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现代技术在全基因组范围内绘制 DNA 中胞嘧啶修饰图谱的综合研究。

Compilation of Modern Technologies To Map Genome-Wide Cytosine Modifications in DNA.

机构信息

State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Department of Chemical Biology and, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering and, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China.

出版信息

Chembiochem. 2019 Aug 1;20(15):1898-1905. doi: 10.1002/cbic.201900035. Epub 2019 May 22.

DOI:10.1002/cbic.201900035
PMID:30809902
Abstract

Over the past few decades, various DNA modification detection methods have been developed; many of the high-resolution methods are based on bisulfite treatment, which leads to DNA degradation, to a degree. Thus, novel bisulfite-free approaches have been developed in recent years and shown to be useful for epigenome analysis in otherwise difficult-to-handle, but important, DNA samples, such as hmC-seal and hmC-CATCH. Herein, an overview of advances in the development of epigenome sequencing methods for these important DNA modifications is provided.

摘要

在过去的几十年中,已经开发出了各种 DNA 修饰检测方法;许多高分辨率方法都是基于亚硫酸氢盐处理的,这会在一定程度上导致 DNA 降解。因此,近年来开发了新型的无亚硫酸盐方法,并且已被证明对于其他难以处理但重要的 DNA 样本中的表观基因组分析很有用,例如 hmC-seal 和 hmC-CATCH。本文提供了这些重要 DNA 修饰的表观基因组测序方法的开发进展概述。

相似文献

1
Compilation of Modern Technologies To Map Genome-Wide Cytosine Modifications in DNA.现代技术在全基因组范围内绘制 DNA 中胞嘧啶修饰图谱的综合研究。
Chembiochem. 2019 Aug 1;20(15):1898-1905. doi: 10.1002/cbic.201900035. Epub 2019 May 22.
2
Targeting of the activation-induced cytosine deaminase is strongly influenced by the sequence and structure of the targeted DNA.活化诱导胞嘧啶脱氨酶的靶向作用受到靶向DNA的序列和结构的强烈影响。
Mol Cell Biol. 2005 Dec;25(24):10815-21. doi: 10.1128/MCB.25.24.10815-10821.2005.
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Evaluation of molecular models for the affinity maturation of antibodies: roles of cytosine deamination by AID and DNA repair.抗体亲和力成熟的分子模型评估:AID介导的胞嘧啶脱氨基作用和DNA修复的作用
Chem Rev. 2006 Feb;106(2):700-19. doi: 10.1021/cr040496t.
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Discovery of cytosine deaminases enables base-resolution methylome mapping using a single enzyme.胞嘧啶脱氨酶的发现使得利用单一酶进行碱基分辨率甲基化组图谱绘制成为可能。
Mol Cell. 2024 Mar 7;84(5):854-866.e7. doi: 10.1016/j.molcel.2024.01.027. Epub 2024 Feb 22.
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Dancin' deaminase.舞蹈脱氨酶。 (不过从专业医学角度看,这个表述可能不太准确规范,正常医学中有“腺苷脱氨酶”英文是“Adenosine deaminase” )
Nat Struct Mol Biol. 2006 May;13(5):380-1. doi: 10.1038/nsmb0506-380.
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Microsoft Word macro for analysis of cytosine methylation by the bisulfite deamination reaction.用于通过亚硫酸氢盐脱氨反应分析胞嘧啶甲基化的Microsoft Word宏。
Biotechniques. 2001 Jan;30(1):116-20. doi: 10.2144/01301bc02.
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Bisulfite genomic sequencing: systematic investigation of critical experimental parameters.亚硫酸氢盐基因组测序:关键实验参数的系统研究
Nucleic Acids Res. 2001 Jul 1;29(13):E65-5. doi: 10.1093/nar/29.13.e65.
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Introduction to epigenomics and epigenome-wide analysis.表观基因组学与全表观基因组分析简介。
Methods Mol Biol. 2010;620:243-65. doi: 10.1007/978-1-60761-580-4_7.
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Studying the epigenome using next generation sequencing.使用下一代测序技术研究表观基因组。
J Med Genet. 2011 Nov;48(11):721-30. doi: 10.1136/jmedgenet-2011-100242. Epub 2011 Aug 8.
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Single-base resolution analysis of DNA epigenome via high-throughput sequencing.高通量测序技术进行 DNA 表观基因组的单碱基分辨率分析。
Sci China Life Sci. 2016 Mar;59(3):219-26. doi: 10.1007/s11427-016-5013-x. Epub 2016 Jan 29.

引用本文的文献

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Quantification and mapping of DNA modifications.DNA修饰的定量与定位
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2
Advances in single-cell multi-omics profiling.单细胞多组学分析技术的进展。
RSC Chem Biol. 2021 Jan 20;2(2):441-449. doi: 10.1039/d0cb00163e. eCollection 2021 Apr 1.
3
Tissue-specific 5-hydroxymethylcytosine landscape of the human genome.人类基因组组织特异性 5-羟甲基胞嘧啶图谱。
Nat Commun. 2021 Jul 12;12(1):4249. doi: 10.1038/s41467-021-24425-w.
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Epigenetic Analysis through MSAP-NGS Coupled Technology: The Case Study of White Poplar Monoclonal Populations/Stands.通过 MSAP-NGS 联合技术进行表观遗传学分析:以白杨单克隆种群/林分为例。
Int J Mol Sci. 2020 Oct 7;21(19):7393. doi: 10.3390/ijms21197393.
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A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT sequencing.通过甲基敏感 DArT 测序进行经济有效的 DNA 甲基化检测方法。
PLoS One. 2020 Jun 4;15(6):e0233800. doi: 10.1371/journal.pone.0233800. eCollection 2020.