| Literature DB >> 26660343 |
Daniel Gackowski1, Ewelina Zarakowska1, Marta Starczak1, Martyna Modrzejewska1, Ryszard Olinski1.
Abstract
BACKGROUND: Replication-independent active/enzymatic demethylation may be an important process in the functioning of somatic cells. The most plausible mechanisms of active 5-methylcytosine demethylation, leading to activation of previously silenced genes, involve ten-eleven translocation (TET) proteins that participate in oxidation of 5-methylcytosine to 5-hydroxymethylcytosine which can be further oxidized to 5-formylcytosine and 5-carboxylcytosine. Recently, 5-hydroxymethylcytosine was demonstrated to be a relatively stable modification, and the previously observed substantial differences in the level of this modification in various murine tissues were shown to depend mostly on cell proliferation rate. Some experimental evidence supports the hypothesis that 5-hydroxymethyluracil may be also generated by TET enzymes and has epigenetic functions.Entities:
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Year: 2015 PMID: 26660343 PMCID: PMC4682766 DOI: 10.1371/journal.pone.0144859
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Transition patterns and specific detector settings for all analyzed compounds.
| compound name | ionization mode | nominal molecular mass (Da) | pseudo-molecular ion formulation | nominal parent ion (Da) | nominal daughter ion (Da) | capillary (kV) | cone (V) | collision (eV) | |
|---|---|---|---|---|---|---|---|---|---|
| 5-hydroxymethyl-2'-deoxycytidine | quantifier | ESI+ | 257 | [M+H]+ | 258 | 124 | 1.2 | 15 | 10 |
| qualifier | ESI+ | 257 | [M+H]+ | 258 | 142 | 1.2 | 15 | 10 | |
| [D3]-5-hydroxymethyl-2'-deoxycytidine | quantifier | ESI+ | 260 | [(M+3)+H]+ | 261 | 127 | 1.2 | 15 | 10 |
| qualifier | ESI+ | 260 | [(M+3)+H]+ | 261 | 145 | 1.2 | 15 | 10 | |
| 5-carboxyl-2'-deoxycytidine | quantifier | ESI- | 271 | [M-H]- | 270 | 110 | 3.5 | 20 | 20 |
| qualifier | ESI- | 271 | [M-H]- | 270 | 93 | 3.5 | 20 | 20 | |
| [13C10, 15N2]-5-carboxyl-2'-deoxycytidine | quantifier | ESI- | 283 | [(M+12)-H]- | 282 | 116 | 3.5 | 20 | 20 |
| qualifier | ESI- | 283 | [(M+12)-H]- | 282 | 99 | 3.5 | 20 | 20 | |
| 5-hydroxymethyl-2'-deoxyuridine | quantifier | ESI- | 258 | [M-H]- | 257 | 124 | 3.5 | 20 | 15 |
| qualifier | ESI- | 258 | [M-H]- | 257 | 214 | 3.5 | 20 | 10 | |
| [13C10, 15N2]-5-hydroxymethyl-2'-deoxyuridine | quantifier | ESI- | 270 | [(M+12)-H]- | 269 | 131 | 3.5 | 20 | 15 |
| qualifier | ESI- | 270 | [(M+12)-H]- | 269 | 224 | 3.5 | 20 | 10 | |
| 5-formyl-2'-deoxycytidine | quantifier | ESI- | 255 | [M-H]- | 254 | 121 | 3.5 | 28 | 18 |
| qualifier | ESI- | 255 | [M-H]- | 254 | 138 | 3.5 | 28 | 18 | |
| [13C10, 15N2]-5-formyl-2'-deoxycytidine | quantifier | ESI- | 267 | [(M+12)-H]- | 266 | 128 | 3.5 | 28 | 18 |
| qualifier | ESI- | 267 | [(M+12)-H]- | 266 | 145 | 3.5 | 28 | 18 |
Compound-specific validation parameters.
| 5-hmdC | 5-fdC | 5-cadC | 5-hmdU | |
|---|---|---|---|---|
| amount spiked (per injection) | 2 pmols | 50 fmols | 10 fmols | 50 fmols |
| recovery [%] | 108% | 93% | 127% | 103% |
| amount spiked (per injection) | 10 pmols | 500 fmols | 50 fmols | 500 fmols |
| recovery [%] | 90% | 97% | 85% | 105% |
| sample to sample RSD, n = 3 | 3.7% | 4.7% | 8.2% | 10.0% |
| within sample RSD, n = 5 | 3.6% | 7.5% | 6.1% | 6.4% |
| matrix factor | 0.993 | 0.901 | 0.891 | 0.957 |
| absolute LOD [fmols] | 3 | 0.3 | 0.05 | 0.5 |
| relative LOD | 0.12/106dN | 0.01/106dN | 2/109dN | 0.02/106dN |
| absolute LOQ [fmols] | 10 | 0.8 | 0.13 | 1.5 |
| relative LOQ | 0.4/106dN | 0.03/106dN | 5.2/109dN | 0.06/106dN |
Fig 1Relationship between tissue-specific proliferation rate and epigenetic DNA modifications.
Relationship between tissue-specific proliferation rate, determined in a murine model and expressed as the percentage of labelled 5-methylcytosine formed in DNA during cellular division (data from [5] kindly supplied by prof. Bachman) and the content of 5-methyl-2’-deoxycytidine and active demethylation products in DNA isolated from various porcine (red) and rat (green) tissues. Coefficients of determination were calculated using a linearized regression model with logarithmic fit for proliferation rate and linear fit for all other variables. Data presented as mean values for biological replicates; error bars correspond to standard deviations.
Fig 2Interrelationships between DNA modifications.
Interrelationships between 5-methyl-2’-deoxycytidine, 5-hydroxymethyl-2’-deoxycytidine, 5-formyl-2’-deoxycytidine, 5-carboxyl-2’-deoxycytidine and 5-hydroxymethyl-2’-deoxyuridine in DNA of various porcine and rat tissues. Coefficients of determination and p-values were calculated using Pearson’s analysis of correlation. Data is presented as mean values for biological replicates; error bars correspond to standard deviations.