TY - JOUR T1 - Deep sequencing of small RNA facilitates tissue and sex specific microRNA discovery in zebrafish JF - bioRxiv DO - 10.1101/019760 SP - 019760 AU - Candida Vaz AU - Choon Wei Wee AU - Gek Ping Serene Lee AU - Philip W Ingham AU - Vivek Tanavde AU - Sinnakaruppan Mathavan Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/05/24/019760.abstract N2 - Role of microRNAs in gene regulation has been well established. Though the number of genes appear to be equal between human and zebrafish, miRNAs detected in zebrafish (∼247) is significantly low compared to human (∼2000; miRBase Release 19). It appears that most of the miRNAs in zebrafish are yet to be discovered. Using next generation sequencing technology, we sequenced small RNAs from brain, gut, liver, ovary, testis, eye, heart and embryo of zebrafish. In few tissues (brain, gut, liver) sequencing was done sex specifically. About 16-62% of the sequenced reads mapped to known miRNAs of zebrafish, with the exceptions of ovary (5.7%) and testis (7.8%). We used miRDeep2, the miRNA predication tool, to discover the novel miRNAs using the un-annotated reads that ranged from 7.6 to 23.0%, with exceptions of ovary (51.4%) and testis (55.2%) that had the largest pool of un-annotated reads. The prediction tool identified a total of 459 novel pre-miRNAs. Comparison of miRNA expression data of the tissues showed the presence of tissue and sex specific miRNAs that could serve as biomarkers. The brain and liver had highest number of tissue specific (36) and sex specific (34) miRNAs, respectively. Taken together, we have made a comprehensive approach to identify tissue and sex specific miRNAs from zebrafish. Further, we have discovered 459 novel pre-miRNAs (∼30% homology to human miRNA) as additional genomic resource for zebrafish. This resource can facilitate further investigations to understand miRNA-mRNA gene regulatory network in zebrafish which will have implications to understand human miRNA function. ER -