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TAB-seq and ACE-seq Data Processing for Genome-Wide DNA hydroxymethylation Profiling


5-Methylcytosine (5mC) is one of the most abundant and well-studied chemical DNA modifications of vertebrate genomes. 5mC plays an essential role in genome regulation including: silencing of retroelements, X chromosome inactivation, and heterochromatin stability. Furthermore, 5mC shapes the activity of cis-regulatory elements crucial for cell fate determination. TET enzymes can oxidize 5mC to form 5-hydroxymethylcytosine (5hmC), thereby adding an additional layer of complexity to the DNA methylation landscape dynamics. The advent of techniques enabling genome-wide 5hmC profiling provided critical insights into its genomic distribution, scope, and function. These methods include immunoprecipitation, chemical labeling and capture-based approaches, as well as single-nucleotide 5hmC profiling techniques such as TET-assisted bisulfite sequencing (TAB-seq) and APOBEC-coupled epigenetic sequencing (ACE-seq). Here we provide a detailed protocol for computational analysis required for the genomic alignment of TAB-seq and ACE-seq data, 5hmC calling, and statistical analysis.

Type Book section
ISBN 1940-6029 (Electronic) 1064-3745 (Linking)
Authors Skvortsova, K.; Bogdanovic, O.
Responsible Garvan Author A/Prof Ozren Bogdanovic
Publisher Name Methods in Molecular Biology
Published Date 2021-05-31
Published Volume 2272
Published Pages 163-178
Status Published in-print
DOI 10.1007/978-1-0716-1294-1_9
URL link to publisher's version