Integrative testis transcriptome analysis reveals differentially expressed miRNAs and their mRNA targets during early puberty in Atlantic salmon

Abstract

BackgroundOur understanding of the molecular mechanisms implementing pubertal maturation of the testis in vertebrates is incomplete. This topic is relevant in Atlantic salmon aquaculture, since precocious male puberty negatively impacts animal welfare and growth. We hypothesize that certain miRNAs modulate mRNAs relevant for the initiation of puberty. To explore which miRNAs regulate mRNAs during initiation of puberty in salmon, we performed an integrated transcriptome analysis (miRNA and mRNA-seq) of salmon testis at three stages of development: an immature, long-term quiescent stage, a prepubertal stage just before, and a pubertal stage just after the onset of single cell proliferation activity in the testis.ResultsDifferentially expressed miRNAs clustered into 5 distinct expression profiles related to the immature, prepubertal and pubertal salmon testis. Potential mRNA targets of these miRNAs were predicted with miRmap and filtered for mRNAs displaying negatively correlated expression patterns. In summary, this analysis revealed miRNAs previously known to be regulated in immature vertebrate testis (miR-101, miR-137, miR-92b, miR-18a, miR-20a), but also miRNAs first reported here as regulated in the testis (miR-new289, miR-30c, miR-724, miR-26b, miR-new271, miR-217, miR-216a, miR-135a, miR-new194 and the novel predicted n268). By KEGG enrichment analysis, progesterone signaling and cell cycle pathway genes were found regulated by these differentially expressed miRNAs. During the transition into puberty we found differential expression of miRNAs previously associated (let7a/b/c), or newly associated (miR-15c, miR-2184, miR-145 and the novel predicted n7a and b) with this stage. KEGG enrichment analysis revealed that mRNAs of the Wnt, Hedgehog and Apelin signaling pathways were potential regulated targets during the transition into puberty. Likewise, several regulated miRNAs in the pubertal stage had earlier been associated (miR-20a, miR-25, miR-181a, miR-202, let7c/d/a, miR-125b, miR-222a/b, miR-190a) or have now been found connected (miR-2188, miR-144, miR-731, miR-8157 and the novel n2) to the initiation of puberty.ConclusionsThis study has - for the first time - linked testis maturation to specific miRNAs and their inversely correlated expressed targets in Atlantic salmon. The study indicates a broad functional conservation of already known miRNAs and associated pathways involved in the transition into puberty in vertebrates. The analysis also reveals miRNAs not previously associated with testis tissue or its maturation, which calls for further functional studies in the testis.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4205-5) contains supplementary material, which is available to authorized users.

Comprehensive Analysis of MicroRNA–Messenger RNA from White Yak Testis Reveals the Differentially Expressed Molecules Involved in Development and Reproduction

“…It is driven by distinct programs of gene regulation and cellular organization [ 22 ]. Previous studies have established functions for specific microRNAs in regulating reproduction [ 23 ]. However, only a few microRNAs and target genes involved in the development and reproduction of testis have been identified in mammals [ 23 , 24 , 25 ].…”

“…Previous studies have established functions for specific microRNAs in regulating reproduction [ 23 ]. However, only a few microRNAs and target genes involved in the development and reproduction of testis have been identified in mammals [ 23 , 24 , 25 ]. Recently, it has been reported that a total of 61 DERs and 80 DEGs have been identified between cattleyak (cattle ♂ and yak ♀ ) and yak testes [ 26 ].…”

“…DEGs were used for enrichment analysis of GO functions [ 49 ] and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis [ 50 ]. Co-expression and interaction predictions were analyzed as described previously [ 9 , 10 , 23 , 51 ]. We calculated the Spearman correlation [ 52 ] for candidate DEGs to construct the correlation coefficient matrix for further investigation and determine the significance co-expressed messenger RNAs and microRNAs.…”

Vitamin K in Vertebrates’ Reproduction: Further Puzzling Pieces of Evidence from Teleost Fish Species

“…Similarly, different miRs have been shown to have great influence on cell mitosis during mammalian gametogenesis (reviewed in [ 170 ]). In fish species, like salmon, not only new specific miRs have been linked to testis maturation, but also a functional conservation in vertebrates of known miRs involved in the transition into puberty have been suggested [ 171 ]. Different clinical studies have been explored the use of miRs as potential biomarkers for human male factor infertility [ 104 , 172 ].…”

Development of innovative methods for induction of European eel (Anguilla anguilla) spermatogenesis

“…The Dhh pathway seems highly involved in spermatogenesis as male mice with a Dhh null mutation are sterile (Bitgood et al 1996;Kroft et al 2001). Furthermore, the Dhh pathway has been shown to be significantly regulated during the salmon transition into puberty (Skaftnesmo et al 2017). Like gli1, myocyte enhancer factor 2A (mef2a) was also found differentially transcribed in the testes between the T10 group and control and was annotated with GO terms related to histone modification and similar to gli1, mef2a has been suggested as an important component of Dhh signaling (Wang et al 2006).…”