression was detected, however, the same being highly expressed in reproductive tissues (PePAL1-labellum; PePAL2-sepal). In case of AsPALs, the expression was found to be highest in reproductive tissues (AsPAL4-maximum in inflorescence). On the other hand, the expression of DcPALs was found to be highest in vegetative tissues (DcPAL2-maximum in root). Based on the medicinal importance of orchids and the significant role of PAL genes in synthesis of bioactive compounds, the functional characterization of PAL genes can be further exploited in genetic improvement of medicinal orchids.Communicated by Ramaswamy H. Sarma.

Plant_SNP_TATA_Z-Tester: A Web Service That Unequivocally Estimates the Impact of Proximal Promoter Mutations on Plant Gene Expression

Synthetic targeted optimization of plant promoters is becoming a part of progress in mainstream postgenomic agriculture along with hybridization of cultivated plants with wild congeners, as well as marker-assisted breeding. Therefore, here, for the first time, we compiled all the experimental data—on mutational effects in plant proximal promoters on gene expression—that we could find in PubMed. Some of these datasets cast doubt on both the existence and the uniqueness of the sought solution, which could unequivocally estimate effects of proximal promoter mutation on gene expression when plants are grown under various environmental conditions during their development. This means that the inverse problem under study is ill-posed. Furthermore, we found experimental data on in vitro interchangeability of plant and human TATA-binding proteins allowing the application of Tikhonov’s regularization, making this problem well-posed. Within these frameworks, we created our Web service Plant_SNP_TATA_Z-tester and then determined the limits of its applicability using those data that cast doubt on both the existence and the uniqueness of the sought solution. We confirmed that the effects (of proximal promoter mutations on gene expression) predicted by Plant_SNP_TATA_Z-tester correlate statistically significantly with all the experimental data under study. Lastly, we exemplified an application of Plant_SNP_TATA_Z-tester to agriculturally valuable mutations in plant promoters.

Identification of potential target genes in Homo sapiens, by miRNA of Triticum aestivum: A cross kingdom computational approach

Plant-derived miRNAs can be found in the human body after dietary intake, and they can affect post-transcriptional gene regulation in human. It is important to identify targets to determine the possible effects in human genes by using computational approach. In this study, 787 possible mRNAs human targets were predicted by 84 miRNAs of wheat. A total of 14 miRNAs were identified with individual binding to 33 mRNAs associated with schizophrenia, epilepsy, neurodevelopmental disorders, and various cancers, located in the 3′UTR of the mRNA. A functional enrichment was carried out, where the results showed associations to pathways such as dopaminergic synapse (hsa04728), and signaling pathways, significantly associated with the target genes. The prediction of target mRNAs in humans by wheat miRNAs, offer candidates that could facilitate the search and verification, which could be of relevance for future projects and therefor contribute in the therapeutic treatment of various human diseases.

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

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.

Identification of Bovine miRNAs with the Potential to Affect Human Gene Expression

Milk and other products from large mammals have emerged during human evolution as an important source of nutrition. Recently, it has been recognized that exogenous miRNAs (mRNA inhibited RNA) contained in milk and other tissues of the mammalian body can enter the human body, which in turn have the ability to potentially regulate human metabolism by affecting gene expression. We studied for exogenous miRNAs from Bos taurus that are potentially contain miRNAs from milk and that could act postprandially as regulators of human gene expression. The interaction of 17,508 human genes with 1025 bta-miRNAs, including 245 raw milk miRNAs was studied. The milk bta-miR-151-5p, bta-miR-151-3p, bta-miRNA-320 each have 11 BSs (binding sites), and bta-miRNA-345-5p, bta-miRNA-614, bta-miRNA-1296b and bta-miRNA-149 has 12, 14, 15 and 26 BSs, respectively. The bta-miR-574-5p from cow’s milk had 209 human genes in mRNAs from one to 25 repeating BSs. We found 15 bta-miRNAs that have 100% complementarity to the mRNA of 13 human target genes. Another 12 miRNAs have BSs in the mRNA of 19 human genes with 98% complementarity. The bta-miR-11975, bta-miR-11976, and bta-miR-2885 BSs are located with the overlap of nucleotide sequences in the mRNA of human genes. Nucleotide sequences of BSs of these miRNAs in 5′UTR mRNA of human genes consisted of GCC repeats with a total length of 18 nucleotides (nt) in 18 genes, 21 nt in 11 genes, 24 nt in 14 genes, and 27–48 nt in nine genes. Nucleotide sequences of BSs of bta-miR-11975, bta-miR-11976, and bta-miR-2885 in CDS mRNA of human genes consisted of GCC repeats with a total length of 18 nt in 33 genes, 21 nt in 13 genes, 24 nt in nine genes, and 27–36 nt in 11 genes. These BSs encoded polyA or polyP peptides. In only one case, the polyR (SLC24A3 gene) was encoded. The possibility of regulating the expression of human genes by exogenous bovine miRNAs is discussed.

The Challenges and Opportunities in the Development of MicroRNA Therapeutics: A Multidisciplinary Viewpoint

microRNAs (miRs) are emerging as attractive therapeutic targets because of their small size, specific targetability, and critical role in disease pathogenesis. However, <20 miR targeting molecules have entered clinical trials, and none progressed to phase III. The difficulties in miR target identification, the moderate efficacy of miR inhibitors, cell type-specific delivery, and adverse outcomes have impeded the development of miR therapeutics. These hurdles are rooted in the functional complexity of miR's role in disease and sequence complementarity-dependent/-independent effects in nontarget tissues. The advances in understanding miR's role in disease, the development of efficient miR inhibitors, and innovative delivery approaches have helped resolve some of these hurdles. In this review, we provide a multidisciplinary viewpoint on the challenges and opportunities in the development of miR therapeutics.