NCM 2021: Allele-specific DNA methylation in the live-bearing fish Poeciliopsis gracilis

Henri spoke about high-accuracy detection of allele-specific DNA methylation using nanopore sequencing to investigate sex-specific evolution in Poeciliidae. He discussed intralocus sexual conflict: genomic conflict will arise if an allele is advantageous to a male but not a female, and vice versa. Genomic imprinting is a potential solution to the conflict as it would silence the allele by DNA methylation if passed on to offspring of the opposite sex. If there is allele-specific methylation (ASM) due to imprinting then it may be possible to measure the difference in methylation patterns between father to daughter and mother to son. DNA was extracted from muscle/fin tissue of four Poeciliopsis gracilis: male parent, female parent, and a male and female offspring. Since nanopore sequencing can differentiate between methylated and unmethylated cytosines, native DNA was sequenced on a single PromethION Flow Cell using the Rapid Barcoding Kit, to yield 80 GB data (approximately 20–30x coverage per individual fish). The next step was to find allele-specific methylation using heterozygous SNPs. Henri’s results show there are many regions in the genome of Poeciliopsis gracilis showing evidence of ASM, suggesting it is widespread. Henri then went on to test his hypothesis of ‘crosswise imprinting’. Only small differences in methylated sites showing ASM were detected, suggesting imprinting happens at a subset of all the sites. Further analysis was performed after enriching for CpG sites that may be imprinted, by the addition of extra requirements in the analysis: 1) ASM should be present in both offspring at the same CpG sites, 2) there should be no heterozygous SNPs in the CpG sites, and 3) the methylated allele in the daughter should be from a different parent to the son. The results then suggested that the inheritance of the methylated alleles was not random but was inherited more often from the parent of the opposite sex. Analysis of the genes involved suggested they coded for proteins located ‘disproportionally to the brain’: consistent with sex-specific selection on behaviour-related traits.