摘要
为了研究五指山猪背最长肌与半腱肌的遗传差异,鉴定差异甲基化区域(DMRs)和差异甲基化基因(DMGs),采用全基因组重亚硫酸盐测序技术(WGBS)对五指山猪背最长肌和半腱肌进行DNA甲基化水平检测和DMRs分析,对DMGs进行基因本体(GO)功能、京都基因与基因组百科全书(KEGG)通路富集分析,并与已有的转录组数据进行整合分析,探讨基因组甲基化对基因表达差异的影响。结果显示:五指山猪背最长肌和半腱肌全基因组范围内胞嘧啶甲基化主要发生在CG序列上;在CG序列环境下,启动子和第一外显子区域的甲基化水平低于其他基因区域,该环境下五指山猪背最长肌和半腱肌间存在348613个DMRs和17484个DMGs,DMGs主要富集到61个GO条目和289个KEGG通路;在五指山猪背最长肌和半腱肌mRNA差异表达前10位的基因中,锌指结构家族成员4(ZIC4)、锌指结构家族成员1(ZIC1)、成对同源异型结构域蛋白转录因子1(PITX1)、碱性-螺旋-环-螺旋转录因子1(SIM1)、小清蛋白(PVALB)、SEC14类脂质结合因子5(SEC14L5)、丝氨酸蛋白酶抑制剂B家族成员11(SERPINB11)、肌球蛋白结合蛋白H(MYBPH)这8个基因存在DMRs,5个基因(ZIC4、PITX1、SIM1、SEC14L5、MYBPH)存在启动子区甲基化差异。本研究为阐明五指山猪骨骼肌生长发育机制提供表观遗传学依据。
The aim of this study was to investigate the genetic differences in longissimus dorsi and semitendinosus in Wuzhishan pigs,and identify the differentially methylated regions(DMRs)and differentially methylated genes(DMGs).The DNA methylation levels and DMRs of the longissimus dorsi and semitendinosus of Wuzhishan pig were scanned using the genome-wide bisulfite sequencing method(WGBS);and gene ontology(GO)and Kyoto encyclopedia genes and genomes(KEGG)enrichment were conducted using DMGs.Meanwhile,integrative analysis of pre-existing muscle mRNA transcriptome data and the WGBS data were conducted to explore the effect of genomic methylation on gene expression differences.The results showed that genome-wide cytosine methylation in the longissimus dorsi and semitendinosus of Wuzhishan pigs mainly occurred on CG sequences.The DNA methylation level of the promoter and first exon region was lower than that of other gene regions under the CG sequence context.A total of 348613 DMRs and 17484 DMGs were detected between the longissimus dorsi and semitendinosus under the CG sequence context.The DMGs were significantly enriched in 60 GO terms and 289 signal pathways.Among the abundances ranked in the top 10 differentially expressed mRNAs between the longissimus dorsi and semitendinosus,8 genes(ZIC4,ZIC1,PITX1,SIM1,PVALB,SEC14L5,SERPINB11,and MYBPH)contained DMRs,and 5 genes(ZIC4,PITX1,SIM1,SEC14L5,and MYBPH)contained differentially methylated promoter regions.Taken together,these results provided a good foundation for future research on the epigenetic mechanisms of skeletal muscles in Wuzhishan pigs.
作者
张庆玲
任钰为
孙瑞萍
刘海隆
王峰
李丹丹
晁哲
ZHANG Qingling;REN Yuwei;SUN Ruiping;LIU Hailong;WANG Feng;LI Dandan;CHAO Zhe(Institute of Animal Science and Veterinary Medicine,Hainan Academy of Agricultural Sciences/Hainan Province Key Laboratory of Tropical Animal Breeding and Disease Research,Haikou 571100,China;College of Veterinary Medicine,Xinjiang Agricultural University,Urumqi 830052,China;Technology Center of Haikou Customs,Haikou 570311,China)
出处
《畜牧与兽医》
CAS
北大核心
2023年第6期16-22,共7页
Animal Husbandry & Veterinary Medicine
基金
国家重点研发计划项目(2021YFD1200802)
海南省自然科学基金高层次人才项目(2019RC358)
海南省农业科学院院本级科研项目(HAAS2022GKPT03)
海南省属科研院所技术创新专项(KYYS-2021-34)。
关键词
五指山猪
背最长肌
半腱肌
全基因组
甲基化
Wuzhishan pig
longissimus dorsi
semitendinosus
genome-wideness
methylation
