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

Liang Zhang, Keith E. Szulwach, Gary C. Hon, Chun-Xiao Song, Beomseok Park, Miao Yu, Xingyu Lu, Qing Dai, Xiao Wang, Craig R. Street, Huiping Tan, Jung-Hyun Min, Bing Ren, Peng Jin and Chuan He ()
Additional contact information
Liang Zhang: University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
Keith E. Szulwach: Emory University School of Medicine, 615 Michael Street, Atlanta, Georgia 30322, USA
Gary C. Hon: Ludwig Institute for Cancer Research, UCSD, Moores Cancer Center, and Institute of Genome Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA
Chun-Xiao Song: University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
Beomseok Park: University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60606, USA
Miao Yu: University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
Xingyu Lu: University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
Qing Dai: University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
Xiao Wang: University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
Craig R. Street: Emory University School of Medicine, 615 Michael Street, Atlanta, Georgia 30322, USA
Huiping Tan: Emory University School of Medicine, 615 Michael Street, Atlanta, Georgia 30322, USA
Jung-Hyun Min: University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60606, USA
Bing Ren: Ludwig Institute for Cancer Research, UCSD, Moores Cancer Center, and Institute of Genome Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA
Peng Jin: Emory University School of Medicine, 615 Michael Street, Atlanta, Georgia 30322, USA
Chuan He: University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA

Nature Communications, 2013, vol. 4, issue 1, 1-10

Abstract: 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.

Date: 2013
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DOI: 10.1038/ncomms2527

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