抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

5-methylcytosine (5mC) in DNA plays an important role in gene expression, genomic imprinting, and suppression of transposable elements. 5mC can be converted to 5-hydroxymethylcytosine (5hmC) by the Tet (ten eleven translocation) proteins. Here, we show that, in addition to 5hmC, the Tet proteins can generate 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) from 5mC in an enzymatic activity–dependent manner. Furthermore, we reveal the presence of 5fC and 5caC in genomic DNA of mouse embryonic stem cells and mouse organs. The genomic content of 5hmC, 5fC, and 5caC can be increased or reduced through overexpression or depletion of Tet proteins. Thus, we identify two previously unknown cytosine derivatives in genomic DNA as the products of Tet proteins. Our study raises the possibility that DNA demethylation may occur through Tet-catalyzed oxidation followed by decarboxylation.

/pdf/tet-proteins-can-convert-5-methylcytosine-to-5-24p29ujcaf.pdf

Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine

The prevalent DNA modification in higher organisms is the methylation of cytosine to 5-methylcytosine (5mC), which is partially converted to 5-hydroxymethylcytosine (5hmC) by the Tet (ten eleven translocation) family of dioxygenases. Despite their importance in epigenetic regulation, it is unclear how these cytosine modifications are reversed. Here, we demonstrate that 5mC and 5hmC in DNA are oxidized to 5-carboxylcytosine (5caC) by Tet dioxygenases in vitro and in cultured cells. 5caC is specifically recognized and excised by thymine-DNA glycosylase (TDG). Depletion of TDG in mouse embyronic stem cells leads to accumulation of 5caC to a readily detectable level. These data suggest that oxidation of 5mC by Tet proteins followed by TDG-mediated base excision of 5caC constitutes a pathway for active DNA demethylation.

https://science.sciencemag.org/content/sci/333/6047/1303.full.pdf

Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA

DNA Methylation and Its Basic Function

http://basicmed.med.ncku.edu.tw/admin/up_img/1007-2.pdf

Oncometabolite 2-Hydroxyglutarate Is a Competitive Inhibitor of α-Ketoglutarate-Dependent Dioxygenases

5-Hydroxymethylcytosine (hmC) was recently detected as the sixth base in mammalian tissue at so far controversial levels. The function of the modified base is currently unknown, but it is certain that the base is generated from 5-methylcytosine (mC). This fuels the hypothesis that it represents an intermediate of an active demethylation process, which could involve further oxidation of the hydroxymethyl group to a formyl or carboxyl group followed by either deformylation or decarboxylation. Here, we use an ultra-sensitive and accurate isotope based LC-MS method to precisely determine the levels of hmC in various mouse tissues and we searched for 5-formylcytosine (fC), 5-carboxylcytosine (caC), and 5-hydroxymethyluracil (hmU) as putative active demethylation intermediates. Our data suggest that an active oxidative mC demethylation pathway is unlikely to occur. Additionally, we show using HPLC-MS analysis and immunohistochemistry that hmC is present in all tissues and cell types with highest concentrations in neuronal cells of the CNS.

/pdf/tissue-distribution-of-5-hydroxymethylcytosine-and-search-2l93a4ukrw.pdf

Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates

Quantification of the sixth DNA base hydroxymethylcytosine in the brain.

Systems‐Based Analysis of Modified tRNA Bases

Parallel isotope-based quantification of modified tRNA nucleosides.

Transfer RNAs (tRNAs) are adapter molecules needed to translate genetic information into a peptide sequence.[1] At the ribosome, the anticodon of each tRNA reads the corresponding codon of the messenger RNA. This anticodon–codon interaction allows the ribosome’s large subunit to catalyze amide-bond formation between the cognate amino acids present at the 3′ terminus of aminoacyl-tRNAs and the growing peptide chain.[2] The tRNA adapters required for this process display a surprisingly large chemical diversity.[3] Aside from the four canonical nucleosides A, C, G, and U, more than 100 modified nucleosides are key constituents (Figure ​(Figure11).[4] The most diverse and complex chemical structures are found in the anticodon stem-loop either in the anticodon at the wobble position or directly adjacent to the 3′ position of the anticodon,[5] suggesting that here the chemical complexity is necessary to establish translational fidelity.[6] The ribosome seems to need the modified anticodon region to better distinguish correctly base-paired tRNA from mispaired interactions in order to prohibit, for example, codon-slippage processes that would lead to frameshifts.[7]

https://www.onlinelibrary.wiley.com/doi/pdf/10.1002/anie.201203769

Tobias Brückl

Papers

Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates

Quantification of the sixth DNA base hydroxymethylcytosine in the brain.

Systems‐Based Analysis of Modified tRNA Bases

Parallel isotope-based quantification of modified tRNA nucleosides.

Isotope‐Based Analysis of Modified tRNA Nucleosides Correlates Modification Density with Translational Efficiency