非cpg甲基化分析的实验和计算方法。

IF 2.5 Q3 GENETICS & HEREDITY
Deepa Ramasamy, Arunagiri Kuha Deva Magendhra Rao, Thangarajan Rajkumar, Samson Mani
{"title":"非cpg甲基化分析的实验和计算方法。","authors":"Deepa Ramasamy,&nbsp;Arunagiri Kuha Deva Magendhra Rao,&nbsp;Thangarajan Rajkumar,&nbsp;Samson Mani","doi":"10.3390/epigenomes6030024","DOIUrl":null,"url":null,"abstract":"<p><p>Cytosine methylation adjacent to adenine, thymine, and cytosine residues but not guanine of the DNA is distinctively known as non-CpG methylation. This CA/CT/CC methylation accounts for 15% of the total cytosine methylation and varies among different cell and tissue types. The abundance of CpG methylation has largely concealed the role of non-CpG methylation. Limitations in the early detection methods could not distinguish CpG methylation from non-CpG methylation. Recent advancements in enrichment strategies and high throughput sequencing technologies have enabled the detection of non-CpG methylation. This review discusses the advanced experimental and computational approaches to detect and describe the genomic distribution and function of non-CpG methylation. We present different approaches such as enzyme-based and antibody-based enrichment, which, when coupled, can also improve the sensitivity and specificity of non-CpG detection. We also describe the current bioinformatics pipelines and their specific application in computing and visualizing the imbalance of CpG and non-CpG methylation. Enrichment modes and the computational suites need to be further developed to ease the challenges of understanding the functional role of non-CpG methylation.</p>","PeriodicalId":55768,"journal":{"name":"Epigenomes","volume":" ","pages":""},"PeriodicalIF":2.5000,"publicationDate":"2022-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9397002/pdf/","citationCount":"0","resultStr":"{\"title\":\"Experimental and Computational Approaches for Non-CpG Methylation Analysis.\",\"authors\":\"Deepa Ramasamy,&nbsp;Arunagiri Kuha Deva Magendhra Rao,&nbsp;Thangarajan Rajkumar,&nbsp;Samson Mani\",\"doi\":\"10.3390/epigenomes6030024\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Cytosine methylation adjacent to adenine, thymine, and cytosine residues but not guanine of the DNA is distinctively known as non-CpG methylation. This CA/CT/CC methylation accounts for 15% of the total cytosine methylation and varies among different cell and tissue types. The abundance of CpG methylation has largely concealed the role of non-CpG methylation. Limitations in the early detection methods could not distinguish CpG methylation from non-CpG methylation. Recent advancements in enrichment strategies and high throughput sequencing technologies have enabled the detection of non-CpG methylation. This review discusses the advanced experimental and computational approaches to detect and describe the genomic distribution and function of non-CpG methylation. We present different approaches such as enzyme-based and antibody-based enrichment, which, when coupled, can also improve the sensitivity and specificity of non-CpG detection. We also describe the current bioinformatics pipelines and their specific application in computing and visualizing the imbalance of CpG and non-CpG methylation. Enrichment modes and the computational suites need to be further developed to ease the challenges of understanding the functional role of non-CpG methylation.</p>\",\"PeriodicalId\":55768,\"journal\":{\"name\":\"Epigenomes\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":2.5000,\"publicationDate\":\"2022-08-16\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9397002/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Epigenomes\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.3390/epigenomes6030024\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Epigenomes","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.3390/epigenomes6030024","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0

摘要

与腺嘌呤、胸腺嘧啶和胞嘧啶残基相邻但不与鸟嘌呤相邻的胞嘧啶甲基化被称为非cpg甲基化。这种CA/CT/CC甲基化占总胞嘧啶甲基化的15%,并且在不同的细胞和组织类型中有所不同。大量的CpG甲基化在很大程度上掩盖了非CpG甲基化的作用。早期检测方法的局限性无法区分CpG甲基化和非CpG甲基化。富集策略和高通量测序技术的最新进展使非cpg甲基化检测成为可能。本文综述了检测和描述非cpg甲基化的基因组分布和功能的先进实验和计算方法。我们提出了不同的方法,如基于酶和基于抗体的富集,当它们耦合时,也可以提高非cpg检测的敏感性和特异性。我们还描述了当前的生物信息学管道及其在计算和可视化CpG和非CpG甲基化失衡方面的具体应用。富集模式和计算套件需要进一步开发,以缓解理解非cpg甲基化的功能作用的挑战。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Experimental and Computational Approaches for Non-CpG Methylation Analysis.

Experimental and Computational Approaches for Non-CpG Methylation Analysis.

Experimental and Computational Approaches for Non-CpG Methylation Analysis.

Cytosine methylation adjacent to adenine, thymine, and cytosine residues but not guanine of the DNA is distinctively known as non-CpG methylation. This CA/CT/CC methylation accounts for 15% of the total cytosine methylation and varies among different cell and tissue types. The abundance of CpG methylation has largely concealed the role of non-CpG methylation. Limitations in the early detection methods could not distinguish CpG methylation from non-CpG methylation. Recent advancements in enrichment strategies and high throughput sequencing technologies have enabled the detection of non-CpG methylation. This review discusses the advanced experimental and computational approaches to detect and describe the genomic distribution and function of non-CpG methylation. We present different approaches such as enzyme-based and antibody-based enrichment, which, when coupled, can also improve the sensitivity and specificity of non-CpG detection. We also describe the current bioinformatics pipelines and their specific application in computing and visualizing the imbalance of CpG and non-CpG methylation. Enrichment modes and the computational suites need to be further developed to ease the challenges of understanding the functional role of non-CpG methylation.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Epigenomes
Epigenomes GENETICS & HEREDITY-
CiteScore
3.80
自引率
0.00%
发文量
38
审稿时长
11 weeks
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信