ORCID Profile
0000-0002-3579-3317
Current Organisation
Ludwig-Maximilians-Universität München
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Publisher: Wiley
Date: 25-08-2016
Abstract: 5‐Formyl‐2′‐deoxycytosine (fdC) is a recently discovered epigenetic base in the genome of stem cells, with yet unknown functions. Sequencing data show that the base is enriched in CpG islands of promoters and hence likely involved in the regulation of transcription during cellular differentiation. fdC is known to be recognized and excised by the enzyme thymine‐DNA‐glycosylase (Tdg). As such, fdC is believed to function as an intermediate during active demethylation. In order to understand the function of the new epigenetic base fdC, it is important to analyze its formation and removal at defined genomic sites. Here, we report a new method that combines sequence‐specific chemical derivatization of fdC with droplet digital PCR that enables such analysis. We show initial data, indicating that the repair protein Tdg removes only 50 % of the fdCs at a given genomic site, arguing that fdC is a semipermanent base.
Publisher: American Chemical Society (ACS)
Date: 21-07-2017
DOI: 10.1021/JACS.7B04131
Abstract: 5-Formyl-dC (fdC) and 5-carboxy-dC (cadC) are newly discovered bases in the mammalian genome that are supposed to be substrates for base excision repair (BER) in the framework of active demethylation. The bases are recognized by the monofunctional thymine DNA glycosylase (Tdg), which cleaves the glycosidic bond of the bases to give potentially harmful abasic sites (AP-sites). Because of the turnover of fdC and cadC during cell state transitions, it is an open question to what extent such harmful AP-sites may accumulate during these processes. Here, we report the development of a new reagent that in combination with mass spectrometry (MS) allows us to quantify the levels of AP-sites. This combination also allowed the quantification of β-elimination (βE) products, which are repair intermediates of bifunctional DNA glycosylases. In combination with feeding of isotopically labeled nucleosides, we were able to trace the intermediates back to their original nucleobases. We show that, while the steady-state levels of fdC and cadC are substantially increased in Tdg-deficient cells, those of both AP- and βE-sites are unaltered. The levels of the detected BER intermediates are 1 and 2 orders of magnitude lower than those of cadC and fdC, respectively. Thus, neither the presence of fdC nor that of cadC in stem cells leads to the accumulation of harmful AP- and βE-site intermediates.
Publisher: American Chemical Society (ACS)
Date: 26-09-2022
DOI: 10.1021/ACS.BIOCONJCHEM.2C00353
Abstract: Here we describe the development of a novel click chemistry-based method for the generation and lification of full-length cDNA libraries from total RNA, while avoiding the need for problematic template-switching (TS) reactions. Compared with prior efforts, our method involves neither random priming nor stochastic cDNA termination, thus enabling lification of transcripts that were previously inaccessible via related click chemistry-based RNA sequencing techniques. A key modification involving the use of PCR primers containing two overhanging 3'-nucleotides substantially improved the read-through compatibility of the 1,4-disubstituted 1,2,3-triazole-containing cDNA, where such modifications typically hinder lification. This allowed us to more than double the possible insert size compared with the state-of-the art click chemistry-based technique, PAC-seq. Furthermore, our method performed on par with a commercially available PCR-cDNA RNA sequencing kit, as determined by Oxford Nanopore sequencing. Given the known advantages of PAC-seq, namely, suppression of PCR artifacts, we anticipate that our contribution could enable erse applications including improved analyses of mRNA splicing variants and fusion transcripts.
Publisher: Wiley
Date: 05-11-2020
Publisher: Wiley
Date: 05-2021
Abstract: The four non‐canonical nucleotides in the human genome 5‐methyl‐, 5‐hydroxymethyl‐, 5‐formyl‐ and 5‐carboxydeoxycytidine (mdC, hmdC, fdC and cadC) form a second layer of epigenetic information that contributes to the regulation of gene expression. Formation of the oxidized nucleotides hmdC, fdC and cadC requires oxidation of mdC by ten‐eleven translocation (Tet) enzymes that require oxygen, Fe(II) and α‐ketoglutarate as cosubstrates. Although these oxidized forms of mdC are widespread in mammalian genomes, experimental evidence for their presence in fungi and plants is ambiguous. This vagueness is caused by the fact that these oxidized mdC derivatives are also formed as oxidative lesions, resulting in unclear basal levels that are likely to have no epigenetic function. Here, we report the xdC levels in the fungus Amanita muscaria in comparison to murine embryonic stem cells (mESCs), HEK cells and induced pluripotent stem cells (iPSCs), to obtain information about the basal levels of hmdC, fdC and cadC as DNA lesions in the genome.
Publisher: Wiley
Date: 25-08-2016
Abstract: Die epigenetische Base 5‐Formyl‐2′‐desoxycytosin (fdC) wurde kürzlich im Genom von Stammzellen entdeckt. Ihre Funktion ist bisher jedoch unbekannt. Daten aus Genomsequenzierungen zeigen eine Anreicherung in CpG‐Inseln von Promotoren, weshalb eine Beteiligung an der Regulation der Transkription während der zellulären Differenzierung angenommen wird. Auch ist fdC dafür bekannt, von dem Enzym Thymin‐DNA‐Glykosylase (Tdg) erkannt und ausgeschnitten zu werden. Folglich wird angenommen, dass fdC als Intermediat während der aktiven Demethylierung auftritt. Um die Funktion von fdC zu verstehen, ist es von großer Bedeutung, seine Bildung und Entfernung an definierten genomischen Positionen analysieren zu können. Im Folgenden beschreiben wir eine neue derartige Methode, die sequenzspezifische chemische Derivatisierung von fdC mit Droplet Digital PCR kombiniert. Erste Ergebnisse zeigen, dass das Reparaturprotein Tdg nur 50 % der fdCs an einer bestimmten Position im Genom entfernt, was auf semipermanente Eigenschaften dieser Base hinweist.
Publisher: Springer Science and Business Media LLC
Date: 27-11-2018
Abstract: Tet enzymes oxidize 5-methyl-deoxycytidine (mdC) to 5-hydroxymethyl-dC (hmdC), 5-formyl-dC (fdC) and 5-carboxy-dC (cadC) in DNA. It was proposed that fdC and cadC deformylate and decarboxylate, respectively, to dC over the course of an active demethylation process. This would re-install canonical dC bases at previously methylated sites. However, whether such direct C-C bond cleavage reactions at fdC and cadC occur in vivo remains an unanswered question. Here we report the incorporation of synthetic isotope- and (R)-2'-fluorine-labeled dC and fdC derivatives into the genome of cultured mammalian cells. Following the fate of these probe molecules using UHPLC-MS/MS provided quantitative data about the formed reaction products. The data show that the labeled fdC probe is efficiently converted into the corresponding labeled dC, most likely after its incorporation into the genome. Therefore, we conclude that fdC undergoes C-C bond cleavage in stem cells, leading to the direct re-installation of unmodified dC.
No related grants have been discovered for Markus Müller.