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Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives
Open accessAbstract
Tet proteins oxidize 5-methylcytosine (mC) to generate 5-hydroxymethyl (hmC), 5-formyl (fC), and 5-carboxylcytosine (caC). The exact function of these oxidative cytosine bases remains elusive. We applied quantitative mass-spectrometry-based proteomics to identify readers for mC and hmC in mouse embryonic stem cells (mESC), neuronal progenitor cells (NPC), and adult mouse brain tissue. Readers for these modifications are only partially overlapping, and some readers, such as Rfx proteins, display strong specificity. Interactions are dynamic during differentiation, as for example evidenced by the mESC-specific binding of Klf4 to mC and the NPC-specific binding of Uhrf2 to hmC, suggesting specific biological roles for mC and hmC. Oxidized derivatives of mC recruit distinct transcription regulators as well as a large number of DNA repair proteins in mouse ES cells, implicating the DNA damage response as a major player in active DNA demethylation.
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“19 proteins were identified that interact preferentially with the methylated DNA probe rather than the non-methylated counterpart in mouse embryonic stem (ES) cell nuclear extracts.”
From Transcription factors as readers and effectors of DNA methylation (2016) · cites this paper as [51]
In the citing paper
“a few proteins such as KLF4 and homeobox A5 (HOXA5) were shown to bind mCpG sites in both species”
From Transcription factors as readers and effectors of DNA methylation (2016) · cites this paper as [51]
In the citing paper
“many TFs (such as MHC class II regulatory factor RFX1, zinc-finger homeobox 3 (ZFHX3), lysine-specific histone demethylase 1A (LSD1), zinc-finger and BTB domain-containing protein 44 (ZBT44) and thymocyte nuclear protein 1 (THYN1; also known as THY28), and the Krüppel-like factors (for example, KLF2, KLF4 and KLF5)), were identified as new mCpG-binding proteins (TABLE 2).”
From Transcription factors as readers and effectors of DNA methylation (2016) · cites this paper as [51]
In the citing paper
“The authors applied the same approach to neuronal progenitor cells and found that a large and distinct set of proteins showed preferential binding to mCpG sites, suggesting that the interaction with mCpG is dynamic and thus varies under different physiological conditions.”
From Transcription factors as readers and effectors of DNA methylation (2016) · cites this paper as [51]
In the citing paper
“this protein was previously shown to bind to methylated DNA47,51.”
From Transcription factors as readers and effectors of DNA methylation (2016) · cites this paper as [51]
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Metadata
- Authors
- Spruijt, C. G., Gnerlich, F., Smits, A. H., Pfaffeneder, T., Jansen, P. W. T. C., Bauer, C., Münzel, M., Wagner, M., Müller, M., Khan, F., Eberl, H. C., Mensinga, A., Brinkman, A. B., Lephikov, K., Müller, U., Walter, J., Boelens, R., van Ingen, H., Leonhardt, H., Carell, T., & Vermeulen, M.
- Affiliations
- University Medical Center Utrecht (NL)
- Center for Integrated Protein Science Munich (DE)
- Utrecht University (NL)
- Max Planck Institute of Biochemistry (DE)
- Radboud University Nijmegen (NL)
- Saarland University (DE)
- Corresponding author
- Carell, Thomas
- Vermeulen, Michiel
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2013-02
- Volume
- 152
- Issue
- 5
- Pages
- 1146-1159
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2157458089
- Cited by
- 973
- References
- 64
- Citations by year
- 2026: 13 · 2025: 26 · 2024: 51 · 2023: 38 · 2022: 43 · 2021: 69 · 2020: 69 · 2019: 89 · 2018: 81 · 2017: 104 · 2016: 115 · 2015: 98 · 2014: 110 · 2013: 65
- FWCI
- 57.81
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Radboud Repository (Radboud University) (submittedVersion)
- Funders
- Max-Planck-Gesellschaft
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Keywords
- 5-hydroxymethylcytosine, 5-methylcytosine, 5-formylcytosine, 5-carboxylcytosine, TET enzymes, DNA demethylation, epigenetic reader protein, KLF4, UHRF2, DNA repair proteins, DNA damage response, mouse embryonic stem cells, neural progenitor cells, brain tissue, cell differentiation
- MeSH terms
- Regulatory Factor X Transcription Factors, Kruppel-Like Factor 4, Animals, Brain, Cytosine, DNA-Binding Proteins, Oxidation-Reduction, Proto-Oncogene Proteins, Mass Spectrometry, Stem Cells, Transcription Factors, DNA Methylation, 5-Methylcytosine, Ubiquitin-Protein Ligases, DNA Glycosylases, Mice, Embryonic Stem Cells
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