Letter | Published:

Tet2 promotes pathogen infection-induced myelopoiesis through mRNA oxidation

Nature volume 554, pages 123127 (01 February 2018) | Download Citation

Abstract

Varieties of RNA modification form the epitranscriptome for post-transcriptional regulation1. 5-Methylcytosine (5-mC) is a sparse RNA modification in messenger RNA (mRNA) under physiological conditions2. The function of RNA 5-hydroxymethylcytosine (5-hmC) oxidized by ten-eleven translocation (Tet) proteins in Drosophila has been revealed more recently3,4. 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 manner5, and is important in resolving inflammatory response in an enzymatic activity-independent way6. 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 methylated cytosines, including ones in the 3′ untranslated region of Socs3, which influences double-stranded RNA formation for Adar1 binding, probably through cytosine methylation-specific readers, such as RNA helicases. Our study reveals a previously unknown regulatory role of Tet2 at the epitranscriptomic level, promoting myelopoiesis during infection in the mammalian system by decreasing 5-mCs in mRNAs. Moreover, the inhibitory function of cytosine methylation on double-stranded RNA formation and Adar1 binding in mRNA reveals its new physiological role in the mammalian system.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from $8.99

All prices are NET prices.

Accessions

Primary accessions

Gene Expression Omnibus

References

  1. 1.

    , , & Gene expression regulation mediated through reversible m6A RNA methylation. Nat. Rev. Genet. 15, 293–306 (2014)

  2. 2.

    , & Post-transcriptional gene regulation by mRNA modifications. Nat. Rev. Mol. Cell Biol. 18, 31–42 (2017)

  3. 3.

    et al. Transcriptome-wide distribution and function of RNA hydroxymethylcytosine. Science 351, 282–285 (2016)

  4. 4.

    et al. Tet-mediated formation of 5-hydroxymethylcytosine in RNA. J. Am. Chem. Soc. 136, 11582–11585 (2014)

  5. 5.

    , , & Epigenetic control of myeloid cell differentiation, identity and function. Nat. Rev. Immunol. 15, 7–17 (2015)

  6. 6.

    et al. Tet2 is required to resolve inflammation by recruiting Hdac2 to specifically repress IL-6. Nature 525, 389–393 (2015)

  7. 7.

    et al. Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation. Cancer Cell 20, 11–24 (2011)

  8. 8.

    et al. Interleukin-3 amplifies acute inflammation and is a potential therapeutic target in sepsis. Science 347, 1260–1265 (2015)

  9. 9.

    et al. Role for interleukin-3 in mast-cell and basophil development and in immunity to parasites. Nature 392, 90–93 (1998)

  10. 10.

    et al. High-resolution mapping of RNA-binding regions in the nuclear proteome of embryonic stem cells. Mol. Cell 64, 416–430 (2016)

  11. 11.

    et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat. Methods 13, 508–514 (2016)

  12. 12.

    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)

  13. 13.

    A-to-I editing of coding and non-coding RNAs by ADARs. Nat. Rev. Mol. Cell Biol. 17, 83–96 (2016)

  14. 14.

    et al. ADAR2 regulates RNA stability by modifying access of decay-promoting RNA-binding proteins. Nucleic Acids Res. 45, 4189–4201 (2017)

  15. 15.

    et al. ADAR1 controls apoptosis of stressed cells by inhibiting Staufen1-mediated mRNA decay. Nat. Struct. Mol. Biol. 24, 534–543 (2017)

  16. 16.

    , & Pcf11 orchestrates transcription termination pathways in yeast. Genes Dev. 29, 849–861 (2015)

  17. 17.

    , , , & A conserved role for cytoplasmic poly(A)-binding protein 1 (PABPC1) in nonsense-mediated mRNA decay. EMBO J. 26, 1591–1601 (2007)

  18. 18.

    et al. Crystal structure of TET2–DNA complex: insight into TET-mediated 5mC oxidation. Cell 155, 1545–1555 (2013)

  19. 19.

    & TET enzymes, TDG and the dynamics of DNA demethylation. Nature 502, 472–479 (2013)

  20. 20.

    et al. Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science 311, 395–398 (2006)

  21. 21.

    & RNA helicase proteins as chaperones and remodelers. Annu. Rev. Biochem. 83, 697–725 (2014)

  22. 22.

    , & Posttranscriptional methylation of transfer and ribosomal RNA in stress response pathways, cell differentiation, and cancer. Curr. Opin. Oncol. 28, 65–71 (2016)

  23. 23.

    et al. Long non-coding RNAs as targets for cytosine methylation. RNA Biol. 10, 1003–1008 (2013)

  24. 24.

    et al. NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Reports 4, 255–261 (2013)

  25. 25.

    et al. Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA. Nature 421, 859–863 (2003)

  26. 26.

    , , , & Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs. PLoS Genet. 9, e1003602 (2013)

  27. 27.

    , , , & NSun2 deficiency protects endothelium from inflammation via mRNA methylation of ICAM-1. Circ. Res. 118, 944–956 (2016)

  28. 28.

    , , & Immunodesign of experimental sepsis by cecal ligation and puncture. Nat. Protocols 4, 31–36 (2009)

  29. 29.

    et al. Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. Nat. Protocols 7, 2159–2170 (2012)

  30. 30.

    et al. Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome. Nat. Chem. Biol. 12, 311–316 (2016)

  31. 31.

    et al. RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself. Science 349, 1115–1120 (2015)

  32. 32.

    et al. Improvements to the HITS-CLIP protocol eliminate widespread mispriming artifacts. BMC Genomics 17, 338 (2016)

  33. 33.

    & Mapping in vivo protein–RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat. Biotechnol. 29, 607–614 (2011)

  34. 34.

    , & RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat. Protocols 1, 302–307 (2006)

  35. 35.

    , , , & Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing. Nat. Protocols 8, 176–189 (2013)

  36. 36.

    et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protocols 7, 562–578 (2012)

  37. 37.

    , & HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015)

  38. 38.

    & Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010)

  39. 39.

    et al. Identifying RNA editing sites using RNA sequencing data alone. Nat. Methods 10, 128–132 (2013)

  40. 40.

    et al. Comprehensive analysis of RNA-seq data reveals extensive RNA editing in a human transcriptome. Nat. Biotechnol. 30, 253–260 (2012)

  41. 41.

    et al. BS-RNA: an efficient mapping and annotation tool for RNA bisulfite sequencing data. Comput. Biol. Chem. 65, 173–177 (2016)

Download references

Acknowledgements

We thank R. L. Levine for providing Tet2 knockout mice, and K. Wang and C. Yi for helping with LC–MS analysis of RNA methylation. We thank C. Hu and W. Huang for technician support. This work was supported by grants from the National Natural Science Foundation of China (81788101, 31390431, 91542204, 31670884), the Shanghai Rising-Star Program (17QA1405300) and the CAMS Innovation Fund for Medical Science (2016-12M-1-003).

Author information

Author notes

    • Qicong Shen
    •  & Qian Zhang

    These authors contributed equally to this work.

Affiliations

  1. National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai 200433, China

    • Qicong Shen
    • , Qian Zhang
    • , Yanyan Jiang
    • , Yan Gu
    • , Nan Li
    •  & Xuetao Cao
  2. Department of Immunology & Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100005, China

    • Qian Zhang
    • , Xia Li
    • , Kai Zhao
    • , Chunmei Wang
    •  & Xuetao Cao
  3. Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China

    • Yang Shi
    • , Qingzhu Shi
    •  & Zhiqing Li

Authors

  1. Search for Qicong Shen in:

  2. Search for Qian Zhang in:

  3. Search for Yang Shi in:

  4. Search for Qingzhu Shi in:

  5. Search for Yanyan Jiang in:

  6. Search for Yan Gu in:

  7. Search for Zhiqing Li in:

  8. Search for Xia Li in:

  9. Search for Kai Zhao in:

  10. Search for Chunmei Wang in:

  11. Search for Nan Li in:

  12. Search for Xuetao Cao in:

Contributions

X.C. designed and supervised the study. X.C., Q.Z. and Q.She. analysed the data and wrote the manuscript. Q.She. established pathogen infection mouse models. Q.She. and Q.Z. confirmed and genotyped mice, performed RNA methylation- and RNA editing-related experiments and analysed all the data of this study. Q.She. and Q.Z. performed CLIP, bisulfite sequencing and analysed the sequencing data. Y.S. performed the dot plot assays. Q.She. and Q. Shi constructed plasmids with aid from Q.Z. Y.J. performed parasite infections of mice. Y.G. and Z.L. sorted and analysed immune cells. X.L., K.Z., C.W. and N.L. provided reagents and advice.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Xuetao Cao.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Figure 1

    This file contains the uncropped gels.

  2. 2.

    Life Sciences Reporting Summary

Excel files

  1. 1.

    Supplementary Data

    This file contains Supplementary Tables 1-4.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nature25434

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.