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@ARTICLE{Dehnen:306182,
      author       = {J. A. Dehnen and A. V. Gopanenko and C. Scholz and M. U.
                      Musheev and C. Niehrs$^*$},
      title        = {5-{F}ormylcytosine is not a prevalent {RNA} modification in
                      mammalian cells.},
      journal      = {Nature Communications},
      volume       = {16},
      number       = {1},
      issn         = {2041-1723},
      address      = {[London]},
      publisher    = {Springer Nature},
      reportid     = {DKFZ-2025-02422},
      pages        = {9925},
      year         = {2025},
      note         = {#LA:A050# / DKFZ-ZMBH Alliance},
      abstract     = {The RNA modification 5-formylcytidine (f5C) is poorly
                      explored in mammals. Low f5C levels reported in mRNA may
                      reflect spurious 5-methylcytidine (m5C) oxidation or
                      targeted demethylation by TET or ALKBH1 dioxygenases. We
                      analyzed f5C in RNA of mouse embryonic stem cells (mESCs)
                      using LC-MS/MS and chemical-assisted sequencing. We reveal
                      that the previously reported pyridine-borane-sequencing
                      misidentifies N4-acetylcytidine (ac4C) and unmodified,
                      hyper-reactive cytidines in a CUMC context as f5C. To
                      overcome these limitations, we developed FIBo-seq with
                      enhanced specificity and sensitivity for f5C-sequencing. We
                      find no evidence for a role of TET enzymes in generating
                      f5C, unlike for ALKBH1. Moreover, no f5C sites are
                      detectable in mRNA. Instead, the bulk of mammalian f5C
                      resides in the well-established mitochondrial tRNA
                      Methionine (mt-tRNAMet) and is mediated by ALKBH1. The
                      results argue against an instructive function for f5C
                      outside tRNA in mammals.},
      keywords     = {Animals / Mice / Cytosine: analogs $\&$ derivatives /
                      Cytosine: metabolism / Cytidine: analogs $\&$ derivatives /
                      Cytidine: metabolism / AlkB Homolog 1, Histone H2a
                      Dioxygenase: metabolism / AlkB Homolog 1, Histone H2a
                      Dioxygenase: genetics / Mouse Embryonic Stem Cells:
                      metabolism / RNA, Messenger: metabolism / RNA, Messenger:
                      genetics / RNA, Transfer, Met: metabolism / RNA, Transfer,
                      Met: genetics / Proto-Oncogene Proteins: metabolism /
                      Proto-Oncogene Proteins: genetics / RNA: metabolism / RNA
                      Processing, Post-Transcriptional / Tandem Mass Spectrometry
                      / DNA-Binding Proteins / Cytosine (NLM Chemicals) / Cytidine
                      (NLM Chemicals) / 5-formylcytosine (NLM Chemicals) / AlkB
                      Homolog 1, Histone H2a Dioxygenase (NLM Chemicals) / RNA,
                      Messenger (NLM Chemicals) / RNA, Transfer, Met (NLM
                      Chemicals) / Alkbh1 protein, mouse (NLM Chemicals) /
                      Proto-Oncogene Proteins (NLM Chemicals) / RNA (NLM
                      Chemicals) / N-acetylcytidine (NLM Chemicals) / TET1
                      protein, mouse (NLM Chemicals) / DNA-Binding Proteins (NLM
                      Chemicals)},
      cin          = {A050},
      ddc          = {500},
      cid          = {I:(DE-He78)A050-20160331},
      pnm          = {311 - Zellbiologie und Tumorbiologie (POF4-311)},
      pid          = {G:(DE-HGF)POF4-311},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:41219180},
      pmc          = {pmc:PMC12606350},
      doi          = {10.1038/s41467-025-66090-3},
      url          = {https://inrepo02.dkfz.de/record/306182},
}