Genome-wide Mapping of 5-hydroxymethylcytosine in Embryonic Stem Cells

Overview

Journal Nature

Specialty Science

Date 2011 May 10

PMID 21552279

Citations 422

Authors

William A Pastor

Utz J Pape

Yun Huang

Hope R Henderson

Ryan Lister

Myunggon Ko

Erin M McLoughlin

Yevgeny Brudno

Sahasransu Mahapatra

Philipp Kapranov

Mamta Tahiliani

George Q Daley

X Shirley Liu

Joseph R Ecker

Patrice M Milos

Suneet Agarwal

Anjana Rao

Affiliations

Soon will be listed here.

Abstract

5-hydroxymethylcytosine (5hmC) is a modified base present at low levels in diverse cell types in mammals. 5hmC is generated by the TET family of Fe(II) and 2-oxoglutarate-dependent enzymes through oxidation of 5-methylcytosine (5mC). 5hmC and TET proteins have been implicated in stem cell biology and cancer, but information on the genome-wide distribution of 5hmC is limited. Here we describe two novel and specific approaches to profile the genomic localization of 5hmC. The first approach, termed GLIB (glucosylation, periodate oxidation, biotinylation) uses a combination of enzymatic and chemical steps to isolate DNA fragments containing as few as a single 5hmC. The second approach involves conversion of 5hmC to cytosine 5-methylenesulphonate (CMS) by treatment of genomic DNA with sodium bisulphite, followed by immunoprecipitation of CMS-containing DNA with a specific antiserum to CMS. High-throughput sequencing of 5hmC-containing DNA from mouse embryonic stem (ES) cells showed strong enrichment within exons and near transcriptional start sites. 5hmC was especially enriched at the start sites of genes whose promoters bear dual histone 3 lysine 27 trimethylation (H3K27me3) and histone 3 lysine 4 trimethylation (H3K4me3) marks. Our results indicate that 5hmC has a probable role in transcriptional regulation, and suggest a model in which 5hmC contributes to the 'poised' chromatin signature found at developmentally-regulated genes in ES cells.

Citing Articles

5-Hydroxymethylcytosine modifications in circulating cell-free DNA: frontiers of cancer detection, monitoring, and prognostic evaluation.

Song D, Zhang Z, Zheng J, Zhang W, Cai J Biomark Res. 2025; 13(1):39.

PMID: 40055844 PMC: 11887266. DOI: 10.1186/s40364-025-00751-9.

TET-mediated 5hmC in breast cancer: mechanism and clinical potential.

Zhang J, Aishan N, Zheng Z, Ju S, He Q, Meng Q Epigenetics. 2025; 20(1):2473250.

PMID: 40014756 PMC: 11869774. DOI: 10.1080/15592294.2025.2473250.

TET2-mediated 5-hydroxymethylcytosine of TXNIP promotes cell cycle arrest in systemic anaplastic large cell lymphoma.

Yu Z, Zhong L, Tang W, Zhang W, Lin T, Zhu W Clin Epigenetics. 2025; 17(1):10.

PMID: 39838392 PMC: 11749379. DOI: 10.1186/s13148-025-01816-0.

Profiling the epigenome using long-read sequencing.

Liu T, Conesa A Nat Genet. 2025; 57(1):27-41.

PMID: 39779955 DOI: 10.1038/s41588-024-02038-5.

Unravelling 2-oxoglutarate turnover and substrate oxidation dynamics in 5-methylcytosine-oxidising TET enzymes.

Simelis K, Belle R, Kawamura A Commun Chem. 2024; 7(1):305.

PMID: 39706884 PMC: 11662004. DOI: 10.1038/s42004-024-01382-1.

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