DNA Demethylation in the Processes of Repair and Epigenetic Regulation Performed by 2-Ketoglutarate-Dependent DNA Dioxygenases

Site-specific DNA methylation plays an important role in epigenetic regulation of gene expression. Chemical methylation of DNA, including the formation of various methylated nitrogenous bases, leads to the formation of genotoxic modifications that impair DNA functions. Despite the fact that different pathways give rise to methyl groups in DNA, the main pathway for their removal is oxidative demethylation, which is catalyzed by nonheme Fe(II)/α-ketoglutarate–dependent DNA dioxygenases. DNA dioxygenases share a common catalytic mechanism of the oxidation of the alkyl groups on nitrogenous bases in nucleic acids. This review presents generalized data on the catalytic mechanism of action of DNA dioxygenases and on the participation of typical representatives of this superfamily, such as prokaryotic enzyme AlkB and eukaryotic enzymes ALKBH1–8 and TET1–3, in both processes of direct repair of alkylated DNA adducts and in the removal of an epigenetic mark (5-methylcytosine).

Nuclear RNA-acetylation can be erased by the deacetylase SIRT7

A large number of RNA modifications are known to affect processing and function of rRNA, tRNA and mRNA 1. The N4-acetylcytidine (ac4C) is the only known RNA acetylation event and is known to occur on rRNA, tRNA and mRNA 2,3. RNA modification by acetylation affects a number of biological processes, including translation and RNA stability 2. For a few RNA methyl modifications, a reversible nature has been demonstrated where specific writer proteins deposit the modification and eraser proteins can remove them by oxidative demethylation 4–6. The functionality of RNA modifications is often mediated by interaction with reader proteins that bind dependent on the presence of specific modifications 1. The NAT10 acetyltransferase has been firmly identified as the main writer of acetylation of cytidine ribonucleotides, but so far neither readers nor erasers of ac4C have been identified 2,3. Here we show, that ac4C is bound by the nucleolar protein NOP58 and deacetylated by SIRT7, for the first time demonstrating reversal by another mechanism than oxidative demethylation. NOP58 and SIRT7 are involved in snoRNA function and pre-ribosomal RNA processing 7–10, and using a NAT10 deficient cell line we can show that the reduction in ac4C levels affects both snoRNA sub-nuclear localization and pre-rRNA processing. SIRT7 can deacetylate RNA in vitro and endogenous levels of ac4C on snoRNA increase in a SIRT7 deficient cell line, supporting its endogenous function as an RNA deacetylase. In summary, we identify the first eraser and reader proteins of the RNA modification ac4C, respectively, and suggest an involvement of RNA acetylation in snoRNA function and pre-rRNA processing.

Metabolic control of histone demethylase activity involved in plant response to high temperature

Jumonji (Jmj)-C domain proteins are histone lysine demethylases that require ferrous iron and alpha-ketoglutarate (or α-KG) as cofactors in the oxidative demethylation reaction. In plants, α-KG is produced by isocitrate dehydrogenases (ICDH) in different metabolic pathways. It remains unclear whether fluctuation of α-KG levels affects JmjC demethylase activity and epigenetic regulation of plant gene expression. In this work, we studied the impact of loss of function of the cytosolic ICDH (or cICDH) gene on the function of histone demethylases in Arabidopsis thaliana. Loss of cICDH resulted in increases of overall histone H3 lysine 4 trimethylation (H3K4me3) and enhanced mutation defects of the H3K4me3 demethylase gene JMJ14. Genetic analysis suggested that the cICDH mutation may affect the activity of other demethylases, including JMJ15 and JMJ18 that function redundantly with JMJ14 in the plant thermosensory response. Furthermore, we show that mutation of JMJ14 affected both the gene activation and repression programs of the plant thermosensory response and that JMJ14 and JMJ15 repressed a set of genes that are likely to play negative roles in the process. The results provide evidence that histone H3K4 demethylases are involved in the plant response to elevated ambient temperature.

Access to fused π-extended acridone derivatives through a regioselective oxidative demethylation

The oxidative demethylation of ortho-dimethoxyacridone with ceric ammonium nitrate (CAN) regioselectively furnished an ortho-quinone leaving a methoxyl unreacted, which further condensed with aromatic ortho-diamines to afford angularly fused π-extended acridone...