In silico genome wide mining of conserved and novel miRNAs in the brain and pineal gland of Danio rerio using small RNA sequencing data.

Suyash Agarwal,Naresh Sahebrao Nagpure,Ravindra Kumar,Shreya Srivastava,Prachi Srivastava,Manmohan Pandey,Basdeo Kushwaha

doi:10.1016/j.gdata.2015.11.013

Suyash Agarwal, Naresh Sahebrao Nagpure + Show 5 more

Open Access

https://doi.org/10.1016/j.gdata.2015.11.013

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Abstract

MicroRNAs (miRNAs) are small, non-coding RNA molecules that bind to the mRNA of the target genes and regulate the expression of the gene at the post-transcriptional level. Zebrafish is an economically important freshwater fish species globally considered as a good predictive model for studying human diseases and development. The present study focused on uncovering known as well as novel miRNAs, target prediction of the novel miRNAs and the differential expression of the known miRNA using the small RNA sequencing data of the brain and pineal gland (dark and light treatments) obtained from NCBI SRA. A total of 165, 151 and 145 known zebrafish miRNAs were found in the brain, pineal gland (dark treatment) and pineal gland (light treatment), respectively. Chromosomes 4 and 5 of zebrafish reference assembly GRCz10 were found to contain maximum number of miR genes. The miR-181a and miR-182 were found to be highly expressed in terms of number of reads in the brain and pineal gland, respectively. Other ncRNAs, such as tRNA, rRNA and snoRNA, were curated against Rfam. Using GRCz10 as reference, the subsequent bioinformatic analyses identified 25, 19 and 9 novel miRNAs from the brain, pineal gland (dark treatment) and pineal gland (light treatment), respectively. Targets of the novel miRNAs were identified, based on sequence complementarity between miRNAs and mRNA, by searching for antisense hits in the 3′-UTR of reference RNA sequences of the zebrafish. The discovery of novel miRNAs and their targets in the zebrafish genome can be a valuable scientific resource for further functional studies not only in zebrafish but also in other economically important fishes.

Highlights

The discovery of the first miRNAs in Caenorhabditis elegans in 1993 paved the way for unearthing of thousands of the mature miRNAs in a wide variety of organisms, including animals, plants and even viruses [1,2,3]
In order to infer the functional annotation of the novel miRs, gene ontology (GO) analysis was done for the predicted Zebrafish targets, which indicated their involvement in the regulation of diverse physiological processes (Fig. 7)
The novel miRNAs were found to play a major role in transcription regulation, signal transduction, organism development, RNA polymerase II promoter regulation, protein transport and homophilic cell adhesion

Summary

Introduction

The discovery of the first miRNAs in Caenorhabditis elegans in 1993 paved the way for unearthing of thousands of the mature miRNAs in a wide variety of organisms, including animals, plants and even viruses [1,2,3]. Intensive studies have been carried out on identification of novel miRNAs and their targets, with the addition of newly discovered miRNAs to miRBase and subsequently resulting in its new version release. The current miRBase release 21 has miR information on 9 fish species. MicroRNAs (miRNAs) are small, non-coding RNA molecules that function as master regulators of the genome. They bind to the mRNA of the target genes; regulating the gene expression at the post-transcriptional level. Many miR-related discoveries have come from zebrafish investigations [5,6,7,8,9,10]. After the release of Zv9 (zebrafish genome draft), the zebrafish genome project joined the Genome

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