Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing

• Type of Material: Article
• Authors: Liang Zhang, University of Chicago; Keith E. Szulwach, Emory University; Gary C. Hon, University of California San Diego; Chun-Xiao Song, University of Chicago; Beomseok Park, University of Illinois; Miao Yu, University of Chicago; Xingyu Lu, University of Chicago; Qing Dai, University of Chicago; Xiao Wang, University of Chicago; Craig R. Street, Emory University; Huiping Tan, Emory University; Jung-Hyun Min, University of Illinois; Bing Ren, University of California San Diego; Peng Jin, Emory University; Chuan He, University of Chicago
• Language: English
• Date: 2013-02-01
• Publisher: Nature Publishing Group
• Publication Version: Final Published Version
• Copyright Statement: © 2013 Macmillan Publishers Limited. All rights reserved.
• Final Published Version (URL): http://dx.doi.org/10.1038/ncomms2527
• Title of Journal or Parent Work: Nature Communications
• ISSN: 2041-1723
• Volume: 4
• Start Page: 1517
• End Page: 1517
• Grant/Funding Information: This study was supported by National Institutes of Health (GM071440 to C.H., NS051630 and MH076090 to P.J., U01 ES017166 to B.R.), a Catalyst Award (C.H. and J.-H.M.) from the Chicago Biomedical Consortium, with support from the Searle Funds at The Chicago Community Trust, the Ludwig Institute for Cancer Research (B.R.) and the Emory Genetics Discovery Fund (P.J.).
• Keywords: 5-FORMYLCYTOSINE; SINGLE-BASE RESOLUTION; 5-HYDROXYMETHYLCYTOSINE; BREAST-CANCER; METHYLOME; DNA IMMUNOPRECIPITATION MEDIP; Science & Technology - Other Topics; 5-CARBOXYLCYTOSINE; Science & Technology; CELLS; METHYLATION; MAMMALIAN DNA; Multidisciplinary Sciences
• Research Categories: Biology, Genetics; Chemistry, General

Abstract

5-methylcytosine is an epigenetic mark that affects a broad range of biological functions in mammals. The chemically inert methyl group prevents direct labelling for subsequent affinity purification and detection. Therefore, most current approaches for the analysis of 5-methylcytosine still have limitations of being either density-biased, lacking in robustness and consistency, or incapable of analysing 5-methylcytosine specifically. Here we present an approach, TAmC-Seq, which selectively tags 5-methylcytosine with an azide functionality that can be further labelled with a biotin for affinity purification, detection and genome-wide mapping. Using this covalent labelling approach, we demonstrate high sensitivity and specificity for known methylated loci, as well as increased CpG dinucleotide coverage at lower sequencing depth as compared with antibody-based enrichment, providing an improved efficiency in the 5-methylcytosine enrichment and genome-wide profiling. © 2013 Macmillan Publishers Limited.