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YTHDF2 in dentate gyrus is the m6A reader mediating m6A modification in hippocampus-dependent learning and memory

Molecular Psychiatry volume 28, pages 1679–1691 (2023)Cite this article

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Abstract

N6-methyladenosine (m6A) has been demonstrated to regulate learning and memory in mice. To investigate the mechanism by which m6A modification exerts its function through its reader proteins in the hippocampus, as well as to unveil the specific subregions of the hippocampus that are crucial for memory formation, we generated dentate gyrus (DG)-, CA3-, and CA1-specific Ythdf1 and Ythdf2 conditional knockout (cKO) mice, respectively. Surprisingly, we found that only the DG-specific Ythdf2 cKO mice displayed impaired memory formation, which is inconsistent with the previous report showing that YTHDF1 was involved in this process. YTHDF2 controls the stability of its target transcripts which encode proteins that regulate the elongation of mossy fibers (MF), the axons of DG granule cells. DG-specific Ythdf2 ablation caused MF overgrowth and impairment of the MF-CA3 excitatory synapse development and transmission in the stratum lucidum. Thus, this study identifies the m6A reader YTHDF2 in dentate gyrus as the only regulator that mediates m6A modification in hippocampus-dependent learning and memory.

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Fig. 1: YTHDF1 and YTHDF2 are highly expressed in the early postnatal mouse hippocampus.
Fig. 2: Ythdf2 conditional knockout in dentate gyrus but not in other hippocampal subregions disturbs learning and memory.
Fig. 3: Loss-of-function of YTHDF2 in DG granule cells enhances axon growth both in vitro and in vivo.
Fig. 4: DG-CA3 synapse development and transmission are impaired in the DG-specific Ythdf2 cKO mice.
Fig. 5: Target mRNAs of YTHDF2 were identified by integrating anti-YTHDF2 RIP-seq and RNAseq of DG-specific Ythdf2 cKO.
Fig. 6: YTHDF2 destabilizes its m6A-modified target mRNAs to control DG granule cell axon growth.

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Data availability

RNAseq of Ythdf2 cKO in DG and anti-YTHDF2 RIPseq data have been deposited in NCBI’s Gene Expression Omnibus (GEO) and are accessible through accession numbers GSE171790 and GSE171791.

References

  1. Squire LR, Stark CE, Clark RE. The medial temporal lobe. Annu Rev Neurosci. 2004;27:279–306.

    Article  CAS  PubMed  Google Scholar 

  2. Kraus BJ, Robinson RJ 2nd, White JA, Eichenbaum H, Hasselmo ME. Hippocampal “time cells”: time versus path integration. Neuron. 2013;78:1090–101.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Goode TD, Tanaka KZ, Sahay A, McHugh TJ. An integrated index: engrams, place cells, and hippocampal memory. Neuron. 2020;107:805–20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Basu J, Siegelbaum SA. The corticohippocampal circuit, synaptic plasticity, and memory. Cold Spring Harb Perspect Biol. 2015;7:a021733.

    Article  PubMed  PubMed Central  Google Scholar 

  5. van Strien NM, Cappaert NL, Witter MP. The anatomy of memory: an interactive overview of the parahippocampal-hippocampal network. Nat Rev Neurosci. 2009;10:272–82.

    Article  PubMed  Google Scholar 

  6. Wiener D, Schwartz S. The epitranscriptome beyond m(6)A. Nat Rev Genet. 2021;22:119–31.

    Article  CAS  PubMed  Google Scholar 

  7. Livneh I, Moshitch-Moshkovitz S, Amariglio N, Rechavi G, Dominissini D. The m(6)A epitranscriptome: transcriptome plasticity in brain development and function. Nat Rev Neurosci. 2020;21:36–51.

    Article  CAS  PubMed  Google Scholar 

  8. Yu J, She Y, Ji SJ. m(6)A modification in mammalian nervous system development, functions, disorders, and injuries. Front Cell Dev Biol. 2021;9:679662.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Walters BJ, Mercaldo V, Gillon CJ, Yip M, Neve RL, Boyce FM, et al. The role of The RNA demethylase FTO (Fat Mass and Obesity-associated) and mRNA methylation in hippocampal memory formation. Neuropsychopharmacology. 2017;42:1502–10.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Widagdo J, Zhao QY, Kempen MJ, Tan MC, Ratnu VS, Wei W, et al. Experience-dependent accumulation of N6-methyladenosine in the prefrontal cortex is associated with memory processes in mice. J Neurosci. 2016;36:6771–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Zhang Z, Wang M, Xie D, Huang Z, Zhang L, Yang Y, et al. METTL3-mediated N(6)-methyladenosine mRNA modification enhances long-term memory consolidation. Cell Res. 2018;28:1050–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Shi H, Zhang X, Weng YL, Lu Z, Liu Y, Lu Z, et al. m(6)A facilitates hippocampus-dependent learning and memory through YTHDF1. Nature. 2018;563:249–53.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Remondes M, Schuman EM. Role for a cortical input to hippocampal area CA1 in the consolidation of a long-term memory. Nature. 2004;431:699–703.

    Article  CAS  PubMed  Google Scholar 

  14. Li M, Zhao X, Wang W, Shi H, Pan Q, Lu Z, et al. Ythdf2-mediated m(6)A mRNA clearance modulates neural development in mice. Genome Biol. 2018;19:69.

    Article  PubMed  PubMed Central  Google Scholar 

  15. Zhuang M, Li X, Zhu J, Zhang J, Niu F, Liang F, et al. The m6A reader YTHDF1 regulates axon guidance through translational control of Robo3.1 expression. Nucleic Acids Res. 2019;47:4765–77.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Yu J, She Y, Yang L, Zhuang M, Han P, Liu J, et al. The m(6) A readers YTHDF1 and YTHDF2 synergistically control cerebellar parallel fiber growth by regulating local translation of the key Wnt5a signaling components in axons. Adv Sci. 2021;8:e2101329.

    Article  Google Scholar 

  17. Wu M, Tian HL, Liu X, Lai JHC, Du S, Xia J. Impairment of inhibitory synapse formation and motor behavior in mice lacking the NL2 binding partner LHFPL4/GARLH4. Cell Rep. 2018;23:1691–705.

    Article  CAS  PubMed  Google Scholar 

  18. Huang H, Zhang G, Ruan GX, Li Y, Chen W, Zou J, et al. Mettl14-mediated m6A modification is essential for germinal center B cell response. J Immunol. 2022;208:1924–36.

    Article  CAS  PubMed  Google Scholar 

  19. Bromley-Brits K, Deng Y, Song W. Morris water maze test for learning and memory deficits in Alzheimer’s disease model mice. J Vis Exp. 2011;20:2920.

    Google Scholar 

  20. Beaudoin GM 3rd, Lee SH, Singh D, Yuan Y, Ng YG, Reichardt LF, et al. Culturing pyramidal neurons from the early postnatal mouse hippocampus and cortex. Nat Protoc. 2012;7:1741–54.

    Article  CAS  PubMed  Google Scholar 

  21. Yu J, Chen M, Huang H, Zhu J, Song H, Zhu J, et al. Dynamic m6A modification regulates local translation of mRNA in axons. Nucleic Acids Res. 2018;46:1412–23.

    Article  CAS  PubMed  Google Scholar 

  22. Kim JY, Ash RT, Ceballos-Diaz C, Levites Y, Golde TE, Smirnakis SM, et al. Viral transduction of the neonatal brain delivers controllable genetic mosaicism for visualising and manipulating neuronal circuits in vivo. Eur J Neurosci. 2013;37:1203–20.

    Article  PubMed  PubMed Central  Google Scholar 

  23. Cetin A, Komai S, Eliava M, Seeburg PH, Osten P. Stereotaxic gene delivery in the rodent brain. Nat Protoc. 2006;1:3166–73.

    Article  CAS  PubMed  Google Scholar 

  24. Bischofberger J, Engel D, Li L, Geiger JR, Jonas P. Patch-clamp recording from mossy fiber terminals in hippocampal slices. Nat Protoc. 2006;1:2075–81.

    Article  CAS  PubMed  Google Scholar 

  25. Wang Y, Li Y, Yue M, Wang J, Kumar S, Wechsler-Reya RJ, et al. N(6)-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications. Nat Neurosci. 2018;21:195–206.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR. Comprehensive analysis of mRNA methylation reveals enrichment in 3’ UTRs and near-stop codons. Cell. 2012;149:1635–46.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Nakamura NH, Akiyama K, Naito T. Quantitative gene-expression analysis of the ligand-receptor system for classical neurotransmitters and neuropeptides in hippocampal CA1, CA3, and dentate gyrus. Hippocampus. 2011;21:1228–39.

    Article  CAS  PubMed  Google Scholar 

  28. Farris S, Ward JM, Carstens KE, Samadi M, Wang Y, Dudek SM. Hippocampal subregions express distinct dendritic transcriptomes that reveal differences in mitochondrial function in CA2. Cell Rep. 2019;29:522–39.e6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. McHugh TJ, Jones MW, Quinn JJ, Balthasar N, Coppari R, Elmquist JK, et al. Dentate gyrus NMDA receptors mediate rapid pattern separation in the hippocampal network. Science. 2007;317:94–9.

    Article  CAS  PubMed  Google Scholar 

  30. Nakazawa K, Quirk MC, Chitwood RA, Watanabe M, Yeckel MF, Sun LD, et al. Requirement for hippocampal CA3 NMDA receptors in associative memory recall. Science. 2002;297:211–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Tsien JZ, Chen DF, Gerber D, Tom C, Mercer EH, Anderson DJ, et al. Subregion- and cell type-restricted gene knockout in mouse brain. Cell. 1996;87:1317–26.

    Article  CAS  PubMed  Google Scholar 

  32. Guo N, McDermott KD, Shih YT, Zanga H, Ghosh D, Herber C, et al. Transcriptional regulation of neural stem cell expansion in the adult hippocampus. Elife. 2022;11:e72195.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Kheirbek MA, Drew LJ, Burghardt NS, Costantini DO, Tannenholz L, Ahmari SE, et al. Differential control of learning and anxiety along the dorsoventral axis of the dentate gyrus. Neuron. 2013;77:955–68.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Licht T, Kreisel T, Biala Y, Mohan S, Yaari Y, Anisimov A, et al. Age-Dependent remarkable regenerative potential of the dentate gyrus provided by intrinsic stem cells. J Neurosci. 2020;40:974–95.

    Article  PubMed  PubMed Central  Google Scholar 

  35. Sun Y, Nguyen AQ, Nguyen JP, Le L, Saur D, Choi J, et al. Cell-type-specific circuit connectivity of hippocampal CA1 revealed through Cre-dependent rabies tracing. Cell Rep. 2014;7:269–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Dong C, Madar AD, Sheffield MEJ. Distinct place cell dynamics in CA1 and CA3 encode experience in new environments. Nat Commun. 2021;12:2977.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Kilonzo K, Strahnen D, Prex V, Gems J, van der Veen B, Kapanaiah SKT, et al. Distinct contributions of GluA1-containing AMPA receptors of different hippocampal subfields to salience processing, memory and impulse control. Transl Psychiatry. 2022;12:102.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Srinivas S, Watanabe T, Lin CS, William CM, Tanabe Y, Jessell TM, et al. Cre reporter strains produced by targeted insertion of EYFP and ECFP into the ROSA26 locus. BMC Dev Biol. 2001;1:4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Phillips RG, LeDoux JE. Differential contribution of amygdala and hippocampus to cued and contextual fear conditioning. Behav Neurosci. 1992;106:274–85.

    Article  CAS  PubMed  Google Scholar 

  40. Muzumdar MD, Tasic B, Miyamichi K, Li L, Luo L. A global double-fluorescent Cre reporter mouse. Genesis. 2007;45:593–605.

    Article  CAS  PubMed  Google Scholar 

  41. Picard M, Petrie RJ, Antoine-Bertrand J, Saint-Cyr-Proulx E, Villemure JF, Lamarche-Vane N. Spatial and temporal activation of the small GTPases RhoA and Rac1 by the netrin-1 receptor UNC5a during neurite outgrowth. Cell Signal. 2009;21:1961–73.

    Article  CAS  PubMed  Google Scholar 

  42. Sun T, Yu N, Zhai LK, Li N, Zhang C, Zhou L, et al. c-Jun NH2-terminal kinase (JNK)-interacting protein-3 (JIP3) regulates neuronal axon elongation in a kinesin- and JNK-dependent manner. J Biol Chem. 2013;288:14531–43.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Watt D, Dixit R, Cavalli V. JIP3 activates kinesin-1 motility to promote axon elongation. J Biol Chem. 2015;290:15512–25.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Toth K, Suares G, Lawrence JJ, Philips-Tansey E, McBain CJ. Differential mechanisms of transmission at three types of mossy fiber synapse. J Neurosci. 2000;20:8279–89.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Lanore F, Labrousse VF, Szabo Z, Normand E, Blanchet C, Mulle C. Deficits in morphofunctional maturation of hippocampal mossy fiber synapses in a mouse model of intellectual disability. J Neurosci. 2012;32:17882–93.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Viana da Silva S, Zhang P, Haberl MG, Labrousse V, Grosjean N, Blanchet C, et al. Hippocampal mossy fibers synapses in CA3 pyramidal cells are altered at an early stage in a mouse model of Alzheimer’s disease. J Neurosci. 2019;39:4193–205.

    Article  PubMed  PubMed Central  Google Scholar 

  47. Kobayashi K. Targeting the hippocampal mossy fiber synapse for the treatment of psychiatric disorders. Mol Neurobiol. 2009;39:24–36.

    Article  CAS  PubMed  Google Scholar 

  48. Zaccara S, Jaffrey SR. A unified model for the function of YTHDF proteins in regulating m(6)A-modified mRNA. Cell. 2020;181:1582–95.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Lasman L, Krupalnik V, Viukov S, Mor N, Aguilera-Castrejon A, Schneir D, et al. Context-dependent functional compensation between Ythdf m(6)A reader proteins. Genes Dev. 2020;34:1373–91.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Kontur C, Jeong M, Cifuentes D, Giraldez AJ. Ythdf m(6)A readers function redundantly during zebrafish development. Cell Rep. 2020;33:108598.

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank Xin Ren for technical assistance, and other members of Ji and Dong laboratories for help, technical support, and comments on the manuscript. We thank Yu Chung Tse and Yilin Wang of SUSTech Core Research Facilities for their help in imaging and analysis of DG dendrites and spines after Golgi staining. We thank Prof. Shengtao Hou for support in the behavioral tests. We thank Prof. Jun Xia at The Hong Kong University of Science and Technology (HKUST) for co-mentoring the Ph.D. student in the SUSTech-HKUST Joint Ph.D. Program. This work was supported by National Natural Science Foundation of China (31871038 and 32170955 to S-JJ, 31871031 to WD), Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions (2022SHIBS0002), High-Level University Construction Fund for Department of Biology (internal grant no. G02226301), Science and Technology Innovation Commission of Shenzhen Municipal Government (ZDSYS20200811144002008), Ministry of Science and Technology of the People’s Republic of China (2019YFE0120600), and Department of Science and Technology of Sichuan Province (2019YJ0481).

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Author notes

  1. These authors contributed equally: Mengru Zhuang, Xiaoqi Geng, Peng Han, Pengfei Che, Fanghao Liang, Chao Liu.

Authors and Affiliations

  1. School of Life Sciences, Department of Neuroscience and Department of Biology, Brain Research Center, Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China

    Mengru Zhuang, Peng Han, Pengfei Che, Fanghao Liang, Lixin Yang, Jun Yu, Zhuxia Zhang & Sheng-Jian Ji

  2. SUSTech-HKUST Joint PhD Program, Division of Life Science and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China

    Mengru Zhuang

  3. Key Laboratory of Medical Electrophysiology of Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan, 646000, China

    Xiaoqi Geng, Chao Liu & Wei Dong

  4. Department of Neurosurgery, Neurosurgical Clinical Research Center of Sichuan Province, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China

    Xiaoqi Geng & Wei Dong

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Contributions

S-JJ conceived the idea and designed the experiments. MZ, PH, and PC performed and analyzed the major experiments. XG and CL performed the electrophysiology experiments. MZ, PC, FL, and ZZ performed the behavioral tests. FL, LY, and JY performed the RIPseq and RNAseq analysis. MZ, S-JJ and WD wrote the manuscript with input from all authors.

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Correspondence to Wei Dong or Sheng-Jian Ji.

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Zhuang, M., Geng, X., Han, P. et al. YTHDF2 in dentate gyrus is the m6A reader mediating m6A modification in hippocampus-dependent learning and memory. Mol Psychiatry 28, 1679–1691 (2023). https://doi.org/10.1038/s41380-023-01953-z

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