Transcription Profiles of Age-at-Maturity-Associated Genes Suggest Cell Fate Commitment Regulation as a Key Factor in the Atlantic Salmon Maturation Process

Abstract

Despite recent taxonomic diversification in studies linking genotype with phenotype, follow-up studies aimed at understanding the molecular processes of such genotype-phenotype associations remain rare. The age at which an individual reaches sexual maturity is an important fitness trait in many wild species. However, the molecular mechanisms regulating maturation timing processes remain obscure. A recent genome-wide association study in Atlantic salmon (Salmo salar) identified large-effect age-at-maturity-associated chromosomal regions including genes vgll3, akap11 and six6, which have roles in adipogenesis, spermatogenesis and the hypothalamic-pituitary-gonadal (HPG) axis, respectively. Here, we determine expression patterns of these genes during salmon development and their potential molecular partners and pathways. Using Nanostring transcription profiling technology, we show development- and tissue-specific mRNA expression patterns for vgll3, akap11 and six6. Correlated expression levels of vgll3 and akap11, which have adjacent chromosomal location, suggests they may have shared regulation. Further, vgll3 correlating with arhgap6 and yap1, and akap11 with lats1 and yap1 suggests that Vgll3 and Akap11 take part in actin cytoskeleton regulation. Tissue-specific expression results indicate that vgll3 and akap11 paralogs have sex-dependent expression patterns in gonads. Moreover, six6 correlating with slc38a6 and rtn1, and Hippo signaling genes suggests that Six6 could have a broader role in the HPG neuroendrocrine and cell fate commitment regulation, respectively. We conclude that Vgll3, Akap11 and Six6 may influence Atlantic salmon maturation timing via affecting adipogenesis and gametogenesis by regulating cell fate commitment and the HPG axis. These results may help to unravel general molecular mechanisms behind maturation.

Cis-regulatory differences in isoform expression associate with life history strategy variation in Atlantic salmon

“…Vgll3 expression in the heart was high relative to other tissues (Fig 2A), but also very variable, similar to results from three-year old juveniles from natural populations [28]. Expression in liver showed a linear downward trend from younger to older individuals, although the overall expression level remained very low relative to other tissues (S4 Fig).…”

“…Consistent with this, by analyzing RNAsequencing data from immature, prepubertal and pubertal testes, we found that vgll3 and yap1 showed opposite expression patterns with respect to maturity status. Salmon vgll3 expression was also found to negatively correlate with yap1 expression in early development [28]. We hypothesize that changes in vgll3 isoform abundance associated with vgll3 � E and vgll3 � L alleles may influence the tendency of cell differentiation in immature testes by changing interaction between Vgll3 and TEADs and/or Vgll3-Yap (Fig 6).…”

“…The transcription co-factor function of vgll3 suggests that isoform changes in vgll3 expression may transmit downstream to expression changes in gene regulatory networks associated with cell proliferation and organ development [37]. Like its vertebrate and invertebrate homologs, the salmon vgll3 has been proposed to control cell differentiation through interacting with the TEAD-family of transcription factors of the Hippo signaling pathway [27,28]. Vgll3, like related co-factors in mice, humans and Drosophila, is predicted to compete for TEAD accessibility with alternative co-factors downstream of the Hippo signaling pathway controlling for organ size (Yap/Taz co-factors) [26,36].…”

“…While the effects of vgll3 down-regulation on the downstream transcriptional landscape of testes cell types remain largely unknown, transcriptomic studies indicate that vgll3 expression correlates with changes in the Hippo signaling pathway, known to control cell differentiation and organ size [27,28]. To gain additional insight into the expression patterns of key players of Hippo signaling pathway and vgll3 during male puberty, we re-analyzed RNA-sequencing data from immature, prepubertal and pubertal testes from an independent dataset [34].…”

“…Uncertainty remains regarding the tissues and developmental stages during which vgll3 expression potentially influences the maturation phenotype. Vgll3 expression and function has been linked to diverse processes such as adipocyte differentiation and myogenesis in mice [25,26], immune function, adiposity and puberty timing in humans [16,17] and cell fate commitment in salmon tissues including adipose and gonads [27,28], but genotype comparisons, vgll3 transcript structure or cis-regulation have not been investigated. We determined vgll3 temporal expression dynamics during the first year of salmon development up to male maturation by way of a time-series sampling of ten tissues from a total of 273 individuals, characterized vgll3 transcript structure and further tested the importance of cis-regulatory mechanisms among vgll3 genotypes by assaying vgll3 allele-specific expression in heterozygotes.…”