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Tet2 promotes pathogen infection-induced myelopoiesis through mRNA oxidation
Abstract
Varieties of RNA modification form the epitranscriptome for post-transcriptional regulation. 5-Methylcytosine (5-mC) is a sparse RNA modification in messenger RNA (mRNA) under physiological conditions. The function of RNA 5-hydroxymethylcytosine (5-hmC) oxidized by ten-eleven translocation (Tet) proteins in Drosophila has been revealed more recently. However, the turnover and function of 5-mC in mammalian mRNA have been largely unknown. Tet2 suppresses myeloid malignancies mostly in an enzymatic activity-dependent manner, and is important in resolving inflammatory response in an enzymatic activity-independent way. Myelopoiesis is a common host immune response in acute and chronic infections; however, its epigenetic mechanism needs to be identified. Here we demonstrate that Tet2 promotes infection-induced myelopoiesis in an mRNA oxidation-dependent manner through Adar1-mediated repression of Socs3 expression at the post-transcription level. Tet2 promotes both abdominal sepsis-induced emergency myelopoiesis and parasite-induced mast cell expansion through decreasing mRNA levels of Socs3, a key negative regulator of the JAK-STAT pathway that is critical for cytokine-induced myelopoiesis. Tet2 represses Socs3 expression through Adar1, which binds and destabilizes Socs3 mRNA in a RNA editing-independent manner. For the underlying mechanism of Tet2 regulation at the mRNA level, Tet2 mediates oxidation of 5-mC in mRNA. Tet2 deficiency leads to the transcriptome-wide appearance of me…
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“Other studies also reported RNA m5C oxidation by TET2 or Drosophila TET homologue17–20.”
From RNA m5C oxidation by TET2 regulates chromatin state and leukaemogenesis (2024) · cites this paper as [19]
In the citing paper
“Both proteins have been associated with additional functions beyond DNA modification.30,31,32,33,34,35,36,37”
From Selective advantage of mutant stem cells in human clonal hematopoiesis is associated with attenuated response to inflammation and aging (2024) · cites this paper as [33]
In the citing paper
“In mast cells, Tet2 loss has contrasting effects -either suppressing mast cell differentiation and stimulating mast cell proliferation via C/EBP transcription factors 141 , or suppressing mast cell expansion in response to Schistosoma infection 142 .”
From Clonal haematopoiesis and dysregulation of the immune system (2023) · cites this paper as [141]
Citations
Cites
HTSeq—a Python framework to work with high-throughput sequencing data
Anders, S., Pyl, P. T., & Huber, W. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu638 · Cited by 21,464
TET enzymes, TDG and the dynamics of DNA demethylation
Kohli, R. M., & Zhang, Y. (2013) · Nature · doi:10.1038/nature12750 · Cited by 1,623
Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation
Moran-Crusio, K., Reavie, L., Shih, A., Abdel-Wahab, O., Ndiaye-Lobry, D., Lobry, C., Figueroa, M. E., Vasanthakumar, A., Patel, J., Zhao, X., et al. (2011) · Cancer Cell · doi:10.1016/j.ccr.2011.06.001 · Cited by 1,339
Tet2 is required to resolve inflammation by recruiting Hdac2 to specifically repress IL-6
Zhang, Q., Zhao, K., Shen, Q., Han, Y., Gu, Y., Li, X., Zhao, D., Liu, Y., Wang, C., Zhang, X., et al. (2015) · Nature · doi:10.1038/nature15252 · Cited by 807
Self-citationHuman and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA
Aas, P. A., Otterlei, M., Falnes, P. Ø., Vågbø, C. B., Skorpen, F., Akbari, M., Sundheim, O., Bjørås, M., Slupphaug, G., Seeberg, E., et al. (2003) · Nature · doi:10.1038/nature01363 · Cited by 638
Research works printed but not linked: 36
- Fu, Y., Dominissini, D., Rechavi, G. & He, C. Gene expression regulation mediated through reversible m6A RNA methylation. Nat. Rev. Genet. 15, 293–306 (2014) · DOI
- Zhao, B. S., Roundtree, I. A. & He, C. Post-transcriptional gene regulation by mRNA modifications. Nat. Rev. Mol. Cell Biol. 18, 31–42 (2017) · DOI
- Delatte, B. et al. Transcriptome-wide distribution and function of RNA hydroxymethylcytosine. Science 351, 282–285 (2016) · DOI · Paper page
- Fu, L. et al. Tet-mediated formation of 5-hydroxymethylcytosine in RNA. J. Am. Chem. Soc. 136, 11582–11585 (2014) · DOI · Paper page
- Álvarez-Errico, D., Vento-Tormo, R., Sieweke, M. & Ballestar, E. Epigenetic control of myeloid cell differentiation, identity and function. Nat. Rev. Immunol. 15, 7–17 (2015) · DOI
- Weber, G. F. et al. Interleukin-3 amplifies acute inflammation and is a potential therapeutic target in sepsis. Science 347, 1260–1265 (2015) · DOI
- Lantz, C. S. et al. Role for interleukin-3 in mast-cell and basophil development and in immunity to parasites. Nature 392, 90–93 (1998) · DOI
- He, C. et al. High-resolution mapping of RNA-binding regions in the nuclear proteome of embryonic stem cells. Mol. Cell 64, 416–430 (2016) · DOI
- Van Nostrand, E. L. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat. Methods 13, 508–514 (2016) · DOI · Paper page
- Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010) · DOI · Paper page
- Nishikura, K. A-to-I editing of coding and non-coding RNAs by ADARs. Nat. Rev. Mol. Cell Biol. 17, 83–96 (2016) · DOI · Paper page
- Anantharaman, A. et al. ADAR2 regulates RNA stability by modifying access of decay-promoting RNA-binding proteins. Nucleic Acids Res. 45, 4189–4201 (2017)
- Sakurai, M. et al. ADAR1 controls apoptosis of stressed cells by inhibiting Staufen1-mediated mRNA decay. Nat. Struct. Mol. Biol. 24, 534–543 (2017) · DOI
- Grzechnik, P., Gdula, M. R. & Proudfoot, N. J. Pcf11 orchestrates transcription termination pathways in yeast. Genes Dev. 29, 849–861 (2015) · DOI
- Behm-Ansmant, I., Gatfield, D., Rehwinkel, J., Hilgers, V. & Izaurralde, E. A conserved role for cytoplasmic poly(A)-binding protein 1 (PABPC1) in nonsense-mediated mRNA decay. EMBO J. 26, 1591–1601 (2007) · DOI
- Hu, L. et al. Crystal structure of TET2–DNA complex: insight into TET-mediated 5mC oxidation. Cell 155, 1545–1555 (2013) · DOI
- Goll, M. G. et al. Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science 311, 395–398 (2006) · DOI
- Jarmoskaite, I. & Russell, R. RNA helicase proteins as chaperones and remodelers. Annu. Rev. Biochem. 83, 697–725 (2014) · DOI
- Popis, M. C., Blanco, S. & Frye, M. Posttranscriptional methylation of transfer and ribosomal RNA in stress response pathways, cell differentiation, and cancer. Curr. Opin. Oncol. 28, 65–71 (2016) · DOI
- Amort, T. et al. Long non-coding RNAs as targets for cytosine methylation. RNA Biol. 10, 1003–1008 (2013) · DOI
- Hussain, S. et al. NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Reports 4, 255–261 (2013) · DOI
- Edelheit, S., Schwartz, S., Mumbach, M. R., Wurtzel, O. & Sorek, R. Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs. PLoS Genet. 9, e1003602 (2013) · DOI
- Luo, Y., Feng, J., Xu, Q., Wang, W. & Wang, X. NSun2 deficiency protects endothelium from inflammation via mRNA methylation of ICAM-1. Circ. Res. 118, 944–956 (2016) · DOI
- Rittirsch, D., Huber-Lang, M. S., Flierl, M. A. & Ward, P. A. Immunodesign of experimental sepsis by cecal ligation and puncture. Nat. Protocols 4, 31–36 (2009) · DOI · Paper page
- Yu, M. et al. Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. Nat. Protocols 7, 2159–2170 (2012) · DOI
- Li, X. et al. Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome. Nat. Chem. Biol. 12, 311–316 (2016) · DOI
- Liddicoat, B. J. et al. RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself. Science 349, 1115–1120 (2015) · DOI
- Austin, E. G. et al. Improvements to the HITS-CLIP protocol eliminate widespread mispriming artifacts. BMC Genomics 17, 338 (2016) · DOI
- Zhang, C. & Darnell, R. B. Mapping in vivo protein–RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat. Biotechnol. 29, 607–614 (2011) · DOI
- Keene, J. D., Komisarow, J. M. & Friedersdorf, M. B. RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat. Protocols 1, 302–307 (2006) · DOI
- Dominissini, D., Moshitch-Moshkovitz, S., Salmon-Divon, M., Amariglio, N. & Rechavi, G. Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing. Nat. Protocols 8, 176–189 (2013) · DOI
- Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protocols 7, 562–578 (2012) · DOI
- Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010) · DOI · Paper page
- Ramaswami, G. et al. Identifying RNA editing sites using RNA sequencing data alone. Nat. Methods 10, 128–132 (2013) · DOI
- Peng, Z. et al. Comprehensive analysis of RNA-seq data reveals extensive RNA editing in a human transcriptome. Nat. Biotechnol. 30, 253–260 (2012) · DOI
- Liang, F. et al. BS-RNA: an efficient mapping and annotation tool for RNA bisulfite sequencing data. Comput. Biol. Chem. 65, 173–177 (2016) · DOI
Cited by
Epigenetic regulation of the innate immune response to infection
Zhang, Q., & Cao, X. (2019) · Nature Reviews Immunology · doi:10.1038/s41577-019-0151-6 · Cited by 366
Self-citationClonal haematopoiesis and dysregulation of the immune system
Belizaire, R., Wong, W. J., Robinette, M. L., & Ebert, B. L. (2023) · Nature Reviews Immunology · doi:10.1038/s41577-023-00843-3 · Cited by 161
Jakobsen, N. A., Turkalj, S., Zeng, A. G. X., Stoilova, B., Metzner, M., Rahmig, S., Nagree, M. S., Shah, S., Moore, R., Usukhbayar, B., et al. (2024) · Cell Stem Cell · doi:10.1016/j.stem.2024.05.010 · Cited by 130
RNA m5C oxidation by TET2 regulates chromatin state and leukaemogenesis
Zou, Z., Dou, X., Li, Y., Zhang, Z., Wang, J., Gao, B., Xiao, Y., Wang, Y., Zhao, L., Sun, C., et al. (2024) · Nature · doi:10.1038/s41586-024-07969-x · Cited by 103
Matatall, K. A., Wathan, T. K., Nguyen, M., Chen, H., McDonald, A., Qi, G., Belk, J. A., Florez, M. A., Le, D. T., Olarinde, T., et al. (2025) · Cell Stem Cell · doi:10.1016/j.stem.2025.06.006 · Cited by 23
The bone marrow hematopoietic niche and its adaptation to infection
Gomes, A. C., Saraiva, M., & Gomes, M. S. (2021) · Seminars in Cell & Developmental Biology · doi:10.1016/j.semcdb.2020.05.014 · Cited by 18
Metadata
- Authors
- Shen, Q., Zhang, Q., Shi, Y., Shi, Q., Jiang, Y., Gu, Y., Li, Z., Li, X., Zhao, K., Wang, C., Li, N., & Cao, X.
- Venue
- Nature
- Published
- 2018-01-24
- Volume
- 554
- Issue
- 7690
- Pages
- 123-127
- ISSN
- 0028-0836
- 1476-4687
- Cited by
- 243
- References
- 5
- Language
- en
- Licence
- www.springer.com/tdm (tdm)
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