Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion identifies evolutionarily unconserved CpGs as TET targets.

Date publication

mars 2016

Journal

Genome biology

Auteurs

Membres identifiés du Cancéropôle Est :
Dr WEBER Mickaël

Tous les auteurs :
Sérandour AA, Avner S, Mahé EA, Madigou T, Guibert S, Weber M, Salbert G

Lien Pubmed

https://www.ncbi.nlm.nih.gov/pubmed/27025842

Résumé

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.

Mots clés

5-Methylcytosine, analogs & derivatives, Animals, Cells, Cultured, CpG Islands, Cytosine, analogs & derivatives, DNA, chemistry, DNA Methylation, Embryonic Stem Cells, chemistry, Epigenesis, Genetic, Epigenomics, methods, Exonucleases, metabolism, Mice, Sequence Analysis, DNA, methods, Staining and Labeling

Référence

Genome Biol.. 2016 Mar 29;17:56