Expanding the annotation of zebrafish microRNAs based on small RNA sequencing

Abstract

MicroRNAs (miRs) are short non-coding RNAs that fine-tune the regulation of gene expression to coordinate a wide range of biological processes. Because of their role in the regulation of gene expression, miRs are essential players in development by acting on cell fate determination and progression towards cell differentiation and are increasingly relevant to human health and disease. Although the zebrafish Danio rerio is a major model for studies of development, genetics, physiology, evolution, and human biology, the annotation of zebrafish miR-producing genes remains limited. In the present work, we report deep sequencing data of zebrafish smallRNAs from brain, heart, testis, and ovary. Results provide evidence for the expression of 56 un-annotated mir genes and 248 un-annotated mature strands, increasing the number of zebrafish mir genes over those already deposited in miRBase by 16% and the number of mature sequences by 63%. We also describe the existence of three pairs of mirror-mir genes and two mirtron genes, genetic features previously undescribed in non-mammalian vertebrates. This report provides information that substantially increases our knowledge of the zebrafish miRNome and will benefit the entire miR community.

miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants

“…Sequences originating from orthologous regions of Y_RNA or vaultRNA genes were previously annotated in human as MIR1979 and MIR886, respectively, but have now been removed from the miRBase database [33]. Short reads originating from several Y_RNA and vaultRNA genes were also recently reported in zebrafish [62]; one, mir733 , from the vault.4 gene and another one, mir735 , from the Y_RNA.2 gene continue to appear in miRBase (MI0004778 and MI0004781, respectively). Even though those fragments appear in various datasets and show evolutionary conservation, a function in repressing translation has been shown only for vault fragments [63] and not yet for Y_RNA fragments [64,65], although the tests performed on Y_RNA fragments might have involved sub-optimal conditions [66].…”

“…Mirror-MiRs are pri-MiRNAs independently transcribed from both DNA strands [34,62,82,83]. Although mirror-mir pairs are evolutionarily associated, they may be transcribed independently and are unlikely to have a conserved seed; thus, mirror-miRs may act on different target protein coding genes.…”

Genome-wide identification and characterization of teleost-specific microRNAs within zebrafish

“…A total of 35,828 known mature miRNAs in miRBase derived from 223 species, which include 1637 mature miRNAs from 9 teleost fishes and 34,191 mature miRNAs from 214 non-teleost species, were obtained. Speciesspecific miRNAs from teleost fishes were collected from previous studies, including bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix) (Chi et al, 2011), common carp (Cyprinus carpio) (Yan et al, 2012;Zhu et al, 2012), channel catfish (Ictalurus punctatus) (Xu et al, 2013), rainbow trout (Oncorhynchus mykiss) (Ma et al, 2012), and zebrafish (Desvignes et al, 2014), which has not been included in the most recent miRBase version 21.…”

Genomic conservation of erythropoietic microRNAs (erythromiRs) in white-blooded Antarctic icefish

“…MiR144-5p additionally displays a seed-shift of one nucleotide at the 5’ end in Antarctic fish, which is a change in the position of the seed region of the miRNA by one nucleotide (Figure 1C), and which can potentially have major functional repercussions (Desvignes et al, 2015). Given that the reference MiR144-5p sequences for human, spotted gar and zebrafish were obtained from tissues other than pronephric kidney (Braasch et al, 2016; Desvignes et al, 2014) and/or miRBase (Kozomara and Griffiths-Jones, 2013), we cannot, however, rule out the possibility that the most expressed MiR144-5p isomiR in some tissue other than pronephric kidney has a 5’ start similar to the one observed in human, gar and zebrafish, and that, in the pronephric-kidney specifically, the most expressed MiR144-5p isomiR has a 5’ start similar to the one observed in notothenioid fish. SmallRNA sequencing of pronephric-kidney from other teleost species, especially those closely related to notothenioids should provide answers to this issue.…”

“…Briefly, raw reads were trimmed from adapter sequences, filtered for quality using the FASTX-Toolkit, size-selected for lengths between 17 and 25 nucleotides, filtered for a minimum of five identical reads, and grouped by genomic location using the published N. coriiceps genome assembly as a reference genome (Shin et al, 2014). Groups of sequences were then annotated against mature and hairpin sequences present in miRBase Release 21 (Kozomara and Griffiths-Jones, 2013), the extended zebrafish miRNA annotation (Desvignes et al, 2014), and the spotted gar annotation (Braasch et al, 2016). Gene nomenclature follows recent conventions (Desvignes et al, 2015), including those for zebrafish (Bradford et al, 2011).…”