In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattle

Abstract

The modern cattle was domesticated from aurochs, sharing its physiological traits into two subspecies Bos taurus and Bos indicus. MicroRNAs (miRNAs) are a class of non-coding short RNAs of ~22nt which have a key role in the regulation of many cellular and physiological processes in the animal. The current study was aimed to predict and annotate the potential mutations in indicine miRNAs throughout the genome using de novo and homology-based in silico approaches. Genome-wide mapping was performed in available indicine assembly by the homology-based approach and 768 miRNAs were recovered out of 808 reported taurine miRNAs belonging to 521 unique mature miRNA families. While 42 precursors were dropped due to lack of secondary miRNA structure, increasing stringency or decreasing similarity between the two genomes’ miRNA. Increasing tendency of miRNAs incidence was observed on chr5, chr7, chr8, chr12 and chr21 with 19 polycistronic miRNA within 1-kilobase distance throughout the indicine genome. Notably, 12 miRNAs showed copy number variation. Eighteen miRNAs showed a mutation in their mature sequences in which eight were found in their seed region. Whilst in de novo based approach, 12 novel potential miRNAs on Y chromosome in indicine cattle along with a new miRNA (bind-miR-1264) on chrX were found. The final data set is annotated and explains the impending target genes that are responsible for enhanced immunity, heat tolerance and disease tolerance regulation in indicine. The study conforms to better understanding and perceptive approach towards indicine genome.

Analysis of the role of the Hippo pathway in cancer

“…The mature miRNA is located to an Argonaute protein with assistance from additional chaperone proteins in a complex known as the RNA-induced silencing complex (RISC) [41]. The RISC-associated miRNA is then guided by the “seed region” (nucleotides 2 to 8) to the complementary seed match” site of a target mRNA, resulting in the degradation of mRNA [42]. Importantly, the seed area of any particular miRNA is expected to target thousands of mRNA, and each mRNA can have hundreds of miRNA seed matching sites in their 3′UTR [42].…”

“…The RISC-associated miRNA is then guided by the “seed region” (nucleotides 2 to 8) to the complementary seed match” site of a target mRNA, resulting in the degradation of mRNA [42]. Importantly, the seed area of any particular miRNA is expected to target thousands of mRNA, and each mRNA can have hundreds of miRNA seed matching sites in their 3′UTR [42]. Due to this broad regulatory potential, miRNAs are considered to be the largest type of gene regulator capable of “fine-tuning” gene expression, and influencing the pathogenesis/progression of a variety of diseases [43].…”

Integrative Network Analysis of Predicted miRNA-Targets Regulating Expression of Immune Response Genes in Bovine Coronavirus Infection

“…Numerous existing algorithms have proven useful as tools for predicting miRNA targets using seed matches or other compensating factors (Griffiths-Jones et al, 2008;Agarwal et al, 2015;Fan et al, 2016;Hanif et al, 2018). Databases are available to compile associations and interactions between proteins for purposes such as identifying disease genes or biomarkers (Hayashida and Akutsu, 2016;Khurana et al, 2017).…”

Identification and Profiling of Pituitary microRNAs of Sheep during Anestrus and Estrus Stages

“…There are still clusters of different miRNA families found in humans and other related species not yet discovered in cattle. Currently, 2588 miRNAs of human and 1915 miRNAs from mouse genomes are deposited in miRBasev21 [21]. The involvement of miRNAs in sheep muscle development was recently reported [22].…”