Dynamic epimarks in sex-related genes predict gonad phenotype in seabass, a fish with mixed genetic and environmental sex determination

Date 2018-09
Author(s) Anastasiadi DafniORCID, Vandeputte MarcORCID, Sanchez-Baizan Núria, Allal FrancoisORCID, Piferrer FrancescORCID
Affiliation(s) Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC).Passeig Marítim, 37-49, 08003, Barcelona, Spain.
MARBEC, Univ. Montpellier, Ifremer-CNRS-IRD. Chemin de Maguelone, 34250 Palavas-les-Flots, France.
GABI, INRA, AgroParisTech, Université Paris-Saclay. Domaine de Vilvert, 78352 Jouy-en-Josas, France.
DOI 10.17882/57246
Publisher SEANOE
Keyword(s) early development, environmental temperature, DNA methylation, sex determination, aromatase, cyp19a1a, dmrt1, epigenetic marks, DNA methylation threshold, epigenetic inheritance
Abstract

The integration of genomic and environmental influences into methylation patterns to bring about a phenotype is of central interest in developmental epigenetics, but many details are still unclear. The sex ratios of the species used here, the European sea bass, are determined by genetic and temperature influences. We created four families from parents known to produce offspring with different sex ratios, exposed larvae to masculinizing temperatures and examined, in juvenile gonads, the DNA methylation of seven genes related to sexual development by a targeted sequencing approach. The genes most affected by both genetics and environment were cyp19a1a and dmrt1, with contrasting sex-specific methylation and temperature responses. The relationship between cyp19a1a methylation and expression is relevant to the epigenetic regulation of sex, and we report the evidence of such relationship only below a methylation threshold, ~80%, and that it was sex-specific: negatively correlated in females but positively correlated in males. From parents to offspring, the methylation in gonads was midway between oocytes and sperm, with bias towards oocytes for amh-r2, er-β2, fsh-r and cyp19a1a. In contrast, dmrt1 levels resembled those of sperm. The methylation of individual CpGs from foxl2, er-β2 and nr3c1 were conserved from parents to offspring, whereas those of cyp19a1a, dmrt1 and amh-r2 were affected by temperature. Utilizing a machine-learning procedure based on the methylation levels of a selected set of CpGs, we present the first, to our knowledge, system based on epigenetic marks capable of predicting sex in an animal with ~90% accuracy and discuss possible applications.

Licence CC-BY-NC-ND
Data
File Size Format Processing Access
Experimental database of sex ratios and biometric measurements 53 KB XLS, XLSX Quality controlled data Open access
qRT-PCR 1 MB XLS, XLSX Quality controlled data Open access
Multiplex bisulfite sequencing library 22 KB XLS, XLSX Quality controlled data Open access
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How to cite 

Anastasiadi Dafni, Vandeputte Marc, Sanchez-Baizan Núria, Allal Francois, Piferrer Francesc (2018). Dynamic epimarks in sex-related genes predict gonad phenotype in seabass, a fish with mixed genetic and environmental sex determination. SEANOE. https://doi.org/10.17882/57246