Analysis of DNA methylation in rainbow trout spermatozoa: the strengths and limitations of RRBS

Abstract

DNA methylation is an important epigenetic mark in fish spermatozoa since it has been shown that some sperm methylome features are transmitted to the offspring. To ensure the transmission of unaltered information to the offspring, the characterization of this mark and its stability in spermatozoa is essential. DNA methylation status can be assessed at the whole genome level with an identification of the methylated and unmethylated cytosines using RRBS (reduced representation bisulfite sequencing). This method allows the sequencing of a subset of the genome expected to be enriched in CpGs. We aim to characterize the data provided by RRBS in rainbow trout spermatozoa, in order to evaluate the suitability of this approach for sperm biotechnologies studies. We observed that RRBS did provide a reduced amount of genomic data, thus allowing the processing of many biological replicates. Although, in our dataset, only a small fraction of the whole genome CpGs was present in all 6 to 12 replicates, the sum of the analyzed CpGs spanned 9 % of the total genomic CpGs. They distributed evenly all over the genome, and all genomic features were represented. RRBS is therefore an effective method to scan the DNA methylation of the along genome in a reduced pattern. However, one should be aware of the choices that are to be made regarding fragment size selection and regarding the options during bioinformatic data processing.