Expanding the miRNA Repertoire in Atlantic Salmon; Discovery of IsomiRs and miRNAs Highly Expressed in Different Tissues and Developmental Stages

• Published in: Cells
• Main Authors: Woldemariam, Nardos Tesfaye, Agafonov, Oleg, Hoyheim, Bjørn, Houston, Ross D, Taggart, John B, Andreassen, Rune
• Other Authors: Norwegian Research Council, Oslo Metropolitan University, University of Oslo, Norwegian University of Life Sciences, University of Edinburgh, Institute of Aquaculture, orcid:0000-0002-3843-9663
• Format: Article in Journal/Newspaper
• Language: English
• Published: MDPI 2019
• Subjects: Teleostei; embryogenesis; tissue-enriched miRNAs; post-transcriptional gene regulation; Atlantic salmon
• Online Access: http://hdl.handle.net/1893/28654; https://doi.org/10.3390/cells8010042; http://dspace.stir.ac.uk/bitstream/1893/28654/1/cells-08-00042.pdf

MicroRNAs (miRNAs) are important post-transcriptional gene expression regulators. Here, 448 different miRNA genes, including 17 novel miRNAs, encoding for 589 mature Atlantic salmon miRNAs were identified after sequencing 111 samples (fry, pathogen challenged fry, various developmental and adult tissues). This increased the reference miRNAome with almost one hundred genes. Prior to isomiR characterization (mature miRNA variants), the proportion of erroneous sequence variants (ESVs) arising in the analysis pipeline was assessed. The ESVs were biased towards 5’ and 3’ end of reads in unexpectedly high proportions indicating that measurements of ESVs rather than Phred score should be used to avoid misinterpreting ESVs as isomiRs. Forty-three isomiRs were subsequently discovered. The biological effect of the isomiRs measured as increases in target diversity was small (