滩羊和湖羊背最长肌全基因组甲基化差异分析

doi:10.16431/j.cnki.1671-7236.2020.10.003

摘要/Abstract

摘要： 本研究旨在通过不同品种绵羊背最长肌的全基因组甲基化差异分析，鉴定差异甲基化区域（DMR）和差异甲基化基因（DMG），为解析绵羊骨骼肌发育差异奠定基础。采用全基因组重亚硫酸盐测序（WGBS）技术开展了周岁龄滩羊、湖羊和滩湖F2代背最长肌全基因组DNA的甲基化水平检测和差异甲基化区域分析，探讨品种间DNA甲基化水平的差异。结果显示，全基因组范围内滩羊、湖羊和滩湖F2代胞嘧啶（C）甲基化（mC）率分别为3.55%、3.18%和3.56%，3个群体的甲基化水平基本一致。对滩羊和湖羊的甲基化水平进行比较，在不同序列环境下共检测到97 731个DMRs和10 784个DMGs。在CG、CHH、CHG序列环境下3个群体甲基化水平无显著差异。对DMGs通过基因本体（GO）和相关信号通路（KEGG）分析，共检测到419个GO条目和20个信号通路，显著富集在细胞过程、细胞组分、结合、长期抑制等相关条目中。筛选出5个与肌肉调控有关的候选基因ACTA2、ROCK1、CALD1、MYH3、MYH10。本研究绘制了滩羊、湖羊和滩湖F2代全基因组甲基化图谱，为表观遗传调控肌肉发育研究和肉质候选基因的筛选提供理论参考。

关键词: 绵羊; 背最长肌; 全基因组; 甲基化

Abstract: It aimed to identify the differential methylation region (DMR) and differential methylation gene (DMG) through the analysis of the genome-wide methylation difference of the longest muscle of the sheep's back of different breeds of sheep,and laid the foundation for the analysis of the differences in sheep skeletal muscle development.In this study,one-year-old sheep(Tan sheep and Hu sheep and Tan-Hu F2) were sanned by the whole genome bisulfite sequencing method(WGBS).The degree of methylation and differentially methylated region in the whole genome DNA of longissimus dorsi(LD) muscle were studied to explore the difference of DNA methylation in level in sheep.The results showed that the methylation (mC) rates of cytosine (C) were 3.55%,3.18% and 3.56% in Tan sheep,Hu sheep and Tan-Hu F2,respectively.A total of 97 731 DMRs and 10 784 related DMGs were detected.In CG,CHH and CHG sequences,the methylation levels of the three groups were not significantly different.419 GO terms and 20 related signal pathways were detected by GO and KEGG analysis,respectively,which were showed to be significantly enriched in cellular process,cell part,binding,long-term depression,and so on.Five candidate genes,ACTA2、ROCK1、CALD1、MYH3 and MYH10 were sreened out in muscle tissues.This study provided genome-wide methylation of pattern of three groups (Tan sheep and Hu sheep and Tan-Hu F2).The results provided reference information for the epigenetic study of Tan sheep and screened candidate genes related to muscle development and meat quality.

Key words: sheep; longissimus dorsi; genome-wide; methylation

中图分类号:

S826

岳彩娟, 梁小军, 王秀琴, 马青, 马吉锋, 张俊丽, 王晓薇, 额尔和花. 滩羊和湖羊背最长肌全基因组甲基化差异分析[J]. 中国畜牧兽医, 2020, 47(10): 3058-3068.

YUE Caijuan, LIANG Xiaojun, WANG Xiuqin, MA Qing, MA Jifeng, ZHANG Junli, WANG Xiaowei, Eerhehua. Whole Genome Methylation Variation Analysis of Longissimus Dorsi Between Tan Sheep and Hu Sheep[J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(10): 3058-3068.

参考文献 37

[1]	MEISSNER A.Epigenetic modifications in pluripotent and differentiated cells[J].Nature Biotechnology,2010,28(10):1079-1088.
[2]	HUYNH K D,LEE J T.X-chromosome inactivation:Ahypothesis linking ontogeny and phylogeny[J].Nature Reviews Genetics,2005,6(5):410-418.
[3]	AMANDINE H,PHILIPPE A.Genome-wide identification of new imprinted genes[J].Briefings in Functional Genomics,2010,9(4):304.
[4]	SMITH Z D,CHAN M M,MIKKELSEN T S,et al.A unique regulatory phase of DNA methylation in the early mammalian embryo[J].Nature,2012,484(7394):339-344.
[5]	SPISÁK S,KALMÁR A,GALAMB O,et al.Genome-wide screening of genes regulated by DNA methylation in colon cancer development[J].PLoS One,2012,7(10):e46215.
[6]	郭添福,张志燕,陈冬,等.不同性别大白猪肌肉全基因组高分辨率单碱基甲基化差异分析[J].畜牧兽医学报,2018,49(11):2326-2339. GUO T F,ZHANG Z Y,CHEN D,et al.High resolution and single base genome-wide methylation variance analysis of muscle of Large White pigs with different sexes[J].Chinese Journal of Animal and Veterinary Sciences,2018,49(11):2326-2339.(in Chinese)
[7]	WILKINSOM M F.Evidence than DNA methylation engenders dynamic gene regulation[J].Proceedings of the National A-cademy of Sciences USA,2015,112(17):E2116.
[8]	楼平儿.猪不同年龄段骨骼肌的差异甲基化组分析[D].雅安:四川农业大学,2013. LOU P E.Aging-related DNA methylomes in porcine skeletal muscles[D].Ya'an:Sichuan Agricultural University,2013.(in Chinese)
[9]	张小丽.猪背部浅层和背部深层脂肪组织全基因组甲基化研究[D].雅安:四川农业大学,2013. ZHANG X L.Genome-wide DNA methylation changes between the superficial and deep backfat tissues of the pig[D]].Ya'an:Sichuan Agricultural University,2013.(in Chinese)
[10]	曹阳.杜寒杂交羊与小尾寒羊背最长肌全基因组甲基化与转录组比较分析[D].长春:吉林大学,2017. CAO Y.Comparative analysis of genome-wide methylation and RNA-seq in longissimus dorsi muscle between Dorper X small Tailed Han crossbred and Small Tailed Han sheep[D].Changchun:Jilin University,2017.(in Chinese)
[11]	XI Y X,WEI L.BSMAP:Whole genome bisulfite sequence MAPping program[J].BMC Bioinformatics,2009,10:232.
[12]	ALTUNA A,MATTHIAS K,LI S,et al.Methyl kit:A comprehensive R package for the analysis of genome-wide DNA methylation profiles[J].Genome Biology,2012,13(10):R87.
[13]	KANEHISA M,GOTO S.KEGG:Kyoto encyclopedia of genes and genomes[J].Nucleic Acids Research,2000,28:27-30.
[14]	JONES P A.Functions of DNA methylation:Islands,start sites,gene bodies and beyond[J].Nature Reviews Genetics,2012,13(7):484-492.
[15]	JIN L,JIANG Z,XIA Y,et al.Genome-wide DNA methylation changes in skeletal muscle between young and middle-aged pigs[J].BMC Genomics,2014,15(1):653.
[16]	SU Y Y,FAN Z P,WU X S,et al.Genome-wide DNA methylation profile of developing deciduous tooth germ im miniature pigs[J].BMC Genomics,2016,17:134.
[17]	WANG H F,WANG J Y,NING C,et al.Genome-wide DNA methylation and transcriptome analyses reveal genes imvolved in immune responses of pig peripheral blood monomuclear cells to poly Ⅰ:C[J].Scientific Reports,2017,7(1):9709.
[18]	KIM W,PARK H,SEO K S,et al.Characterization and functional inferences of a genome-wide DNA methylation profile in the loin (longissimus dorsi) muscle of swine[J].Asian-Australasian Journal of Animal Sciences,2018,31(1):3-12.
[19]	LI M Z,WU H,LUO Z G,et al.An atlas of DNA methylomes in porcine adipose and muscle tissues[J].Nature Communications,2012,3:850.
[20]	YANG Y L,LIANG G M,NIU G L,et al.Comparative analysis of DNA methylome and transcriptome of skeletal muscle in lean,obese,and mini-type pigs[J].Scientific Reports,2017,7:39883.
[21]	KWAK W,KIM J N,KI D,et al.Genlome-wide DNA mmethylation profiles of small imtestine and liver in fast-growing and slow-growing weaning piglets[J].Asian-Australasian Journal of Animal Sciences,2014,27(11):1532-1539.
[22]	SCHACHTSCHNEIDER K M,MADSEN O,PARK C,et al.Adult porcine genome-wide DNA methylation patterns support pigs as a biomedical model[J].BMC Genomics,2015,16:743
[23]	CHOI M,LEEJ,LE M T,et al.Genome-wide analysis of DNA methylation in pigs using reduced representation bisulfite sequencing[J].DNA Research,2015,22(5):343-355.
[24]	LI Z,LIU J,ZHAO F,et al.Genome-wide association studies for growth and meat production traits in sheep[J].PloS One,2013,8(6):e66569.
[25]	STRATZ P,WELLMANN R,PREUSS S,et al.Genome-wide association analysis for growth,muscularity and meat quality in Pietrain pigs[J].Animal Genetics,2014,45(3):350.
[26]	KADARMIDEEN H N.Biochemical,ECF18R,and RYR1 gene polymorphisms and their associations with osteochondral diseases and production traits in pigs[J].Biochemical Genetics,2008,46(1-2):41.
[27]	YUAN X L,GAO N,XING Y,et al.Profiling the genome-wide DNA methyation pattern of porcine ovaries using reduced representation bisulfite sequencing[J].Scientific Reports,2016,6:22138.
[28]	HAO Y,CUI Y J,GU X H.Genome-wide DNA methylation profiles associated with constant heat stress in pigs as measured by bisulfite sequencing[J].Scientific Reports,2016:27507.
[29]	张恬.猪肌内脂肪全基因组甲基化差异分析及候选基因研究[D].北京:中国农业科学院,2016. ZHANG T.Genomic methylation analysis and candidate genes of porcine intramuscular fat[D].Beijing:Chinese Academy of Agricultural Sciences,2016.(in Chinese)
[30]	WHITESELL T R,CHRYSTAL P W,RYU J R,et al.Foxc1 is required for embryonic head vascular smooth muscle differentiation in zebrafish[J].Developmental Biology,2019,453(1):34-47.
[31]	MA X,WANG L,SHI Z,et al.Mechanism of continuous high temperature affecting growth performance,meat quality,and muscle biochemical properties of finishing pigs[J].Genes & Nutrition,2019,14(1):23.
[32]	LUDVIGSEN T P,OLSEN L H,PEDERSEN H D,et al.Hyperglycemia-induced transcriptional regulation of ROCK1 and TGM2 expression is involved in small artery remodeling in obese diabetic Göttingen minipigs[J].Clinical Science,2019,133(24):2499-2516.
[33]	SHILEI C,ISAO I,HITOSHI N,et al.Induction of airway remodeling and persistent cough by repeated citric acid exposure in a guinea pig cough model[J].Respiratory Physiology & Neurobiology,2019,263:1-8.
[34]	FISICARO N,SALVARIS E J,PHILIP G K,et al.FokI-dCas9 mediates high-fidelity genome editing in pigs[J].Xenotransplantation,2019,21(1):e12551.
[35]	CHO I C,PARK H B,AHN J S,et al.A functional regulatory variant of MYH3 influences muscle fiber-type composition and intramuscular fat content in pigs[J].PLoS Genetics,2019,15(10):e1008279.
[36]	ALBUQUERQUE A.Identification of Differentially Expressed Key Genes of Longissimus Lumborum Samples from Portuguese Alentejano and Bísaro Local Pig Breeds[M].Florença,Itália:The X International Symposium on Mediterranean Pig,2019.
[37]	YANG Z,ZHAO X,XIONG X,et al.Uncovering the mechanism whereby dietary nicotinic acid increases the intramuscular fat content in finishing steers by RNA sequencing analysis[J].Animal Production Science,2019,59:1620-1630.