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

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Title In silico genome wide mining of conserved and novel miRNAs in the brain and pineal gland of Danio rerio using small RNA sequencing data
Not Available
 
Creator Suyash Agarwal
Naresh Sahebrao Nagpure
Prachi Srivastava
Basdeo Kushwaha
Ravindra Kumar
Manmohan Pandey
Shreya Srivastava
 
Subject MiRNA
NcRNAs
Novel miRs
Phylogenetic analysis
Zebrafish
 
Description Not Available
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.
Department of Biotechnology, Ministry of Science and Technology,Gov. of India, New Delhi, India vide Sanction Grant No. BT/PR3688/AAQ/3/571/2011 dated 10.09.201
 
Date 2021-07-19T09:52:36Z
2021-07-19T09:52:36Z
2015-11-26
 
Type Research Paper
 
Identifier Agarwal, S., Nagpure, N.S., Srivastava, P., Kushwaha, B., Kumar, R., Pandey, M. and Srivastava, S., 2016. In silico genome wide mining of conserved and novel miRNAs in the brain and pineal gland of Danio rerio using small RNA sequencing data. Genomics data, 7, pp.46-53.
2213-5960
2213-5960
http://krishi.icar.gov.in/jspui/handle/123456789/48829
 
Language English
 
Relation Not Available;
 
Publisher Elsevier