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Nat Protoc. 2012 Dec;7(12):2159-70. doi: 10.1038/nprot.2012.137. Epub 2012 Nov 29.

Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine.

Author information

1
Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.

Abstract

A complete understanding of the potential function of 5-hydroxymethylcytosine (5-hmC), a DNA cytosine modification in mammalian cells, requires an accurate single-base resolution sequencing method. Here we describe a modified bisulfite-sequencing method, Tet-assisted bisulfite sequencing (TAB-seq), which can identify 5-hmC at single-base resolution, as well as determine its abundance at each modification site. This protocol involves β-glucosyltransferase (β-GT)-mediated protection of 5-hmC (glucosylation) and recombinant mouse Tet1(mTet1)-mediated oxidation of 5-methylcytosine (5-mC) to 5-carboxylcytosine (5-caC). After the subsequent bisulfite treatment and PCR amplification, both cytosine and 5-caC (derived from 5-mC) are converted to thymine (T), whereas 5-hmC reads as C. The treated genomic DNA is suitable for both whole-genome and locus-specific sequencing. The entire procedure (which does not include data analysis) can be completed in 14 d for whole-genome sequencing or 7 d for locus-specific sequencing.

PMID:
23196972
PMCID:
PMC3641661
DOI:
10.1038/nprot.2012.137
[Indexed for MEDLINE]
Free PMC Article

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