DNA甲基化和羟甲基化比例的生物信息学评估

Bioinformatic Estimation of DNA Methylation and Hydroxymethylation Proportions.

作者信息

Kiihl Samara Flamini

机构信息

Department of Statistics, State University of Campinas, Campinas, SP, Brazil.

出版信息

Methods Mol Biol. 2021;2272:141-162. doi: 10.1007/978-1-0716-1294-1_8.

DOI:10.1007/978-1-0716-1294-1_8

PMID:34009612

Abstract

Simultaneous measurement of 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) at the single-nucleotide level can be obtained by combining data from DNA processing methods including traditional bisulfite (BS), oxidative bisulfite (oxBS), or Tet-assisted (TAB) bisulfite conversion. Array-based technologies have been widely used in this task, due to their time and cost efficiency. For methylation studies using BS data, many protocols and related packages have been suggested in the literature to deal with limitations and confounders that arise from array data. In this chapter, we illustrate how the reader can make small adjustments to these protocols to obtain estimates of methylation and hydroxymethylation proportions.

摘要

通过整合来自包括传统亚硫酸氢盐（BS）、氧化亚硫酸氢盐（oxBS）或四氢叶酸辅助（TAB）亚硫酸氢盐转化等DNA处理方法的数据，能够在单核苷酸水平上同时测量5-甲基胞嘧啶（5-mC）和5-羟甲基胞嘧啶（5-hmC）。基于芯片的技术因其时间和成本效率，已在这项任务中得到广泛应用。对于使用BS数据的甲基化研究，文献中已提出许多方案和相关软件包，以处理芯片数据中出现的局限性和混杂因素。在本章中，我们将说明读者如何对这些方案进行小的调整，以获得甲基化和羟甲基化比例的估计值。