Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression

文献类型： 外文期刊

第一作者： Zhou, Yang

作者： Zhou, Yang;Chen, Hong;Zhou, Yang;Bickhart, Derek M.;Schroeder, Steven G.;Connor, Erin E.;Van Tassell, Curtis P.;Liu, George E.;Xu, Lingyang;Hay, El Hamidi abdel;Alexander, Leeson J.;Sonstegard, Tad S.

作者机构：

关键词： Cattle genome;Somatic tissue;DNA methylation;RRBS (reduced representation bisulphite sequencing)

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2016 年 17 卷

页码：

收录情况： SCI

摘要： Background: As a major epigenetic component, DNA methylation plays important functions in individual development and various diseases. DNA methylation has been well studied in human and model organisms, but only limited data exist in economically important animals like cattle. Results: Using reduced representation bisulphite sequencing (RRBS), we obtained single-base-resolution maps of bovine DNA methylation from ten somatic tissues. In total, we evaluated 1,868,049 cytosines in CG-enriched regions. While we found slightly low methylation levels (29.87 to 38.06 %) in cattle, the methylation contexts (CGs and non-CGs) of cattle showed similar methylation patterns to other species. Non-CG methylation was detected but methylation levels in somatic tissues were significantly lower than in pluripotent cells. To study the potential function of the methylation, we detected 10,794 differentially methylated cytosines (DMCs) and 836 differentially methylated CG islands (DMIs). Further analyses in the same tissues revealed many DMCs (including non-CGs) and DMIs, which were highly correlated with the expression of genes involved in tissue development. Conclusions: In summary, our study provides a baseline dataset and essential information for DNA methylation profiles of cattle.

分类号：

  • 相关文献

[1]Systematic Profiling of Short Tandem Repeats in the Cattle Genome. Xu, Lingyang,Li, Junya,Xu, Lingyang,Zhou, Yang,Bickhart, Derek M.,Sonstegard, Tad S.,Van Tassell, Curtis P.,Liu, George E.,Xu, Lingyang,Song, Jiuzhou,Haasl, Ryan J.,Sun, Jiajie,Zhou, Yang,Sonstegard, Tad S.,Lewin, Harris A.. 2017

[2]Rapid alterations of gene expression and cytosine methylation in newly synthesized Brassica napus allopolyploids. Xu, Yanhao,Zhong, Lan,Wang, Jianbo,Wu, Xiaoming,Fang, Xiaoping.

[3]Widespread and evolutionary analysis of a MITE family Monkey King in Brassicaceae. Dai, Shutao,Hou, Jinna,Long, Yan,Wang, Jing,Li, Cong,Xiao, Qinqin,Jiang, Xiaoxue,Zou, Xiaoxiao,Zou, Jun,Meng, Jinling,Hou, Jinna. 2015

[4]Genome-wide high-resolution mapping of DNA methylation identifies epigenetic variation across embryo and endosperm in Maize (Zea may). Wang, Pengfei,Ma, Chuanxi,Wang, Pengfei,Xia, Han,Zhang, Ye,Zhao, Shuzhen,Zhao, Chuanzhi,Hou, Lei,Li, Changsheng,Li, Aiqin,Wang, Xingjun. 2015

[5]Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity. Qi, Yueying,Xu, Wenjing,Xing, Tian,Zhao, Mingming,Yan, Li,Xia, Guangmin,Wang, Mengcheng,Li, Nana. 2015

[6]Alteration of the DNA methylation status of donor cells impairs the developmental competence of porcine cloned embryos. Huan, Yan Jun,Zhu, Jiang,Xie, Bing Teng,Wang, Jian Yu,Li, Jing Yu,Xue, Bing Hua,Kong, Qing Ran,Liu, Zhong Hua,Huan, Yan Jun,Wu, Zhan Feng,Zhang, Ji Guang.

[7]Study on DNA Cytosine Methylation of Cotton (Gossypium hirsutum L.) Genome and Its Implication for Salt Tolerance. ZHAO Yun-lei,YU Shu-xun,YE Wu-wei,WANG Hong-mei,WANG Jun-juan,FANG Bao-xing. 2010

[8]Induced Pib Expression and Resistance to Magnaporthe grisea are Compromised by Cytosine Demethylation at Critical Promoter Regions in Rice. Li, Yuan,Xia, Qiong,Wu, Ying,Xu, Chunming,Liu, Bao,Li, Yuan,Xia, Qiong,Wu, Ying,Xu, Chunming,Liu, Bao,Kou, Hongping,Wang, Dan,Lin, Xiuyun,Xing, Shaochen. 2011

[9]Effect of different light quality on DNA methylation variation for brown cotton (Gossypium hirstum). Li, Tingchun,Fan, Honghong,Li, Zhengpeng,Wei, Jun,Cai, Yongping,Lin, Yi,Li, Tingchun. 2011

[10]Laser Irradiation-Induced DNA Methylation Changes Are Heritable and Accompanied with Transpositional Activation of mPing in Rice. Li, Siyuan,Xia, Qiong,Yu, Xiaoming,Gao, Xiang,Liu, Bao,Li, Siyuan,Wang, Fang,Ma, Jian,Kou, Hongping,Lin, Xiuyun. 2017

[11]Performances of Different Fragment Sizes for Reduced Representation Bisulfite Sequencing in Pigs. Yuan, Xiao-Long,Zhang, Zhe,Pan, Rong-Yang,Gao, Ning,Deng, Xi,Li, Bin,Zhang, Hao,Li, Jia-Qi,Yuan, Xiao-Long,Sangild, Per Torp,Gao, Ning. 2017

[12]Molecular characterizations of DNA methyltransferase 3 and its roles in temperature tolerance in the whitefly, Bemisia tabaci Mediterranean. Hong, X. -Y.,Dai, T. -M,Lu, Z. -C.,Wang, Y. -S.,Liu, W. -X.,Wan, F. -H.,Wan, F. -H.. 2018

[13]Promoter methylation negatively correlated with mRNA expression but not tissue differential expression after heat stress. Gan, J. K.,Zhang, D. X.,Zhang, X. Q.,Chen, Z. Y.,Luo, Q. B.,Gan, J. K.,Zhang, D. X.,He, D. L.,Zhang, X. Q.,Chen, Z. Y.,Luo, Q. B.,He, D. L.. 2013

[14]Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice. Wang, Ningning,Zhang, Di,Wang, Zhenhui,Xun, Hongwei,Wang, Hui,Huang, Wei,Liu, Ying,Li, Ning,Ou, Xiufang,Zhang, Chunyu,Liu, Bao,Wang, Ningning,Ma, Jian,Lin, Xiuyun,Zhang, Chunyu,Wang, Ningning,Wang, Ming-Bo. 2014

[15]A Comparative Analysis of DNA Methylation in Diploid and Tetraploid Apple (Malus x domestica Borkh.). He, Ping,Cheng, Lailiang,Li, Huifeng,Wang, Haibo,Li, Linguang. 2017

[16]Comparative analysis of DNA methylation changes in two rice genotypes under salt stress and subsequent recovery. Wang, Wensheng,Huang, Fei,Qin, Qiao,Zhao, Xiuqin,Li, Zhikang,Fu, Binying,Li, Zhikang,Fu, Binying.

[17]Expression and methylation of microsomal triglyceride transfer protein and acetyl-CoA carboxylase are associated with fatty liver syndrome in chicken. Liu, Zhen,Li, Qinghe,Liu, Ranran,Zhao, Guiping,Zhang, Yonghong,Zheng, Maiqing,Cui, Huanxian,Li, Peng,Cui, Xiaoyan,Liu, Jie,Wen, Jie,Liu, Zhen,Li, Qinghe,Liu, Ranran,Zhao, Guiping,Zheng, Maiqing,Cui, Huanxian,Li, Peng,Cui, Xiaoyan,Liu, Jie,Wen, Jie,Zhang, Yonghong.

[18]Polymorphisms and DNA methylation level in the CpG site of the GHR1 gene associated with mRNA expression, growth traits and hormone level of half-smooth tongue sole (Cynoglossus semilaevis). Zhao, J. L.,Si, Y. F.,He, F.,Wen, H. S.,Li, J. F.,Ren, Y. Y.,Zhao, M. L.,Huang, Z. J.,Zhao, J. L.,Si, Y. F.,He, F.,Wen, H. S.,Li, J. F.,Ren, Y. Y.,Zhao, M. L.,Huang, Z. J.,Chen, S. L..

[19]The Demethylating Agent 5-Aza-2 '-Deoxycytidine (5-AZA-CdR) Inhibits The Development of Preimplantation Mouse Embryos. Yu Jian-Ning,Li Shao-Hua,Wang Dan-Qiu,Wang Meng,Lin Fen,Liu Hong-Lin,Yu Jian-Ning. 2009

[20]DNA methylation pattern of Photoperiod-B1 is associated with photoperiod insensitivity in wheat (Triticum aestivum). Sun, Han,Guo, Zhiai,Gao, Lifeng,Zhao, Guangyao,Zhang, Wenping,Zhou, Ronghua,Wu, Yongzhen,Jia, Jizeng,Sun, Han,An, Hailong,Wang, Haiyang.

作者其他论文 更多>>

微信小程序