Methods for analysis of specific DNA methylation status.

Fecha de publicación: 05/07/2020 Fecha Ahead of Print: 05/07/2020

Autores de IIS La Fe

Participantes ajenos a IIS La Fe

Pajares MJ
Urtasun R

Grupos

Unidad de Biomarcadores y Medicina de Precisión (UBYMP)

Leader

Agustín Lahoz Rodríguez

Abstract

Methylation of CpG dinucleotides plays a crucial role in the regulation of gene expression and therefore in the development of different pathologies. Aberrant methylation has been associated to the majority of the diseases, including cancer, neurodegenerative, cardiovascular and autoimmune disorders. Analysis of DNA methylation patterns is crucial to understand the underlying molecular mechanism of these diseases. Moreover, DNA methylation patterns could be used as biomarker for clinical management, such as diagnosis, prognosis and treatment response. Nowadays, a variety of high throughput methods for DNA methylation have been developed to analyze the methylation status of a high number of CpGs at once or even the whole genome. However, identification of specific methylation patterns at specific loci is essential for validation and also as a tool for diagnosis. In this review, we describe the most commonly used approaches to evaluate specific DNA methylation. There are three main groups of techniques that allow the identification of specific regions that are differentially methylated: bisulfite conversion-based methods, restriction enzyme-based approaches, and affinity enrichment-based assays. In the first group, specific restriction enzymes recognize and cleave unmethylated DNA, leaving methylated sequences intact. Bisulfite conversion methods are the most popular approach to distinguish methylated and unmethylated DNA. Unmethylated cytosines are deaminated to uracil by sodium bisulfite treatment, while the methyl cytosines remain unconverted. In the last group, proteins with methylation binding domains or antibodies against methyl cytosines are used to recognize methylated DNA. In this review, we provide the theoretical basis and the framework of each technique as well as the analysis of their strength and the weaknesses.

Datos de la publicación

ISSN/ISSNe:: 1046-2023, 1095-9130
Tipo:: Article
Páginas:: 3-12
DOI:: 10.1016/j.ymeth.2020.06.021
Factor de Impacto:: 2,080 SCImago ℠
Cuartil:: Q1 SCImago ℠

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Filiaciones

Pajares MJ:: Biochemistry Area, Department of Health Science, Public University of Navarre, 31008 Pamplona, Spain

IDISNA Navarra's Health Research Institute, 31008 Pamplona, Spain
Palanca-Ballester C:: Instituto de Investigación. Biomarkers and Precision Medicine Unit, Health Research Institute la Fe, 46026 Valencia, Spain
Urtasun R:: Biochemistry Area, Department of Health Science, Public University of Navarre, 31008 Pamplona, Spain
Alemany-Cosme E:: Instituto de Investigación. Biomarkers and Precision Medicine Unit, Health Research Institute la Fe, 46026 Valencia, Spain
Lahoz A:: Instituto de Investigación. Biomarkers and Precision Medicine Unit, Health Research Institute la Fe, 46026 Valencia, Spain
Sandoval J:: Instituto de Investigación. Biomarkers and Precision Medicine Unit, Health Research Institute la Fe, 46026 Valencia, Spain

Instituto de Investigación. Epigenomics Core Facility, Health Research Institute la Fe, 46026 Valencia, Spain