MeDIP based methylome analysis of muscle from two pig breeds with varying muscularity

We report the application of methylated DNA immunopreciptation (MeDIP)-next generation sequencing for examining methylome in two different breeds of pigs. Two muscle samples from each animal/breed processed to isolated DNA. DNA was isolated from two muscle samples (one per breed) was used for methylated DNA immunoprecipitation (MeDIP). 5 methyl cytosine regions were immunoprecipitated and processed for next generation sequencing in Hiseq 2500 (Illumina). The pre-processed reads were mapped to the Sus scrofa genome v11.1 downloaded from UCSC (http://genome.ucsc.edu/) with Burrows–Wheeler alignment (BWA) (version 0.7.17). The MeDIP data generated was used for identification of differentially methylated regions (DMRs) across the chromosome between the breeds using Burrrows Eheeler Alignment (BWA version 0.7.17. Uniquely mapped reads were processed further with MEDIPS. A total of 1545 and 25 DMRs (P<0.1) were identified across the pig chromosome and mitochondrial DNA respectively. Methylome analysis of muscle from two pig breeds with varying muscularity was conducted to provide insights into muscle development.

本研究报道了甲基化DNA免疫沉淀（methylated DNA immunoprecipitation, MeDIP）-下一代测序技术在两种不同品种猪的甲基化组分析中的应用。本研究从每个品种的每头动物中采集两份肌肉样本用于DNA提取，取两个品种各一份肌肉样本提取的DNA开展甲基化DNA免疫沉淀（MeDIP）实验。对5个甲基胞嘧啶区域进行免疫沉淀后，在Illumina HiSeq 2500平台上完成下一代测序。使用Burrows-Wheeler比对工具（Burrows–Wheeler alignment, BWA，版本0.7.17），将预处理后的测序reads比对至从加州大学圣克鲁兹分校基因组数据库（UCSC，http://genome.ucsc.edu/）下载的家猪（Sus scrofa）参考基因组v11.1版本。本研究利用生成的MeDIP测序数据，采用Burrows-Wheeler比对工具（BWA版本0.7.17），鉴定两个猪品种间全染色体及线粒体DNA上的差异甲基化区域（differentially methylated regions, DMRs），随后使用MEDIPS工具对唯一比对上的reads进行后续分析。最终分别在猪核染色体与线粒体DNA中鉴定出1545个和25个差异甲基化区域（P<0.1）。本研究针对两种肌肉发育特性存在差异的猪品种的肌肉组织开展甲基化组分析，旨在为肌肉发育相关研究提供参考见解。