Couldrey Christine, Brauning Rudiger, Bracegirdle Jeremy, Maclean Paul, Henderson Harold V, McEwan John C
AgResearch Ltd., Ruakura Research Centre, Hamilton, New Zealand.
AgResearch Ltd., Invermay Agricultural Centre, Puddle Alley, Mosgiel, New Zealand.
PLoS One. 2014 Jul 10;9(7):e101853. doi: 10.1371/journal.pone.0101853. eCollection 2014.
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.
DNA甲基化通过调控基因表达在哺乳动物生长发育的多个方面发挥核心作用。新一代测序技术的发展为使用称为简化代表性亚硫酸氢盐测序（RRBS）的方法对DNA甲基化图谱进行全基因组、高分辨率分析铺平了道路。虽然RRBS已被证明在理解人类、小鼠和大鼠的DNA甲基化图谱方面有效，但迄今为止，很少有研究利用这种强大的方法来研究家畜的DNA甲基化。在这里，我们描述了利用RRBS研究绵羊背最长肌中的DNA甲基化。对背最长肌约1%的基因组进行RRBS分析，为从全基因组到单个核苷酸的所有分辨率水平的DNA甲基化分析提供了具有足够高精度和准确性的数据。将RRBS数据与mRNAseq数据相结合，使得能够将绵羊背最长肌甲基化组与其他物种的甲基化组进行比较。虽然识别出了一些物种差异，但在绵羊和其他更常研究的物种的DNA甲基化模式之间观察到了许多相似之处。这里呈现的RRBS数据突出了基因表观遗传调控的复杂性。然而，跨物种观察到的相似性是有前景的，因为从人类和小鼠的表观遗传研究中获得的知识可以谨慎地应用于农业物种。准确测量家畜DNA甲基化的能力将为目前用于最大限度提高这些物种生产收益的遗传分析增加一层额外的信息。
