Transcriptome-wide miRNA identification of Bacopa monnieri: a cross-kingdom approach

Abstract

Bacopa monnieri known as 'Brahmi' is a well-known medicinal plant belonging to Scrophulariaceae family for its nootropic properties. To the best of our knowledge, no characterization data is available on the potential role of micro RNAs (miRNAs) from this plant till date. We present here the first report of computational characterizations of miRNAs from B. monnieri. Owing to the high conservation of miRNAs in nature, new and potential miRNAs can be identified in plants using in silico techniques. Using the plant miRNA sequences present in the miRBase repository, a total of 12 miRNAs were identified from B. monnieri which pertained to 11 miRNA families from the shoot and root transcriptome data. Furthermore, gene ontology analysis of the identified 68 human target genes exhibited significance in various biological processes. These human target genes were associated with signaling pathways like NF-kB and MAPK with TRAF2, CBX1, IL1B, ITGA4 and ITGB1BP1 as the top five hub nodes. This crosskingdom study provides initial insights about the potential of miRNA-mediated cross-kingdom regulation and unravels the essential target genes of human with implications in numerous human diseases including cancer.

Characterization and identification of microRNA from Andrographis paniculata and its role in Cancer: A Cross Kingdom Approach

“…1). Characteristics of all the predicted potential miRNAs were found to be in compliance with secondary structure prediction norms (Gadhavi et al 2019). It has been reported that a plant derived miRNAs regulate host gene expression by binding to complementary mRNAs.…”

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

“…Identifying mammalian gene targets in a timely manner by plant miRNA offers a reliable, effective and economical way to determine the possible effects of interactions given by exogenous molecules, regardless of their origin, on human mRNA [ [ [9] , [10] , [11] , [12] , [13] , [14] ]].…”

Identifying potential human and medicinal plant microRNAs against SARS-CoV-2 3′UTR region: A computational genomics assessment

“…The resulted hits with a minimum of two substitutions (including gap and mismatches) on the genomic region were fetched together with their flanking region up to 350 bases. An in-house Perl script automation utilizing mfold (standalone version 3.6) [ 31 ] and VARNA [ 32 ] was applied on these captured regions, which retrieved the predicted RNA secondary structures that fulfilled the following criteria [ [33] , [34] , [35] , [36] , [37] ] including i. The miRNA sequences with breaks or loops were circumvented, ii.…”