Computational prediction and characterisation of miRNAs and their pathway genes in human schistosomiasis caused by Schistosoma haematobium

Abstract

BACKGROUND Key genes control the infectivity of the Schistosoma haematobium causing schistosomiasis. A method for understanding the regulation of these genes might help in developing new disease strategies to control schistosomiasis, such as the silencing mediated by microRNAs (miRNAs). The miRNAs have been studied in schistosome species and they play important roles in the post-transcriptional regulation of genes, and in parasite-host interactions. However, genome-wide identification and characterisation of novel miRNAs and their pathway genes and their gene expression have not been explored deeply in the genome and transcriptome of S. haematobium.OBJECTIVES Identify and characterise mature and precursor miRNAs and their pathway genes in the S. haematobium genome.METHODS Computational prediction and characterisation of miRNAs and genes involved in miRNA pathway from S. haematobium genome on SchistoDB. Conserved domain analysis was performed using PFAM and CDD databases. A robust algorithm was applied to identify mature miRNAs and their precursors. The characterisation of the precursor miRNAs was performed using RNAfold, RNAalifold and Perl scripts. FINDINGS We identified and characterised 14 putative proteins involved in miRNA pathway including ARGONAUTE and DICER in S. haematobium. Besides that, 149 mature miRNAs and 131 precursor miRNAs were identified in the genome including novel miRNAs. MAIN CONCLUSIONS miRNA pathway occurs in the S. haematobium, including endogenous miRNAs and miRNA pathway components, suggesting a role of this type of non-coding RNAs in gene regulation in the parasite. The results found in this work will open up a new avenue for studying miRNAs in the S. haematobium biology in helping to understand the mechanism of gene silencing in the human parasite Schistosome.

Satellite-Like W-Elements: Repetitive, Transcribed, and Putative Mobile Genetic Factors with Potential Roles for Biology and Evolution of Schistosoma mansoni

“…glabrata/S . mansoni interaction has been discussed ( Queiroz et al 2017 ; Cardoso et al 2020 ). Furthermore, miRNAs of S. mansoni and S. japonicum may participate in male–female interaction, sexual development, and pathological processes in the final host ( Zhu et al 2014 ; Cai et al 2016 ; Yu et al 2019 ).…”

Multifunctional Roles of MicroRNAs in Schistosomiasis

“…Adults of both sexes have been identified by transcriptome analysis and deep-sequencing technique, which provided a broader view of parasite sncRNAs ( Han et al, 2020 ). In addition, crucial molecules associated with miRNA biogenesis, such as Dicer, Argonaute, and Drosha, are differentially expressed at different developmental stages of schistosomes ( Gomes et al, 2009 ; Chen et al, 2010 ; Luo et al, 2010 ; Cai et al, 2012 ; Cardoso et al, 2020 ). Hence, miRNAs appear to play important roles in schistosome development.…”

Roles of microRNAs and Long Non-Coding RNAs Encoded by Parasitic Helminths in Human Carcinogenesis

“…It was predicted that 89 microRNAs were encoded and expressed by adult S. haematobium worms [ 56 ]. However, a recent in silico analysis identified 149 mature miRNAs and 131 precursor miRNAs, mainly in intergenic regions [ 57 ]. Considering the seed sequence of miRNAs from S. haematobium , homology with S. mansoni and S. japonicum in 43 miRNAs was described [ 56 ]; additionally, 34 miRNAs specific to S. haematobium were predicted [ 56 ].…”

“…Considering the seed sequence of miRNAs from S. haematobium , homology with S. mansoni and S. japonicum in 43 miRNAs was described [ 56 ]; additionally, 34 miRNAs specific to S. haematobium were predicted [ 56 ]. Additionally, another study reported 41 conserved miRNAs in the Schistosoma genus [ 57 ]. Interestingly, 64 miRNAs were differentially expressed in male and female adults of S. haematobium, suggesting possible functional roles in reproductive biology [ 56 ].…”