下一代测序技术在表观遗传学研究中的重要应用及进展

doi:10.3724/SP.J.1005.2014.0256

[an error occurred while processing this directive]

HEREDITAS ›› 2014, Vol. 36 ›› Issue (3): 256-275.doi: 10.3724/SP.J.1005.2014.0256

Previous Articles Next Articles

The application of next generation sequencing on epigenetic study

Sheng Shen, Yanchun Qu, Jun Zhang

COE for Neuroscience, Texas Tech University Health Sciences Center, El Paso, Texas 79905, USA

Received:2013-10-16 Revised:2013-12-07 Online:2014-03-20 Published:2014-02-25

Abstract

Abstract:

The application of next generation sequencing (NGS) technique has a great impact on epigenetic studies. Coupled with NGS, a number of sequencing-based methodologies have been developed and applied in epigenetic studies, such as Whole Genome Bisulfite Sequencing (WGBS), Reduced Representation Bisulfite Sequencing (RRBS), Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq), Chromatin Immunoprecipitation-Sequencing (ChIP-seq), TAB-seq (Tet-assisted Bisulfite Sequencing), Chromosome Conformation Capture Sequencing (3C-seq) and various of 3C-seq de-rivatives, DNaseⅠ-seq/MNase-seq/FAIRE-seqand RNA Sequencing (RNA-seq). These new techniques were used to iden-tify DNA methylation patterns and a broad range of protein/nucleic acid interactions, and to analyze chromatin conforma-tion.With these new technologies, researchers have gained a broader view and better tools to investigate the distributions and dynamic changes of epigenetic markers affected by both internal and external factors. The principles and characteristics of major applications of NGS technologies on epigenetics were summarized; and the recent advances and the future direc-tions in NGS-based epigenetic studies were further discussed.

Key words: next generation sequencing, epigenetics, DNA methylation, histone modifications, chromosome con-formation capture

Sheng Shen, Yanchun Qu, Jun Zhang. The application of next generation sequencing on epigenetic study[J]. HEREDITAS, 2014, 36(3): 256-275.

References

[1] Waddington CH. The epigenotype. 1942. Int J Epidemiol, 2012, 41(1): 10–13. <\p>

[2] Jaenisch R, Bird A. Epigenetic regulation of gene expres-sion: how the genome integrates intrinsic and environ-mental signals. Nat Genet, 2003, 33(Suppl.): 245–254. <\p>

[3] Bird A. Perceptions of epigenetics. Nature, 2007, 447 (7143): 396–398. <\p>

[4] Ziller MJ, Gu HC, Muller F, Donaghey J, Tsai LTY, Kohlbacher O, De Jager PL, Rosen ED, Bennett DA, Bernstein BE, Gnirke A, Meissner A. Charting a dynamic DNA methylation landscape of the human genome. Nature, 2013, 500(7463): 477–481. <\p>

[5] Fu BS, Wang HW, Wang JH, Barouhas I, Liu WQ, Shuboy A, Bushinsky DA, Zhou DS, Favus MJ. Epigenetic regu-lation of BMP2 by 1, 25-dihydroxyvitamin D3 through DNA methylation and histone modification. PLoS ONE, 2013, 8(4): e61423. <\p>

[6] Martinowich K, Hattori D, Wu H, Fouse S, He F, Hu Y, Fan GP, Sun YE. DNA methylation-related chromatin re-modeling in activity-dependent Bdnf gene regulation. Sci-ence, 2003, 302(5646): 890–893. <\p>

[7] Cruickshanks HA, Vafadar-Isfahani N, Dunican DS, Lee A, Sproul D, Lund JN, Meehan RR, Tufarelli C. Expression of a large LINE-1-driven antisense RNA is linked to epi-genetic silencing of the metastasis suppressor gene TFPI-2 in cancer. Nucleic Acids Res, 2013, 41(14): 6857–6869. <\p>

[8] Andolfo I, Liguori L, De Antonellis P, Cusanelli E, Mari-naro F, Pistollato F, Garzia L, De Vita G, Petrosino G, Ac-cordi B, Migliorati R, Basso G, Iolascon A, Cinalli G, Zollo M. The micro-RNA 199b-5p regulatory circuit in-volves Hes1, CD15, and epigenetic modifications in me-dulloblastoma. Neuro Oncol, 2012, 14(5): 596–612. <\p>

[9] Bastet L, Dubé A, Massé E, Lafontaine DA. New insights into riboswitch regulation mechanisms. Mol Microbiol, 2011, 80(5): 1148–1154. <\p>

[10] Voelkerding KV, Dames SA, Durtschi JD. Next-generation sequencing: from basic research to diagnostics. Clin Chem, 2009, 55(4): 641–658. <\p>

[11] Mardis ER. A decade's perspective on DNA sequencing technology. Nature, 2011, 470(7333): 198–203. <\p>

[12] Metzker ML. Sequencing technologies - the next genera-tion. Nat Rev Genet, 2010, 11(1): 31–46. <\p>

[13] Taylor KH, Kramer RS, Davis JW, Guo JY, Duff DJ, Xu D, Caldwell CW, Shi HD. Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res, 2007, 67(18): 8511–8518. <\p>

[14] Barski A, Cuddapah S, Cui KR, Roh TY, Schones DE, Wang ZB, Wei G, Chepelev I, Zhao KJ. High-resolution profiling of histone methylations in the human genome. Cell, 2007, 129(4): 823–837. <\p>

[15] Mikkelsen TS, Ku MC, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie XH, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature, 2007, 448(7153): 553–560. <\p>

[16] Hurd PJ, Nelson CJ. Advantages of next-generation se-quencing versus the microarray in epigenetic research. Brief Funct Genomic Proteomic, 2009, 8(3): 174–183. <\p>

[17] Feinberg AP, Gehrke CW, Kuo KC, Ehrlich M. Reduced genomic 5-methylcytosine content in human colonic neo-plasia. Cancer Res, 1988, 48(5): 1159–1161. <\p>

[18] Ogino S, Nosho K, Kirkner GJ, Kawasaki T, Chan AT, Schernhammer ES, Giovannucci EL, Fuchs CS. A cohort study of tumoral LINE-1 hypomethylation and prognosis in colon cancer. J Natl Cancer Inst, 2008, 100(23): 1734–1738. <\p>

[19] He XJ, Chen TP, Zhu JK. Regulation and function of DNA methylation in plants and animals. Cell Res, 2011, 21(3): 442&n

Metrics

Comments

www.chinagene.cn
备案号：京ICP备09063187号

The application of next generation sequencing on epigenetic study

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	Daiyuan Liu, Zhaohui Zhang, Xianjiang Kang. Research progress on the effect of sperm chromatin integrity on function and its detection methods [J]. Hereditas(Beijing), 2024, 46(7): 511-529.
[2]	Yuan Shen, Jintao Li, Miao Yin, Qunying Lei. The roles of branched-chain amino acids metabolism in tumorigenesis and progression [J]. Hereditas(Beijing), 2024, 46(6): 438-451.
[3]	Wei Han, Qingzhen Zhang, Jing Yang, Zhe Zhou. A DNA typing panel of 201 genetic markers for degraded samples: development and validation [J]. Hereditas(Beijing), 2024, 46(4): 306-318.
[4]	Mengnan Cui, Yan Guo, Yarong Wu, Guangqian Pei, Yujun Cui. Progress on the quality control technology of next generation sequencing library [J]. Hereditas(Beijing), 2024, 46(2): 140-148.
[5]	Yanni Wang, Jia Li. Processing pipelines and analytical methods for single-cell DNA methylation sequencing data [J]. Hereditas(Beijing), 2024, 46(10): 807-819.
[6]	Jiahao Wang, Qingyao Zhao, Yueling Zhou, Liangyu Shi, Chuduan Wang, Ying Yu. Application and prospect of gene chip in genetic breeding of livestock and poultry [J]. Hereditas(Beijing), 2023, 45(12): 1114-1127.
[7]	Xiufang Ou, Ying Wu, Ning Li, Lili Jiang, Bao Liu, Lei Gong. Epigenetics comprehensive experimental course based on the integration of science and education to cultivate students' ability of cutting-edge innovation [J]. Hereditas(Beijing), 2023, 45(12): 1158-1168.
[8]	Mengxuan Xu, Ming Zhou. Advances of RNA polymerase IV in controlling DNA methylation and development in plants [J]. Hereditas(Beijing), 2022, 44(7): 567-580.
[9]	Wang Ya'nan, Tao Xu, Wanpeng Wang, Qingzhu Zhang, Xie Li'nan. Role of epigenetic modifications in the development of crops essential traits [J]. Hereditas(Beijing), 2021, 43(9): 858-879.
[10]	Tianyi Wang, Yingxiang Wang, Chenjiang You. Structural and functional characteristics of plant PHD domain-containing proteins [J]. Hereditas(Beijing), 2021, 43(4): 323-339.
[11]	Xiangqian Zhang, Nan Li, Xinming Xie. Design and exploration of epigenetic comprehensive experiments [J]. Hereditas(Beijing), 2021, 43(12): 1179-1187.
[12]	Xinyue Wang, Liang Li, Qiuhui Duan, Dali Li, Jinlian Chen. Effect of Uhrf1 on intestinal development [J]. Hereditas(Beijing), 2021, 43(1): 84-93.
[13]	Yingchu Hu, Haochang Hu, Shaoyi Lin, Xiaomin Chen. The role of DNA hydroxymethylation in the regulation of atherosclerosis [J]. Hereditas(Beijing), 2020, 42(7): 632-640.
[14]	Zhichao Mei, Zhujun Wei, Jiahui Yu, Fengdan Ji, Linan Xie. Multi-omics association analysis revealed the role and mechanism of epialleles in environmental adaptive evolution of Arabidopsis thaliana [J]. Hereditas(Beijing), 2020, 42(3): 321-331.
[15]	Hengzhen Cui, Mizhu Sun, Runzhi Wang, Chenyu Li, Yuxuan Huang, Qiuju Huang, Xiaomeng Qiao. DNA methylation in the medial prefrontal cortex regulates alcohol-related behavior in rats [J]. Hereditas(Beijing), 2020, 42(1): 112-125.