DNAmod: 5-methylcytosine

Description

A pyrimidine that is a derivative of cytosine, having a methyl group at the 5-position.

Chemical properties

Chemical formula	Net charge	Average mass
C5H7N3O	0	125.12860

Recommended notation

Name	5-methylcytosine
Abbreviation	5mC
Symbol	m
Complement	guanine:5-methylcytosine
Symbol	1

Nomenclature

IUPAC	SMILES	InChI	InChIKey	Synonyms
4-amino-5-methylpyrimidin-2(1H)-one	Cc1c[nH]c(=O)nc1N	InChI=1S/C5H7N3O/c1-3-2-7-5(9)8-4(3)6/h2H,1H3,(H3,6,7,8,9)	LRSASMSXMSNRBT-UHFFFAOYSA-N	4-amino-5-methyl-2(1h)-pyrimidinone 4-amino-5-methyl-2-pyrimidinol

Mapping techniques

Method	Method detail	Resolution	Qualifier	References
BS-seq	chemical conversion	single-base		Frommer, M, et al. 1992. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proceedings of the National Academy of Sciences of the United States of America. 89(5). Uhlmann, K, et al. 2002. Evaluation of a potential epigenetic biomarker by quantitative methyl-single nucleotide polymorphism analysis. Electrophoresis. 23(24). Tost, J, et al. 2006. Serial pyrosequencing for quantitative DNA methylation analysis. BioTechniques. 40(6). Taylor, KH, et al. 2007. Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Research. 67(18). Tost, J, et al. 2007. DNA methylation analysis by pyrosequencing. Nature Protocols. 2(9). Lister, R, et al. 2009. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 462(7271). Paul, DS, et al. 2014. Assessment of RainDrop BS-seq as a method for large-scale, targeted bisulfite sequencing. Epigenetics. 9(5).
HELP assay	restriction endonuclease	low	microarray probes	Khulan, B, et al. 2006. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Research. 16(8).
HPoxBS	chemical conversion	single-base	strand-specific	Giehr, P, et al. 2018. Two are better than one: HPoxBS - hairpin oxidative bisulfite sequencing. Nucleic Acids Research. 46(15).
MBD-seq	affinity-based	low		Serre, D, et al. 2009. MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Research. 38(2).
MRE-seq	affinity-based	low		Maunakea, AK, et al. 2010. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 466(7303).
Maxam–Gilbert sequencing		single-base		Maxam, AM, et al. 1977. A new method for sequencing DNA. Proceedings of the National Academy of Sciences of the United States of America. 74(2). Münzel, M, et al. 2010. Chemical discrimination between dC and 5MedC via their hydroxylamine adducts. Nucleic Acids Research. 38(21). Wang, T, et al. 2013. Application of N-halogeno-N-sodiobenzenesulfonamide reagents to the selective detection of 5-methylcytosine in DNA sequences. Journal of the American Chemical Society. 135(4). Huang, R, et al. 2013. A novel combined bisulfite UDG assay for selective 5-methylcytosine detection. Talanta. 117.
MeDIP-seq	affinity-based	low		Pomraning, KR, et al. 2008. Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods (San Diego, Calif.). 47(3).
Methyl-MAPS	affinity-based	low		Edwards, JR, et al. 2010. Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns. Genome Research. 20(7).
Methyl-seq	restriction endonuclease	low		Brunner, AL, et al. 2009. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Research. 19(6).
MethylCap-seq	affinity-based	low	salt gradient stratification	Brinkman, AB, et al. 2010. Whole-genome DNA methylation profiling using MethylCap-seq. Methods (San Diego, Calif.). 52(3).
MspJI recognition	restriction endonuclease	low	specific fragments	Cohen-Karni, D, et al. 2011. The MspJI family of modification-dependent restriction endonucleases for epigenetic studies. Proceedings of the National Academy of Sciences of the United States of America. 108(27).
PBAT	chemical conversion	single-base		Miura, F, et al. 2012. Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. Nucleic Acids Research. 40(17).
RRBS	chemical conversion	single-base	methylation-insensitive restriction digestion	Meissner, A, et al. 2008. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature. 454(7205). Smith, ZD, et al. 2009. High-throughput bisulfite sequencing in mammalian genomes. Methods (San Diego, Calif.). 48(3). Gu, H, et al. 2010. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nature Methods. 7(2). Gu, H, et al. 2011. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nature Protocols. 6(4).
SMRT	direct detection	single-base	target sequences	Flusberg, BA, et al. 2010. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nature Methods. 7(6). Clark, TA, et al. 2011. Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Research. 40(4).
SMRT-BS	chemical conversion	single-base	target sequences	Yang, Y, et al. 2015. Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS). BMC Genomics. 16.
TAPS	chemical conversion	single-base		Liu, Y, et al. 2019. Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution. Nature Biotechnology. 37(4).
TAPSβ	chemical conversion	single-base		Liu, Y, et al. 2019. Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution. Nature Biotechnology. 37(4).
TAmC-seq	chemical tagging	high		Zhang, L, et al. 2013. Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing. Nature Communications. 4.
TOP-seq	enzyme-mediated chemical tagging	high	target sequences	Staševskij, Z, et al. 2017. Tethered Oligonucleotide-Primed Sequencing, TOP-Seq: A High-Resolution Economical Approach for DNA Epigenome Profiling. Molecular Cell. 65(3).
Tn5mC-seq	chemical conversion	single-base		Adey, A, et al. 2012. Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing. Genome Research. 22(6).
cfMeDIP-seq	affinity-based	low	low-input	Shen, SY, et al. 2018. Sensitive tumour detection and classification using plasma cell-free DNA methylomes. Nature. 563(7732). Shen, SY, et al. 2019. Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA. Nature Protocols. 14(10).
coBS-seq	chemical conversion	single-base		Fukuzawa, S, et al. 2016. Simple and accurate single base resolution analysis of 5-hydroxymethylcytosine by catalytic oxidative bisulfite sequencing using micelle incarcerated oxidants. Bioorganic & Medicinal Chemistry. 24(18).
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).
fluorescence microscopy	direct detection	low	target sequences	Cerf, A, et al. 2011. Single DNA molecule patterning for high-throughput epigenetic mapping. Analytical Chemistry. 83(21).
lrTAPS	chemical conversion	single-base		Liu, Y, et al. 2020. Accurate targeted long-read DNA methylation and hydroxymethylation sequencing with TAPS. Genome Biology. 21(1).
nanopore	direct detection	single-base	target sequences	Wallace, EV, et al. 2010. Identification of epigenetic DNA modifications with a protein nanopore. Chemical Communications (Cambridge, England). 46(43). Wanunu, M, et al. 2010. Discrimination of methylcytosine from hydroxymethylcytosine in DNA molecules. Journal of the American Chemical Society. 133(3). Manrao, EA, et al. 2011. Nucleotide discrimination with DNA immobilized in the MspA nanopore. PloS One. 6(10). 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). 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). Rand, AC, et al. 2017. Mapping DNA methylation with high-throughput nanopore sequencing. Nature Methods. 14(4).
oxBS-seq	chemical conversion	single-base		Booth, MJ, et al. 2013. Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine. Nature Protocols. 8(10).

Nature

Origin	Function	Functional detail	Organisms	References
natural	epigenetic mark		Arthrobacter luteus Bacillus amyloliquefaciens Bacillus aneurinolyticus Bacillus stearothermophilus Bos taurus Caldicellulosiruptor kristjanssonii Chlamydomonas reinhardtii Desulfotomaculum nigrificans Desulfovibrio desulfuricans Drosophila melanogaster Escherichia coli Fusobacterium nucleatum Haemophilus aegyptius Haemophilus gallinarum Haemophilus haemolyticus Haemophilus parainfluenzae Homo sapiens Klebsiella pneumoniae Locusta migratoria Moraxella nonliquefaciens Mus musculus Nocardia aerocolonigenes Ovis aries Serratia marcescens Streptomyces achromogenes Xanthomonas campestris	WYATT, GR, et al. 1950. Occurrence of 5-methylcytosine in nucleic acids. Nature. 166(4214). Culp, LA, et al. 1970. Methylated bases in DNA of animal origin. Archives of Biochemistry and Biophysics. 136(1). Ehrlich, M, et al. 1981. 5-Methylcytosine in eukaryotic DNA. Science (New York, N.Y.). 212(4501). 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). Feng, S, et al. 2010. Conservation and divergence of methylation patterning in plants and animals. Proceedings of the National Academy of Sciences of the United States of America. 107(19). Capuano, F, et al. 2014. Cytosine DNA methylation is found in Drosophila melanogaster but absent in Saccharomyces cerevisiae, Schizosaccharomyces pombe, and other yeast species. Analytical Chemistry. 86(8). 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).

Database references:

CHEBI:27551

Citations

Adey, A, et al. 2012. Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing. Genome Research. 22(6).
Bart, A, et al. 2005. Direct detection of methylation in genomic DNA. Nucleic Acids Research. 33(14).
Booth, MJ, et al. 2013. Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine. Nature Protocols. 8(10).
Brinkman, AB, et al. 2010. Whole-genome DNA methylation profiling using MethylCap-seq. Methods (San Diego, Calif.). 52(3).
Brunner, AL, et al. 2009. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Research. 19(6).
Capuano, F, et al. 2014. Cytosine DNA methylation is found in Drosophila melanogaster but absent in Saccharomyces cerevisiae, Schizosaccharomyces pombe, and other yeast species. Analytical Chemistry. 86(8).
Cerf, A, et al. 2011. Single DNA molecule patterning for high-throughput epigenetic mapping. Analytical Chemistry. 83(21).
Clark, TA, et al. 2011. Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Research. 40(4).
Cohen-Karni, D, et al. 2011. The MspJI family of modification-dependent restriction endonucleases for epigenetic studies. Proceedings of the National Academy of Sciences of the United States of America. 108(27).
Culp, LA, et al. 1970. Methylated bases in DNA of animal origin. Archives of Biochemistry and Biophysics. 136(1).
Edwards, JR, et al. 2010. Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns. Genome Research. 20(7).
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).
Ehrlich, M, et al. 1981. 5-Methylcytosine in eukaryotic DNA. Science (New York, N.Y.). 212(4501).
Feng, S, et al. 2010. Conservation and divergence of methylation patterning in plants and animals. Proceedings of the National Academy of Sciences of the United States of America. 107(19).
Flusberg, BA, et al. 2010. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nature Methods. 7(6).
Frommer, M, et al. 1992. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proceedings of the National Academy of Sciences of the United States of America. 89(5).
Fukuzawa, S, et al. 2016. Simple and accurate single base resolution analysis of 5-hydroxymethylcytosine by catalytic oxidative bisulfite sequencing using micelle incarcerated oxidants. Bioorganic & Medicinal Chemistry. 24(18).
Giehr, P, et al. 2018. Two are better than one: HPoxBS - hairpin oxidative bisulfite sequencing. Nucleic Acids Research. 46(15).
Gu, H, et al. 2010. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nature Methods. 7(2).
Gu, H, et al. 2011. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nature Protocols. 6(4).
Hahn, MA, et al. 2014. Single base resolution analysis of 5-methylcytosine and 5-hydroxymethylcytosine by RRBS and TAB-RRBS. Methods in Molecular Biology (Clifton, N.J.). 1238.
Huang, R, et al. 2013. A novel combined bisulfite UDG assay for selective 5-methylcytosine detection. Talanta. 117.
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).
Khulan, B, et al. 2006. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Research. 16(8).
Ko, M, et al. 2014. TET proteins and 5-methylcytosine oxidation in hematological cancers. Immunological Reviews. 263(1).
Kubik, G, et al. 2014. Achieving single-nucleotide resolution of 5-methylcytosine detection with TALEs. Chembiochem : A European Journal of Chemical Biology. 16(2).
Lister, R, et al. 2009. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 462(7271).
Liu, Y, et al. 2019. Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution. Nature Biotechnology. 37(4).
Liu, Y, et al. 2020. Accurate targeted long-read DNA methylation and hydroxymethylation sequencing with TAPS. Genome Biology. 21(1).
Liyanage, VR, et al. 2015. Ethanol deregulates Mecp2/MeCP2 in differentiating neural stem cells via interplay between 5-methylcytosine and 5-hydroxymethylcytosine at the Mecp2 regulatory elements. Experimental Neurology. 265.
Manrao, EA, et al. 2011. Nucleotide discrimination with DNA immobilized in the MspA nanopore. PloS One. 6(10).
Maunakea, AK, et al. 2010. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 466(7303).
Maxam, AM, et al. 1977. A new method for sequencing DNA. Proceedings of the National Academy of Sciences of the United States of America. 74(2).
Meissner, A, et al. 2008. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature. 454(7205).
Miura, F, et al. 2012. Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. Nucleic Acids Research. 40(17).
Moen, EL, et al. 2014. New themes in the biological functions of 5-methylcytosine and 5-hydroxymethylcytosine. Immunological Reviews. 263(1).
Münzel, M, et al. 2010. Chemical discrimination between dC and 5MedC via their hydroxylamine adducts. Nucleic Acids Research. 38(21).
Paul, DS, et al. 2014. Assessment of RainDrop BS-seq as a method for large-scale, targeted bisulfite sequencing. Epigenetics. 9(5).
Pomraning, KR, et al. 2008. Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods (San Diego, Calif.). 47(3).
Rand, AC, et al. 2017. Mapping DNA methylation with high-throughput nanopore sequencing. Nature Methods. 14(4).
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).
Rojas, D, et al. 2014. Prenatal arsenic exposure and the epigenome: identifying sites of 5-methylcytosine alterations that predict functional changes in gene expression in newborn cord blood and subsequent birth outcomes. Toxicological Sciences : An Official Journal of the Society of Toxicology. 143(1).
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).
Serre, D, et al. 2009. MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Research. 38(2).
Shen, SY, et al. 2018. Sensitive tumour detection and classification using plasma cell-free DNA methylomes. Nature. 563(7732).
Shen, SY, et al. 2019. Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA. Nature Protocols. 14(10).
Smith, ZD, et al. 2009. High-throughput bisulfite sequencing in mammalian genomes. Methods (San Diego, Calif.). 48(3).
Staševskij, Z, et al. 2017. Tethered Oligonucleotide-Primed Sequencing, TOP-Seq: A High-Resolution Economical Approach for DNA Epigenome Profiling. Molecular Cell. 65(3).
Tang, Y, et al. 2015. Sensitive and simultaneous determination of 5-methylcytosine and its oxidation products in genomic DNA by chemical derivatization coupled with liquid chromatography-tandem mass spectrometry analysis. Analytical Chemistry. 87(6).
Taylor, KH, et al. 2007. Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Research. 67(18).
Tost, J, et al. 2006. Serial pyrosequencing for quantitative DNA methylation analysis. BioTechniques. 40(6).
Tost, J, et al. 2007. DNA methylation analysis by pyrosequencing. Nature Protocols. 2(9).
Uhlmann, K, et al. 2002. Evaluation of a potential epigenetic biomarker by quantitative methyl-single nucleotide polymorphism analysis. Electrophoresis. 23(24).
WYATT, GR, et al. 1950. Occurrence of 5-methylcytosine in nucleic acids. Nature. 166(4214).
Wallace, EV, et al. 2010. Identification of epigenetic DNA modifications with a protein nanopore. Chemical Communications (Cambridge, England). 46(43).
Wang, T, et al. 2013. Application of N-halogeno-N-sodiobenzenesulfonamide reagents to the selective detection of 5-methylcytosine in DNA sequences. Journal of the American Chemical Society. 135(4).
Wanunu, M, et al. 2010. Discrimination of methylcytosine from hydroxymethylcytosine in DNA molecules. Journal of the American Chemical Society. 133(3).
Widschwendter, M, et al. 2007. 5-methylcytosine--the fifth base of DNA: the fifth wheel on a car or a highly promising diagnostic and therapeutic target in cancer? Disease Markers. 23(1-2).
Yang, Y, et al. 2015. Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS). BMC Genomics. 16.
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).
Zhang, L, et al. 2013. Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing. Nature Communications. 4.