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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 methy...

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Autores principales: Ramasamy, Deepa, Rao, Arunagiri Kuha Deva Magendhra, Rajkumar, Thangarajan, Mani, Samson
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9397002/
https://www.ncbi.nlm.nih.gov/pubmed/35997370
http://dx.doi.org/10.3390/epigenomes6030024
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author Ramasamy, Deepa
Rao, Arunagiri Kuha Deva Magendhra
Rajkumar, Thangarajan
Mani, Samson
author_facet Ramasamy, Deepa
Rao, Arunagiri Kuha Deva Magendhra
Rajkumar, Thangarajan
Mani, Samson
author_sort Ramasamy, Deepa
collection PubMed
description 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.
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spelling pubmed-93970022022-08-24 Experimental and Computational Approaches for Non-CpG Methylation Analysis Ramasamy, Deepa Rao, Arunagiri Kuha Deva Magendhra Rajkumar, Thangarajan Mani, Samson Epigenomes Review 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. MDPI 2022-08-16 /pmc/articles/PMC9397002/ /pubmed/35997370 http://dx.doi.org/10.3390/epigenomes6030024 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Review
Ramasamy, Deepa
Rao, Arunagiri Kuha Deva Magendhra
Rajkumar, Thangarajan
Mani, Samson
Experimental and Computational Approaches for Non-CpG Methylation Analysis
title Experimental and Computational Approaches for Non-CpG Methylation Analysis
title_full Experimental and Computational Approaches for Non-CpG Methylation Analysis
title_fullStr Experimental and Computational Approaches for Non-CpG Methylation Analysis
title_full_unstemmed Experimental and Computational Approaches for Non-CpG Methylation Analysis
title_short Experimental and Computational Approaches for Non-CpG Methylation Analysis
title_sort experimental and computational approaches for non-cpg methylation analysis
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9397002/
https://www.ncbi.nlm.nih.gov/pubmed/35997370
http://dx.doi.org/10.3390/epigenomes6030024
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