DNAmod: N4-methylcytosine

Description

A pyrimidone that is cytosine bearing an N(4)-methyl substituent.

Chemical properties

Chemical formula	Net charge	Average mass
C5H7N3O	0	125.12860

<i>N</i><sup>4</sup>-methylcytosine

Recommended notation

Name	4-methylcytosine
Abbreviation	4mC

Nomenclature

IUPAC	SMILES	InChI	InChIKey	Synonyms
4-(methylamino)pyrimidin-2(1H)-one	CNc1cc[nH]c(=O)n1	InChI=1S/C5H7N3O/c1-6-4-2-3-7-5(9)8-4/h2-3H,1H3,(H2,6,7,8,9)	PJKKQFAEFWCNAQ-UHFFFAOYSA-N	4-methylamino-1h-pyrimidin-2-one n(4)-methylcytosine

Mapping techniques

Method	Method detail	Resolution	Qualifier	References
SMRT	direct detection	single-base	target sequences	Clark, TA, et al. 2011. Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Research. 40(4).
dye-terminator Sanger sequencing	direct detection	single-base		Rao, BS, et al. 1998. Direct visualization of site-specific and strand-specific DNA methylation patterns in automated DNA sequencing data. Nucleic Acids Research. 26(10). Bart, A, et al. 2005. Direct detection of methylation in genomic DNA. Nucleic Acids Research. 33(14).

Nature

Origin	Function	Functional detail	Organisms	References
natural	restriction-modification		Bacillus aneurinolyticus Bacillus cenirosporus Bacillus globigii Bacillus stearothermophilus Caldicellulosiruptor kristjanssonii Clostridium thermoaceticum Clostridium thermoautotrophicum Desulfotomaculum nigrificans Geobacillus stearothermophilus Methanococcus thermolithotrophicus Moraxella bovis Proteus vulgaris Rhodopseudomonas sphaeroides Thermobacteroides acetoethylicus Thermus aquaticus Xanthomonas campestris	Janulaitis, A, et al. 1983. Cytosine modification in DNA by BcnI methylase yields N4-methylcytosine. FEBS Letters. 161(1). Ehrlich, M, et al. 1985. DNA methylation in thermophilic bacteria: N4-methylcytosine, 5-methylcytosine, and N6-methyladenine. Nucleic Acids Research. 13(4). Ehrlich, M, et al. 1987. N4-methylcytosine as a minor base in bacterial DNA. Journal of Bacteriology. 169(3). Yu, M, et al. 2015. Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing. Nucleic Acids Research. 43(21). Sánchez-Romero, MA, et al. 2015. DNA methylation in bacteria: from the methyl group to the methylome. Current Opinion in Microbiology. 25.

Database references:

CHEBI:21839

Citations

Bart, A, et al. 2005. Direct detection of methylation in genomic DNA. Nucleic Acids Research. 33(14).
Clark, TA, et al. 2011. Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Research. 40(4).
Ehrlich, M, et al. 1987. N4-methylcytosine as a minor base in bacterial DNA. Journal of Bacteriology. 169(3).
Ehrlich, M, et al. 1985. DNA methylation in thermophilic bacteria: N4-methylcytosine, 5-methylcytosine, and N6-methyladenine. Nucleic Acids Research. 13(4).
Janulaitis, A, et al. 1983. Cytosine modification in DNA by BcnI methylase yields N4-methylcytosine. FEBS Letters. 161(1).
Rao, BS, et al. 1998. Direct visualization of site-specific and strand-specific DNA methylation patterns in automated DNA sequencing data. Nucleic Acids Research. 26(10).
Roux, A, et al. 2012. Annotation of the human adult urinary metabolome and metabolite identification using ultra high performance liquid chromatography coupled to a linear quadrupole ion trap-Orbitrap mass spectrometer. Analytical Chemistry. 84(15).
Sánchez-Romero, MA, et al. 2015. DNA methylation in bacteria: from the methyl group to the methylome. Current Opinion in Microbiology. 25.
Yu, M, et al. 2015. Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing. Nucleic Acids Research. 43(21).