Identification of an Epigenetically Marked Locus within the Sex Determination Region of Channel Catfish

Abstract

Channel catfish has an XY sex determination system. However, the X and Y chromosomes harbor an identical gene content of 950 genes each. In this study, we conducted comparative analyses of methylome and transcriptome of genetic males and genetic females before gonadal differentiation to provide insights into the mechanisms of sex determination. Differentially methylated CpG sites (DMCs) were predominantly identified on the sex chromosome, most notably within the sex determination region (SDR), although the overall methylation profiles across the entire genome were similar between genetic males and females. The drastic differences in methylation were located within the SDR at nucleotide position 14.0–20.3 Mb of the sex chromosome, making this region an epigenetically marked locus within the sex determination region. Most of the differentially methylated CpG sites were hypermethylated in females and hypomethylated in males, suggesting potential involvement of methylation modification in sex determination in channel catfish. Along with the differential methylation in the SDR, a number of differentially expressed genes within the SDR were also identified between genetic males and females, making them potential candidate genes for sex determination and differentiation in channel catfish.

Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture

“…It was demonstrated that zebrafish achieve a totipotent chromatin state at zygotic genome activation (ZGA) through paternal genome competency and maternal genome DNA methylation reprogramming (Potok et al, 2013). Similar developmental regulation processes for epigenetic factors have been observed in a non-model teleost Yang et al, 2022).…”

“…The position of C in a sequence can be in three different situations: 1) CG motifs; 2) CHG motifs where H is A, C, or T; and 3) CHH, where H is A, C, or T. In many fish species studied to date, approximately 70%–80% CpG sites were found to be methylated. For instance, 74.5%–78.4% of all C’s at the CpG sites were methylated in channel catfish ( Yang et al, 2022 ). This is similar to those observed in other vertebrate animal species, slightly higher than that seen in mice (74%) ( Feng et al, 2010 ) and tilapia (69.60%) ( Wan et al, 2016 ), but slightly lower than that in zebrafish (80.3%) ( Feng et al, 2010 ).…”

“…Methylation rate at CHG and CHH sites are much less frequent, at only miniscule scale as compared to methylation at CpG sites. For example, only 0.3%–0.4% of Cs within the CHG and CHH context were methylated in channel catfish ( Yang et al, 2022 ). Similarly, only 1.22% and 0.91% of Cs within CHG and CHH context were methylated in zebrafish ( Feng et al, 2010 ), 0.47% and 0.57% of Cs within CHG and CHH were methylated in tilapia ( Wan et al, 2016 ).…”

“…In the presence of Foxl2, SdY is translocated to the nucleus where the SdY:Foxl2 complex prevents activation of the aromatase (cyp19a1a) promoter, thereby disrupting the female differentiation pathway, consequently allowing testicular differentiation to proceed ( Bertho et al, 2018 ). In channel catfish, we have identified an epigenetically marked locus within the sex determination region (SDR), where hypermethylation was found on the X chromosomes but hypomethylation was found on the Y chromosome, leading to differential expression of the sex determination gene ( Yang et al, 2022 ). Similarly, with the Siamese fighting fish ( Betta splendens ), genetic sex is determined by an X/Y system with dmrt1 gene as the master sex determination gene, but the expression of the dmrt1 gene on the X chromosome is down-regulated by changes in DNA methylation caused by transposon-induced epigenetic silencing, where a transposon, drbx1, inserted into the fourth intron of the X-linked dmrt1 allele ( Wang et al, 2022 ).…”

“…Detailed examination of the sex differences in methylation patterns differentiates the sexual methylation pattern dimorphism into two categories: 1) The difference is concentrated on sex chromosome, and 2) the differences are general. In this regard, there are many similarities between the situations of three spine stickleback ( Metzger and Schulte, 2018 ) and channel catfish ( Wang et al, 2022 ; Yang et al, 2022 ), where sex dimorphism in DNA methylation is concentrated on the sex chromosome. In both cases, hypermethylation was observed on the X chromosome and hypomethylation was observed on the Y chromosome.…”