Genome-wide CpG density and DNA methylation analysis method (MeDIP, RRBS, and WGBS) comparisons.
Genome-wide CpG density and DNA methylation analysis method (MeDIP, RRBS, and WGBS) comparisons.
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DOI：
10.1080/15592294.2021.1924970
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发表时间：
2022-05
期刊：
影响因子：
3.7
通讯作者：
Skinner, Michael K.
中科院分区：
文献类型：
--
作者：
Beck, Daniel;Ben Maamar, Millissia;Skinner, Michael K.
全基因组 DNA 甲基化分析是用于基因组表征和差异 DNA 甲基化评估的最常见表观遗传过程之一。先前的全基因组分析表明 DNA 甲基化方法中的一个重要变量涉及 CpG 密度。当前的研究旨在研究各种不同物种基因组中的 CpG 密度，并将其与各种 DNA 甲基化分析数据集相关联。大多数基因组的>90%的基因组属于低密度1-3 CpG/100 bp类别，而<10%的基因组属于较高密度>5 CpG/100 bp类别。对人类、大鼠、鸟类和鱼类基因组也观察到了类似的结果。甲基化 DNA 免疫沉淀 (MeDIP) 程序使用抗 5-甲基胞嘧啶抗体免疫沉淀，然后进行新一代测序 (MeDIP-Seq)。 MeDIP 程序偏向于 <5 CpG/100 bp 的较低 CpG 密度，这对应于 >95% 的基因组。简化代表性亚硫酸氢盐 (RRBS) 方案通常在 ≥3 CpG/100 bp 的较高 CpG 密度区域中识别 DMR，该区域对应于大约 20% 的基因组。全基因组亚硫酸氢盐 (WGBS) 分析得出较高的 CpG 密度，通常大于 10 CpG/100bp。 WGBS 通常识别 ≥2 CpG/100bp，相当于基因组的大约 50%。讨论了每种方法的局限性和潜在的优化方法。没有一种程序可以提供对基因组的完整全基因组评估，但 MeDIP-Seq 提供了最高百分比的覆盖率。观察结果表明，CpG 密度是 DNA 甲基化分析中的一个关键变量，不同的分子技术侧重于不同的基因组区域。
Genome-wide DNA methylation analysis is one of the most common epigenetic processes analysed for genome characterization and differential DNA methylation assessment. Previous genome-wide analysis has suggested an important variable in DNA methylation methods involves CpG density. The current study was designed to investigate the CpG density in a variety of different species genomes and correlate this to various DNA methylation analysis data sets. The majority of all genomes had >90% of the genome in the low density 1–3 CpG/100 bp category, while <10% of the genome was in the higher density >5 CpG/100 bp category. Similar observations with human, rat, bird, and fish genomes were observed. The methylated DNA immunoprecipitation (MeDIP) procedure uses the anti-5-methylcytosine antibody immunoprecipitation followed by next-generation sequencing (MeDIP-Seq). The MeDIP procedure is biased to lower CpG density of <5 CpG/100 bp, which corresponds to >95% of the genome. The reduced representation bisulphite (RRBS) protocol generally identifies DMRs in higher CpG density regions of ≥3 CpG/100 bp which corresponds to approximately 20% of the genome. The whole-genome bisulphite (WGBS) analyses resulted in higher CpG densities, often greater than 10 CpG/100bp. WGBS generally identifies ≥2 CpG/100bp, which corresponds to approximately 50% of the genome. Limitations and potential optimization approaches for each method are discussed. None of the procedures can provide complete genome-wide assessment of the genome, but MeDIP-Seq provides coverage of the highest percentage. Observations demonstrate that CpG density is a critical variable in DNA methylation analysis, and different molecular techniques focus on distinct genomic regions.
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影响因子：
16.6
作者：
Berthelot, Camille;Brunet, Frederic;Chalopin, Domitille;Juanchich, Amelie;Bernard, Maria;Noel, Benjamin;Bento, Pascal;Da Silva, Corinne;Labadie, Karine;Alberti, Adriana;Aury, Jean-Marc;Louis, Alexandra;Dehais, Patrice;Bardou, Philippe;Montfort, Jerome;Klopp, Christophe;Cabau, Cedric;Gaspin, Christine;Thorgaard, Gary H.;Boussaha, Mekki;Quillet, Edwige;Guyomard, Rene;Galiana, Delphine;Bobe, Julien;Volff, Jean-Nicolas;Genet, Carine;Wincker, Patrick;Jaillon, Olivier;Roest Crollius, Hugues;Guiguen, Yann
通讯作者：
Guiguen, Yann
影响因子：
12.3
作者：
Liu, Yibin;Cheng, Jingfei;Song, Chun-Xiao
通讯作者：
Song, Chun-Xiao
DOI：
10.1007/978-1-4939-6685-1_15
发表时间：
2017-01-01
期刊：
ORAL BIOLOGY: MOLECULAR TECHNIQUES AND APPLICATIONS, 2ND EDITION
影响因子：
--
作者：
Chatterjee, Aniruddha;Rodger, Euan J.;Stockwell, Peter A.
通讯作者：
Stockwell, Peter A.
影响因子：
46.9
作者：
通讯作者：
--
影响因子：
4.6
作者：
Ben Maamar M;Sadler-Riggleman I;Beck D;Skinner MK
通讯作者：
Skinner MK