Experimental and Computational Approaches for Non-CpG Methylation Analysis.

IF 4.6 Q2 MATERIALS SCIENCE, BIOMATERIALS
Deepa Ramasamy, Arunagiri Kuha Deva Magendhra Rao, Thangarajan Rajkumar, Samson Mani
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引用次数: 0

Abstract

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.

Abstract Image

Abstract Image

非cpg甲基化分析的实验和计算方法。
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。
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来源期刊
ACS Applied Bio Materials
ACS Applied Bio Materials Chemistry-Chemistry (all)
CiteScore
9.40
自引率
2.10%
发文量
464
期刊介绍: ACS Applied Bio Materials is an interdisciplinary journal publishing original research covering all aspects of biomaterials and biointerfaces including and beyond the traditional biosensing, biomedical and therapeutic applications. The journal is devoted to reports of new and original experimental and theoretical research of an applied nature that integrates knowledge in the areas of materials, engineering, physics, bioscience, and chemistry into important bio applications. The journal is specifically interested in work that addresses the relationship between structure and function and assesses the stability and degradation of materials under relevant environmental and biological conditions.
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