Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine

By Chun-Xiao Song, Keith E. Szulwach, Ye Fu, Qing Dai, C. Yi, Xuekun Li, Yujing Li, Chih-Hsin Chen, Wen Zhang, Xing Jian and 9 more. Nature Biotechnology, 2010

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In contrast to 5-methylcytosine (5-mC), which has been studied extensively, little is known about 5-hydroxymethylcytosine (5-hmC), a recently identified epigenetic modification present in substantial amounts in certain mammalian cell types. Here we present a method for determining the genome-wide distribution of 5-hmC. We use the T4 bacteriophage β-glucosyltransferase to transfer an engineered glucose moiety containing an azide group onto the hydroxyl group of 5-hmC. The azide group can be chemically modified with biotin for detection, affinity enrichment and sequencing of 5-hmC–containing DNA fragments in mammalian genomes. Using this method, we demonstrate that 5-hmC is present in human cell lines beyond those previously recognized. We also find a gene expression level–dependent enrichment of intragenic 5-hmC in mouse cerebellum and an age-dependent acquisition of this modification in specific gene bodies linked to neurodegenerative disorders.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/51b13514e33d57bf81574f9d6c660c32da1b9c2d

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Citations in the corpus

DNA Demethylation Dynamics (2011, methodology): “5hmC is especially abundant in tissues such as brain and in pluripotent embryonic stem cells (ESCs), but it is also present at lower levels in blood, lung, kidney, and muscle (Globisch et al., 2010; Kriaucionis and Heintz, 2009; Ruzov et al., 2011; Song et al., 2011; Tahiliani et al., 2009).”
MeCP2 binds to 5hmc enriched within active genes and accessible chromatin in the nervous system (2013, positive): “5hmC was pulled down as described (Song et al., 2010) (see extended protocols).”
LOSS OF 5-HYDROXYMETHYLCYTOSINE IS AN EPIGENETIC HALLMARK OF MELANOMA (2012, background): “However, 5-hmC levels are greatly reduced in most cultured, immortalized tumor cells (Haffner et al., 2011; Song et al., 2011; Yang et al., 2012).”
Reversing DNA Methylation: Mechanisms, Genomics, and Biological Functions (2014, positive): “…Chemical Labeling 5hmCwith Biotin (hMe-Seal or GLIB) By exploiting the naturally occurring glucosylation process of 5hmC by b-GT, several methods were developed to chemically and enzymatically label 5hmC with the biotin tag (Pastor et al., 2011; Song et al., 2011; Szwagierczak et al., 2010).”
DNA methylome analysis using short bisulfite sequencing data (2012, background): “This limitation does not apply to antibody-based techniques, which can be used to specifically enrich 5hmC 26–28 .”
Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome (2012, neutral): “Strategies to label and/or enrich 5hmC in genomic DNA have been developed to investigate the distribution and function of 5hmC in the genome (Ficz et al., 2011; Pastor et al., 2011; Robertson et al., 2012; Robertson et al., 2011; Song et al., 2011; Stroud et al., 2011; Williams et al., 2011; Wu et a”
Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation. (2011, background): “2C; Ficz et al. 2011; Jin et al. 2011; Stroud et al. 2011; Szulwach et al. 2011; Wu et al. 2011a; Y Xu et al. 2011).”