DNAmod: 5-formylcytosine

Description

A nucleobase analogue that is cytosine in which the hydrogen at position 5 is replaced by a formyl group.

Chemical properties

Chemical formula	Net charge	Average mass
C5H5N3O2	0	139.11210

Recommended notation

Name	5-formylcytosine
Abbreviation	5fC
Symbol	f
Complement	guanine:5-formylcytosine
Symbol	3

Nomenclature

IUPAC	SMILES	InChI	InChIKey	Synonyms
4-amino-2-oxo-1,2-dihydropyrimidine-5-carbaldehyde	Nc1nc(=O)[nH]cc1C=O	InChI=1S/C5H5N3O2/c6-4-3(2-9)1-7-5(10)8-4/h1-2H,(H3,6,7,8,10)	FHSISDGOVSHJRW-UHFFFAOYSA-N	4-amino-2-oxopyrimidine-5-carbaldehyde cytosine-5-carbaldehyde

Mapping techniques

Method	Method detail	Resolution	Qualifier	References
CLEVER-seq	chemical tagging	single-base	single-cell	Zhu, C, et al. 2017. Single-Cell 5-Formylcytosine Landscapes of Mammalian Early Embryos and ESCs at Single-Base Resolution. Cell Stem Cell. 20(5).
MAB-seq	chemical conversion	single-base		Wu, H, et al. 2016. Base-resolution profiling of active DNA demethylation using MAB-seq and caMAB-seq. Nature Protocols. 11(6).
MAB-seq	chemical conversion	single-base	low-input or single-cell	Wu, X, et al. 2017. Simultaneous mapping of active DNA demethylation and sister chromatid exchange in single cells. Genes & Development. 31(5).
Pvu-seal-seq	enzyme-mediated chemical tagging	single-base		Sun, Z, et al. 2015. A sensitive approach to map genome-wide 5-hydroxymethylcytosine and 5-formylcytosine at single-base resolution. Molecular Cell. 57(4).
fC-CET	chemical conversion	single-base		Xia, B, et al. 2015. Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale. Nature Methods. 12(11).
fCAB-seq	chemical conversion	single-base		Song, CX, et al. 2013. Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming. Cell. 153(3).
fluorogenic labeling	chemical tagging	single-base		Liu, C, et al. 2017. Fluorogenic labeling and single-base resolution analysis of 5-formylcytosine in DNA. Chemical Science. 8(11).
nanopore	direct detection	single-base	target sequences	Johnson, RP, et al. 2017. Dynamics of a DNA Mismatch Site Held in Confinement Discriminate Epigenetic Modifications of Cytosine. Journal of the American Chemical Society. 139(7).
redBS-seq	chemical conversion	single-base		Booth, MJ, et al. 2014. Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution. Nature Chemistry. 6(5).

Nature

Origin	Function	Functional detail	Organisms	References
natural	demethylation intermediate and epigenetic mark		Homo sapiens Mus musculus	Song, CX, et al. 2013. Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming. Cell. 153(3). Song, CX, et al. 2013. Potential functional roles of DNA demethylation intermediates. Trends in Biochemical Sciences. 38(10). Booth, MJ, et al. 2014. Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution. Nature Chemistry. 6(5). Lu, X, et al. 2015. Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics. Cell Research. 25(3). Bachman, M, et al. 2015. 5-Formylcytosine can be a stable DNA modification in mammals. Nature Chemical Biology. 11(8). Iurlaro, M, et al. 2016. In vivo genome-wide profiling reveals a tissue-specific role for 5-formylcytosine. Genome Biology. 17(1). Jiang, HP, et al. 2017. Determination of formylated DNA and RNA by chemical labeling combined with mass spectrometry analysis. Analytica Chimica Acta. 981.

Database references:

CHEBI:76794

Citations

Bachman, M, et al. 2015. 5-Formylcytosine can be a stable DNA modification in mammals. Nature Chemical Biology. 11(8).
Booth, MJ, et al. 2013. Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine. Nature Protocols. 8(10).
Booth, MJ, et al. 2014. Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution. Nature Chemistry. 6(5).
Cadet, J, et al. 2013. TET enzymatic oxidation of 5-methylcytosine, 5-hydroxymethylcytosine and 5-formylcytosine. Mutation Research. Genetic Toxicology and Environmental Mutagenesis. 764-765.
Hu, J, et al. 2013. Selective chemical labelling of 5-formylcytosine in DNA by fluorescent dyes. Chemistry (Weinheim An Der Bergstrasse, Germany). 19(19).
Ito, S, et al. 2011. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science (New York, N.Y.). 333(6047).
Iurlaro, M, et al. 2016. In vivo genome-wide profiling reveals a tissue-specific role for 5-formylcytosine. Genome Biology. 17(1).
Jiang, HP, et al. 2017. Determination of formylated DNA and RNA by chemical labeling combined with mass spectrometry analysis. Analytica Chimica Acta. 981.
Jin, L, et al. 2014. A new insight into the 5-carboxycytosine and 5-formylcytosine under typical bisulfite conditions: a deamination mechanism study. Physical Chemistry Chemical Physics : PCCP. 16(8).
Johnson, RP, et al. 2017. Dynamics of a DNA Mismatch Site Held in Confinement Discriminate Epigenetic Modifications of Cytosine. Journal of the American Chemical Society. 139(7).
Kellinger, MW, et al. 2012. 5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription. Nature Structural & Molecular Biology. 19(8).
Kizaki, S, et al. 2013. CGmCGCG is a versatile substrate with which to evaluate Tet protein activity. Organic & Biomolecular Chemistry. 12(1).
Liu, C, et al. 2017. Fluorogenic labeling and single-base resolution analysis of 5-formylcytosine in DNA. Chemical Science. 8(11).
Lu, X, et al. 2015. Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics. Cell Research. 25(3).
Maiti, A, et al. 2013. Divergent mechanisms for enzymatic excision of 5-formylcytosine and 5-carboxylcytosine from DNA. Journal of the American Chemical Society. 135(42).
Mao, W, et al. 2013. A convenient method for selective detection of 5-hydroxymethylcytosine and 5-formylcytosine sites in DNA sequences. Organic & Biomolecular Chemistry. 11(21).
Okashita, N, et al. 2013. PRDM14 promotes active DNA demethylation through the ten-eleven translocation (TET)-mediated base excision repair pathway in embryonic stem cells. Development (Cambridge, England). 141(2).
Shen, L, et al. 2013. Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics. Cell. 153(3).
Song, CX, et al. 2013. Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming. Cell. 153(3).
Song, CX, et al. 2013. Potential functional roles of DNA demethylation intermediates. Trends in Biochemical Sciences. 38(10).
Sun, W, et al. 2014. 5-hydroxymethylcytosine-mediated DNA demethylation in stem cells and development. Stem Cells and Development. 23(9).
Sun, Z, et al. 2015. A sensitive approach to map genome-wide 5-hydroxymethylcytosine and 5-formylcytosine at single-base resolution. Molecular Cell. 57(4).
Tian, T, et al. 2013. Systematic investigation of DNAs with modified cytosines under hot alkali treatment. Chemical Communications (Cambridge, England). 49(85).
Wu, H, et al. 2016. Base-resolution profiling of active DNA demethylation using MAB-seq and caMAB-seq. Nature Protocols. 11(6).
Wu, X, et al. 2017. Simultaneous mapping of active DNA demethylation and sister chromatid exchange in single cells. Genes & Development. 31(5).
Xia, B, et al. 2015. Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale. Nature Methods. 12(11).
Yao, B, et al. 2013. Cytosine modifications in neurodevelopment and diseases. Cellular and Molecular Life Sciences : CMLS. 71(3).
Zhu, C, et al. 2017. Single-Cell 5-Formylcytosine Landscapes of Mammalian Early Embryos and ESCs at Single-Base Resolution. Cell Stem Cell. 20(5).