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Title: Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish
Authors: Vaz, Candida
Wee, Choon Wei
Lee, Gek Ping Serene
Ingham, Philip William
Tanavde, Vivek
Mathavan, Sinnakaruppan
Keywords: Tissue associated miRNA
Sex associated miRNA
Novel miRNA prediction
Issue Date: 2015
Source: Vaz, C., Wee, C. W., Lee, G. P. S., Ingham, P. W., Tanavde, V., & Mathavan, S. (2015). Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish. BMC Genomics, 16, 950-.
Series/Report no.: BMC Genomics
Abstract: Background: The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish, substantially less microRNAs have been discovered in zebrafish compared to human (miRBase Release 19). It appears that most of the miRNAs in zebrafish are yet to be discovered. Results: We sequenced small RNAs from brain, gut, liver, ovary, testis, eye, heart and embryo of zebrafish. In brain, gut and liver sequencing was done sex specifically. Majority of the sequenced reads (16–62 %) mapped to known miRNAs, with the exception of ovary (5.7 %) and testis (7.8 %). Using the miRNA discovery tool (miRDeep2), we discovered novel miRNAs from the unannotated reads that ranged from 7.6 to 23.0 %, with exceptions of ovary (51.4 %) and testis (55.2 %). The prediction tool identified a total of 459 novel pre-miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated (22) and sex associated (34) miRNAs, respectively. Conclusions: This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further, we have discovered 459 novel pre-miRNAs (~30 % seed homology to human miRNA) as a genomic resource which can facilitate further investigations to understand miRNA-mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs.
ISSN: 1471-2164
DOI: 10.1186/s12864-015-2135-7
Schools: Lee Kong Chian School of Medicine (LKCMedicine) 
Rights: © 2015 Vaz et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:LKCMedicine Journal Articles

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