DNA repair enzymes ALKBH2, ALKBH3, and AlkB oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in vitro

Bian, Ke; Lenz, Stefan A. P.; Tang, Qi; Chen, Fangyi; Qi, Rui; Jost, Marco; Drennan, Catherine L.; Essigmann, John M.; Wetmore, Stacey D.; Li, Deyu

doi:10.1093/nar/gkz395

Cited by 57 publications

(48 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…RNA extraction and reverse transcription-quantitative PCR (RT-qPCR) RNA was extracted with TRIzol (Invitrogen) or TRI Reagent® [85] according to the manufacturer's instructions. Briefly, cells were suspended in 1 ml TRI Reagent per well, mixed with 200 μl chloroform and incubated for 3 min.…”

Section: Amplicon Bisulfite Rna Sequencing Data Generation and Analysismentioning

confidence: 99%

Multiple links between 5-methylcytosine content of mRNA and translation

et al. 2020

View full text Add to dashboard Cite

Background: 5-Methylcytosine (m 5 C) is a prevalent base modification in tRNA and rRNA but it also occurs more broadly in the transcriptome, including in mRNA, where it serves incompletely understood molecular functions. In pursuit of potential links of m 5 C with mRNA translation, we performed polysome profiling of human HeLa cell lysates and subjected RNA from resultant fractions to efficient bisulfite conversion followed by RNA sequencing (bsRNA-seq). Bioinformatic filters for rigorous site calling were devised to reduce technical noise.Results: We obtained~1000 candidate m 5 C sites in the wider transcriptome, most of which were found in mRNA. Multiple novel sites were validated by amplicon-specific bsRNA-seq in independent samples of either human HeLa, LNCaP and PrEC cells. Furthermore, RNAi-mediated depletion of either the NSUN2 or TRDMT1 m 5 C:RNA methyltransferases showed a clear dependence on NSUN2 for the majority of tested sites in both mRNAs and noncoding RNAs. Candidate m 5 C sites in mRNAs are enriched in 5′UTRs and near start codons and are embedded in a local context reminiscent of the NSUN2-dependent m 5 C sites found in the variable loop of tRNA. Analysing mRNA sites across the polysome profile revealed that modification levels, at bulk and for many individual sites, were inversely correlated with ribosome association. Conclusions: Our findings emphasise the major role of NSUN2 in placing the m 5 C mark transcriptome-wide. We further present evidence that substantiates a functional interdependence of cytosine methylation level with mRNA translation. Additionally, we identify several compelling candidate sites for future mechanistic analysis.

show abstract

Section: Amplicon Bisulfite Rna Sequencing Data Generation and Analysismentioning

confidence: 99%

Multiple links between 5-methylcytosine content of mRNA and translation

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Unlike the well-known ALKB family substrates such as m1A and m 6 A, m 5 C methylation modification occurs on the carbon atom rather than the nitrogen atom. Surprisingly, in 2019 Ke Bian et al Found that ALKB, ALKBH2, and ALKBH3 can oxidize m 5 C in vitro and produce the same intermediates: hm 5 C, f 5 C, and ca 5 C. The experiment used enzymatic reaction conditions similar to TET, and the presence of hm 5 C, f 5 C, and ca 5 C were detected in the oxidation products of the three enzymes [41]. ALKB and ALKBH3 have a clear preference for single-stranded DNA substrates, while ALKBH2 seems to have a slight preference for doublestranded DNA substrates.…”

Section: Intermediates Captured During M5c Demethylationmentioning

confidence: 99%

Oxidative intermediates captured during demethylation of DNA and RNA

Wang

Zhang

2021

E3S Web Conf.

View full text Add to dashboard Cite

DNA and RNA have various methylation modifications or damage that are directly related to some human diseases and physiological regulation. Most of these methylation modifications are reversible and can be dynamically repaired by RNA or DNA demethylases. Over the past few decades, enzymes from the ALKB and TET families have been shown to have the ability to demethylate nucleic acids, which involves intermediates in the oxidative repair process. These intermediates can be accurately captured by advanced methods such as HPLC, LC-MS, TLC, and crystallization, which can significantly promote our understanding of the dynamic mechanism of demethylation. In this review, we discuss recent research advances in this area and raise open questions and constructive opinions about the capture of nucleic acid demethylation intermediates.

show abstract

“…The alkB homolog (ALKBH) family enzymes are α-KG-dependent dioxygenases involved in repairing DNA damage caused by alkylating agents[ 140 , 141 ]. In IDH -mutant LGG cells, the activities of ALKBH enzymes are suppressed, which makes these cells sensitive to alkylation damage[ 142 ].…”

Section: Other Pathways Regulated By Oncometabolitesmentioning

confidence: 99%

Role of succinate dehydrogenase deficiency and oncometabolites in gastrointestinal stromal tumors

Zhao

Feng

Guo

et al. 2020

WJG

View full text Add to dashboard Cite

Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. At the molecular level, GISTs can be categorized into two groups based on the causative oncogenic mutations. Approximately 85% of GISTs are caused by gain-of-function mutations in the tyrosine kinase receptor KIT or platelet-derived growth factor receptor alpha (PDGFRA). The remaining GISTs, referred to as wild-type (WT) GISTs, are often deficient in succinate dehydrogenase complex (SDH), a key metabolic enzyme complex in the tricarboxylic acid (TCA) cycle and electron transport chain. SDH deficiency leads to the accumulation of succinate, a metabolite produced by the TCA cycle. Succinate inhibits α-ketoglutarate-dependent dioxygenase family enzymes, which comprise approximately 60 members and regulate key aspects of tumorigenesis such as DNA and histone demethylation, hypoxia responses, and m6A mRNA modification. For this reason, succinate and metabolites with similar structures, such as D-2-hydroxyglutarate and fumarate, are considered oncometabolites. In this article, we review recent advances in the understanding of how metabolic enzyme mutations and oncometabolites drive human cancer with an emphasis on SDH mutations and succinate in WT GISTs.

show abstract

DNA repair enzymes ALKBH2, ALKBH3, and AlkB oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in vitro

Cited by 57 publications

References 38 publications

Multiple links between 5-methylcytosine content of mRNA and translation

Multiple links between 5-methylcytosine content of mRNA and translation

Oxidative intermediates captured during demethylation of DNA and RNA

Role of succinate dehydrogenase deficiency and oncometabolites in gastrointestinal stromal tumors

Contact Info

Product

Resources

About