In silico genome wide mining of conserved and novel miRNAs in the brain and pineal gland of Danio rerio using small RNA sequencing data
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...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2016-03-01
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| Series: | Genomics Data |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2213596015300830 |
| _version_ | 1811235627629281280 |
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| author | Suyash Agarwal Naresh Sahebrao Nagpure Prachi Srivastava Basdeo Kushwaha Ravindra Kumar Manmohan Pandey Shreya Srivastava |
| author_facet | Suyash Agarwal Naresh Sahebrao Nagpure Prachi Srivastava Basdeo Kushwaha Ravindra Kumar Manmohan Pandey Shreya Srivastava |
| author_sort | Suyash Agarwal |
| collection | DOAJ |
| description | 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. Keywords: MiRNA, NcRNAs, Novel miRs, Phylogenetic analysis, Zebrafish |
| first_indexed | 2024-04-12T11:55:15Z |
| format | Article |
| id | doaj.art-cb69085dec2d4f05a5b0759b75772a82 |
| institution | Directory Open Access Journal |
| issn | 2213-5960 |
| language | English |
| last_indexed | 2024-04-12T11:55:15Z |
| publishDate | 2016-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Genomics Data |
| spelling | doaj.art-cb69085dec2d4f05a5b0759b75772a822022-12-22T03:34:02ZengElsevierGenomics Data2213-59602016-03-0174653In silico genome wide mining of conserved and novel miRNAs in the brain and pineal gland of Danio rerio using small RNA sequencing dataSuyash Agarwal0Naresh Sahebrao Nagpure1Prachi Srivastava2Basdeo Kushwaha3Ravindra Kumar4Manmohan Pandey5Shreya Srivastava6Division of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226 002, Uttar Pradesh, IndiaDivision of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226 002, Uttar Pradesh, IndiaAMITY Institute of Biotechnology, AMITY University Uttar Pradesh, Lucknow Campus, Lucknow 226 028, India; Corresponding author.Division of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226 002, Uttar Pradesh, IndiaDivision of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226 002, Uttar Pradesh, IndiaDivision of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226 002, Uttar Pradesh, IndiaDivision of Molecular Biology and Biotechnology, ICAR-National Bureau of Fish Genetic Resources, Lucknow 226 002, Uttar Pradesh, IndiaMicroRNAs (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. Keywords: MiRNA, NcRNAs, Novel miRs, Phylogenetic analysis, Zebrafishhttp://www.sciencedirect.com/science/article/pii/S2213596015300830 |
| spellingShingle | Suyash Agarwal Naresh Sahebrao Nagpure Prachi Srivastava Basdeo Kushwaha Ravindra Kumar Manmohan Pandey Shreya Srivastava 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 |
| 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 |
| title_full | In silico genome wide mining of conserved and novel miRNAs in the brain and pineal gland of Danio rerio using small RNA sequencing data |
| title_fullStr | In silico genome wide mining of conserved and novel miRNAs in the brain and pineal gland of Danio rerio using small RNA sequencing data |
| title_full_unstemmed | In silico genome wide mining of conserved and novel miRNAs in the brain and pineal gland of Danio rerio using small RNA sequencing data |
| title_short | In silico genome wide mining of conserved and novel miRNAs in the brain and pineal gland of Danio rerio using small RNA sequencing data |
| title_sort | in silico genome wide mining of conserved and novel mirnas in the brain and pineal gland of danio rerio using small rna sequencing data |
| url | http://www.sciencedirect.com/science/article/pii/S2213596015300830 |
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