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Cells. 2019 Jan 11;8(1). pii: E42. doi: 10.3390/cells8010042.

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

Author information

1
Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet⁻Oslo Metropolitan University, Pilestredet 50, N-0130 Oslo, Norway. nate@oslomet.no.
2
Bioinformatics Core Facility, Department of Core Facilities, Institute of Cancer Research, Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway. olegag@ifi.uio.no.
3
Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 0454 Oslo, Norway. bjorn.hoyheim@nmbu.no.
4
Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK. ross.houston@roslin.ed.ac.uk.
5
Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK. j.b.taggart@stir.ac.uk.
6
Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet⁻Oslo Metropolitan University, Pilestredet 50, N-0130 Oslo, Norway. rune.andreassen@oslomet.no.

Abstract

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 (<3%). Five miRNA genes showed allelic variation that had a large impact on target gene diversity if present in the seed. Twenty-one miRNAs were ubiquitously expressed while 31 miRNAs showed predominant expression in one or few tissues, indicating housekeeping or tissue specific functions, respectively. The miR-10 family, known to target Hox genes, were highly expressed in the developmental stages. The proportion of miR-430 family members, participating in maternal RNA clearance, was high at the earliest developmental stage.

KEYWORDS:

Teleostei; embryogenesis; post-transcriptional gene regulation; tissue-enriched miRNAs

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