title: Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine.
abstract: We describe strand-specific, base-resolution detection of 5-hydroxymethylcytosine (5-hmC) in genomic DNA with single-molecule sensitivity, combining a bioorthogonal, selective chemical labeling method of 5-hmC with single-molecule, real-time (SMRT) DNA sequencing. The chemical labeling not only allows affinity enrichment of 5-hmC-containing DNA fragments but also enhances the kinetic signal of 5-hmC during SMRT sequencing. We applied the approach to sequence 5-hmC in a genomic DNA sample with high confidence.
authors.affiliation: Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA.
authors.forename: Chun-Xiao
authors.initials: CX
authors.lastname: Song
authors.forename: Tyson A
authors.initials: TA
authors.lastname: Clark
authors.forename: Xing-Yu
authors.initials: XY
authors.lastname: Lu
authors.forename: Andrey
authors.initials: A
authors.lastname: Kislyuk
authors.forename: Qing
authors.initials: Q
authors.lastname: Dai
authors.forename: Stephen W
authors.initials: SW
authors.lastname: Turner
authors.forename: Chuan
authors.initials: C
authors.lastname: He
authors.forename: Jonas
authors.initials: J
authors.lastname: Korlach
mesh_terms: D044503:5-Methylcytosine / Q000031:analogs & derivatives; D001483:Base Sequence; D003596:Cytosine / Q000031:analogs & derivatives* / Q000032:analysis; D004247:DNA / Q000737:chemistry*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine; D004247:DNA
references.citation: Mol Cell. 2011 May 20;42(4):451-64
references.pmid: 21514197
references.citation: Genes Dev. 2011 Apr 1;25(7):679-84
references.pmid: 21460036
references.citation: Cell. 2011 Sep 16;146(6):866-72
references.pmid: 21925312
references.citation: J Org Chem. 2011 May 20;76(10):4182-8
references.pmid: 21462947
references.citation: Nat Biotechnol. 2011 Jan;29(1):68-72
references.pmid: 21151123
references.citation: Angew Chem Int Ed Engl. 2011 Jul 11;50(29):6460-8
references.pmid: 21688365
references.citation: Nat Methods. 2010 Jun;7(6):461-5
references.pmid: 20453866
references.citation: Methods Enzymol. 2010;472:431-55
references.pmid: 20580975
references.citation: Nature. 2011 May 19;473(7347):398-402
references.pmid: 21460836
references.citation: Science. 2009 Jan 2;323(5910):133-8
references.pmid: 19023044
references.citation: Science. 2009 May 15;324(5929):929-30
references.pmid: 19372393
references.citation: Nature. 2011 May 19;473(7347):394-7
references.pmid: 21552279
references.citation: Science. 2009 May 15;324(5929):930-5
references.pmid: 19372391
references.citation: Nucleic Acids Res. 2010 Aug;38(15):e159
references.pmid: 20571086
references.citation: Nature. 2011 May 19;473(7347):343-8
references.pmid: 21490601
references.citation: PLoS One. 2010 Jan 26;5(1):e8888
references.pmid: 20126651