title: Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion identifies evolutionarily unconserved CpGs as TET targets.
abstract: Conventional techniques for single-base resolution mapping of epigenetic modifications of DNA such as 5-hydroxymethylcytosine (5hmC) rely on the sequencing of bisulfite-modified DNA. Here we present an alternative approach called SCL-exo which combines selective chemical labeling (SCL) of 5hmC in genomic DNA with exonuclease (exo) digestion of the bead-trapped modified DNA molecules. Associated with a straightforward bioinformatic analysis, this new procedure provides an unbiased and fast method for mapping this epigenetic mark at high resolution. Implemented on mouse genomic DNA from in vitro-differentiated neural precursor cells, SCL-exo sheds light on an intrinsic lack of conservation of hydroxymethylated CpGs across vertebrates.
authors.affiliation: EMBL, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
authors.forename: Aurélien A
authors.initials: AA
authors.lastname: Sérandour
authors.affiliation: CNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes cedex, 35042, France.|Université de Rennes 1, Campus de Beaulieu, Rennes Cedex, 35042, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Avner
authors.affiliation: CNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes cedex, 35042, France.|Université de Rennes 1, Campus de Beaulieu, Rennes Cedex, 35042, France.
authors.forename: Elise A
authors.initials: EA
authors.lastname: Mahé
authors.affiliation: CNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes cedex, 35042, France.|Université de Rennes 1, Campus de Beaulieu, Rennes Cedex, 35042, France.
authors.forename: Thierry
authors.initials: T
authors.lastname: Madigou
authors.affiliation: CNRS, Université de Strasbourg, UMR7242, Biotechnologie et signalisation cellulaire, 300 bd Sébastien Brant, Illkirch cedex, 67412, France.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Guibert
authors.affiliation: CNRS, Université de Strasbourg, UMR7242, Biotechnologie et signalisation cellulaire, 300 bd Sébastien Brant, Illkirch cedex, 67412, France.
authors.forename: Michaël
authors.initials: M
authors.lastname: Weber
authors.affiliation: CNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes cedex, 35042, France. gilles.salbert@univ-rennes1.fr.|Université de Rennes 1, Campus de Beaulieu, Rennes Cedex, 35042, France. gilles.salbert@univ-rennes1.fr.
authors.forename: Gilles
authors.identifier: http://orcid.org/0000-0001-6115-4140
authors.initials: G
authors.lastname: Salbert
mesh_terms: D044503:5-Methylcytosine / Q000031:analogs & derivatives; D000818:Animals; D002478:Cells, Cultured; D018899:CpG Islands; D003596:Cytosine / Q000031:analogs & derivatives* / Q000378:metabolism; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D019175:DNA Methylation; D053595:Embryonic Stem Cells / Q000737:chemistry / Q000166:cytology; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods*; D005092:Exonucleases / Q000378:metabolism*; D051379:Mice; D017422:Sequence Analysis, DNA / Q000379:methods; D013194:Staining and Labeling
chemical_list: C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine; D004247:DNA; D005092:Exonucleases
keywords: 5-hydroxymethylcytosine; 5hmC; Selective chemical labeling; Single-CpG resolution