Abstract
DNA methylation plays a central role in regulating many aspects of growth and development in mammals through regulating gene expression. The development of next generation sequencing technologies have paved the way for genome-wide, high resolution analysis of DNA methylation landscapes using methodology known as reduced representation bisulfite sequencing (RRBS). While RRBS has proven to be effective in understanding DNA methylation landscapes in humans, mice, and rats, to date, few studies have utilised this powerful method for investigating DNA methylation in agricultural animals. Here we describe the utilisation of RRBS to investigate DNA methylation in sheep Longissimus dorsi muscles. RRBS analysis of ∼1% of the genome from Longissimus dorsi muscles provided data of suitably high precision and accuracy for DNA methylation analysis, at all levels of resolution from genome-wide to individual nucleotides. Combining RRBS data with mRNAseq data allowed the sheep Longissimus dorsi muscle methylome to be compared with methylomes from other species. While some species differences were identified, many similarities were observed between DNA methylation patterns in sheep and other more commonly studied species. The RRBS data presented here highlights the complexity of epigenetic regulation of genes. However, the similarities observed across species are promising, in that knowledge gained from epigenetic studies in human and mice may be applied, with caution, to agricultural species. The ability to accurately measure DNA methylation in agricultural animals will contribute an additional layer of information to the genetic analyses currently being used to maximise production gains in these species.
Highlights
The rapid advances that have been made in DNA sequencing technologies over the past 20 years [1] have resulted in genomewide selection for production traits becoming a reality in agricultural animals [2]
Sequencing, quality control and mapping The ovine Longissimus dorsi (LD) muscle DNA was used for representation bisulfite sequencing (RRBS) to generate data suitable for analysing DNA methylation from a genome-wide perspective as well as at the level of single nucleotide resolution in sheep
Fragmentation of the genome with restriction enzyme MspI and construction of directional RRBS libraries resulted in high quality sequencing libraries that were generated from approximately 1% of the genome
Summary
The rapid advances that have been made in DNA sequencing technologies over the past 20 years [1] have resulted in genomewide selection for production traits becoming a reality in agricultural animals [2] This is allowing the animal breeding industry to significantly increase the rate of genetic progress. Epigenetic mechanisms include, but are not limited to: DNA methylation, acetylation and methylation of histone proteins that bind and stabilise DNA, and non-coding RNA molecules. These epigenetic processes act in an interrelated manner in order to regulate gene expression. Despite the clear importance of DNA methylation, it remains poorly understood how methylation patterns are set during development, maintained, change in response to environmental conditions, regulate gene expression, and in some cases how they affect gene expression in offspring
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