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PSD-95 is post-transcriptionally repressed during early neural development by PTBP1 and PTBP2

Abstract

Postsynaptic density protein 95 (PSD-95) is essential for synaptic maturation and plasticity. Although its synaptic regulation has been widely studied, the control of PSD-95 cellular expression is not understood. We found that Psd-95 was controlled post-transcriptionally during neural development. Psd-95 was transcribed early in mouse embryonic brain, but most of its product transcripts were degraded. The polypyrimidine tract binding proteins PTBP1 and PTBP2 repressed Psd-95 (also known as Dlg4) exon 18 splicing, leading to premature translation termination and nonsense-mediated mRNA decay. The loss of first PTBP1 and then of PTBP2 during embryonic development allowed splicing of exon 18 and expression of PSD-95 late in neuronal maturation. Re-expression of PTBP1 or PTBP2 in differentiated neurons inhibited PSD-95 expression and impaired the development of glutamatergic synapses. Thus, expression of PSD-95 during early neural development is controlled at the RNA level by two PTB proteins whose sequential downregulation is necessary for synapse maturation.

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Figure 1: PTB proteins repress PSD-95 expression cell-autonomously.
Figure 2: PTB proteins repress AMPA receptor–mediated synaptic transmission in cultured hippocampal neurons.
Figure 3: PTB proteins inhibit dendritic spine maturation.
Figure 4: PTB proteins inhibit Psd-95 exon 18 splicing.
Figure 5: Nonsense-mediated decay of Psd-95Δexon 18 isoforms.
Figure 6: Sequential downregulation of PTBP1 and PTBP2 induce exon 18 splicing during neural development.
Figure 7: Most embryonic Psd-95 transcripts are actively degraded via the NMD pathway.

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References

  1. Funke, L., Dakoji, S. & Bredt, D.S. Membrane-associated guanylate kinases regulate adhesion and plasticity at cell junctions. Annu. Rev. Biochem. 74, 219–245 (2005).

    Article  CAS  PubMed  Google Scholar 

  2. Sheng, M. & Hoogenraad, C.C. The postsynaptic architecture of excitatory synapses: a more quantitative view. Annu. Rev. Biochem. 76, 823–847 (2007).

    Article  CAS  PubMed  Google Scholar 

  3. Migaud, M. et al. Enhanced long-term potentiation and impaired learning in mice with mutant postsynaptic density-95 protein. Nature 396, 433–439 (1998).

    Article  CAS  PubMed  Google Scholar 

  4. Carlisle, H.J., Fink, A.E., Grant, S.G. & O'Dell, T.J. Opposing effects of PSD-93 and PSD-95 on long-term potentiation and spike timing-dependent plasticity. J. Physiol. (Lond.) 586, 5885–5900 (2008).

    Article  CAS  Google Scholar 

  5. El-Husseini, A.E., Schnell, E., Chetkovich, D.M., Nicoll, R.A. & Bredt, D.S. PSD-95 involvement in maturation of excitatory synapses. Science 290, 1364–1368 (2000).

    CAS  PubMed  Google Scholar 

  6. Elias, G.M. et al. Synapse-specific and developmentally regulated targeting of AMPA receptors by a family of MAGUK scaffolding proteins. Neuron 52, 307–320 (2006).

    Article  CAS  PubMed  Google Scholar 

  7. Schlüter, O.M., Xu, W. & Malenka, R.C. Alternative N-terminal domains of PSD-95 and SAP97 govern activity-dependent regulation of synaptic AMPA receptor function. Neuron 51, 99–111 (2006).

    Article  PubMed  Google Scholar 

  8. Ehrlich, I., Klein, M., Rumpel, S. & Malinow, R. PSD-95 is required for activity-driven synapse stabilization. Proc. Natl. Acad. Sci. USA 104, 4176–4181 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Béïque, J.C. et al. Synapse-specific regulation of AMPA receptor function by PSD-95. Proc. Natl. Acad. Sci. USA 103, 19535–19540 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  10. Boutz, P.L. et al. A post-transcriptional regulatory switch in polypyrimidine tract–binding proteins reprograms alternative splicing in developing neurons. Genes Dev. 21, 1636–1652 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Makeyev, E.V., Zhang, J., Carrasco, M.A. & Maniatis, T. The microRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing. Mol. Cell 27, 435–448 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Spellman, R., Llorian, M. & Smith, C.W. Crossregulation and functional redundancy between the splicing regulator PTB and its paralogs nPTB and ROD1. Mol. Cell 27, 420–434 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Chang, Y.F., Imam, J.S. & Wilkinson, M.F. The nonsense-mediated decay RNA surveillance pathway. Annu. Rev. Biochem. 76, 51–74 (2007).

    Article  CAS  PubMed  Google Scholar 

  14. Lejeune, F. & Maquat, L.E. Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells. Curr. Opin. Cell Biol. 17, 309–315 (2005).

    Article  CAS  PubMed  Google Scholar 

  15. Lareau, L.F., Inada, M., Green, R.E., Wengrod, J.C. & Brenner, S.E. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature 446, 926–929 (2007).

    Article  CAS  PubMed  Google Scholar 

  16. Ni, J.Z. et al. Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev. 21, 708–718 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Mendell, J.T., Sharifi, N.A., Meyers, J.L., Martinez-Murillo, F. & Dietz, H.C. Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat. Genet. 36, 1073–1078 (2004).

    Article  CAS  PubMed  Google Scholar 

  18. Weischenfeldt, J. et al. NMD is essential for hematopoietic stem and progenitor cells and for eliminating byproducts of programmed DNA rearrangements. Genes Dev. 22, 1381–1396 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Hyvonen, M.T. et al. Polyamine-regulated unproductive splicing and translation of spermidine/spermine N1-acetyltransferase. RNA 12, 1569–1582 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Gardner, L.B. Hypoxic inhibition of nonsense-mediated RNA decay regulates gene expression and the integrated stress response. Mol. Cell. Biol. 28, 3729–3741 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Chen, L. & Zheng, S. Identify alternative splicing events based on position-specific evolutionary conservation. PLoS ONE 3, e2806 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  22. Sorek, R. & Ast, G. Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. Genome Res. 13, 1631–1637 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Sugnet, C.W. et al. Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLOS Comput. Biol. 2, e4 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  24. Yeo, G.W., Van Nostrand, E., Holste, D., Poggio, T. & Burge, C.B. Identification and analysis of alternative splicing events conserved in human and mouse. Proc. Natl. Acad. Sci. USA 102, 2850–2855 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Amir-Ahmady, B., Boutz, P.L., Markovtsov, V., Phillips, M.L. & Black, D.L. Exon repression by polypyrimidine tract binding protein. RNA 11, 699–716 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Spellman, R. et al. Regulation of alternative splicing by PTB and associated factors. Biochem. Soc. Trans. 33, 457–460 (2005).

    Article  CAS  PubMed  Google Scholar 

  27. Ashiya, M. & Grabowski, P.J. A neuron-specific splicing switch mediated by an array of pre-mRNA repressor sites: evidence of a regulatory role for the polypyrimidine tract binding protein and a brain-specific PTB counterpart. RNA 3, 996–1015 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Liu, H., Zhang, W., Reed, R.B., Liu, W. & Grabowski, P.J. Mutations in RRM4 uncouple the splicing repression and RNA-binding activities of polypyrimidine tract binding protein. RNA 8, 137–149 (2002).

    Article  PubMed  PubMed Central  Google Scholar 

  29. Xue, Y. et al. Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping. Mol. Cell 36, 996–1006 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Carter, M.S. et al. A regulatory mechanism that detects premature nonsense codons in T-cell receptor transcripts in vivo is reversed by protein synthesis inhibitors in vitro. J. Biol. Chem. 270, 28995–29003 (1995).

    Article  CAS  PubMed  Google Scholar 

  31. Sans, N. et al. A developmental change in NMDA receptor–associated proteins at hippocampal synapses. J. Neurosci. 20, 1260–1271 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Medghalchi, S.M. et al. Rent1, a trans-effector of nonsense-mediated mRNA decay, is essential for mammalian embryonic viability. Hum. Mol. Genet. 10, 99–105 (2001).

    Article  CAS  PubMed  Google Scholar 

  33. Iwasato, T. et al. Dorsal telencephalon–specific expression of Cre recombinase in PAC transgenic mice. Genesis 38, 130–138 (2004).

    Article  CAS  PubMed  Google Scholar 

  34. Chen, L. et al. Stargazin regulates synaptic targeting of AMPA receptors by two distinct mechanisms. Nature 408, 936–943 (2000).

    Article  CAS  PubMed  Google Scholar 

  35. Firestein, B.L. & Rongo, C. DLG-1 is a MAGUK similar to SAP97 and is required for adherens junction formation. Mol. Biol. Cell 12, 3465–3475 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Woods, D.F. & Bryant, P.J. The discs-large tumor suppressor gene of Drosophila encodes a guanylate kinase homolog localized at septate junctions. Cell 66, 451–464 (1991).

    Article  CAS  PubMed  Google Scholar 

  37. Bruno, I.G. et al. Identification of a microRNA that activates gene expression by repressing nonsense-mediated RNA decay. Mol. Cell 42, 500–510 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Guo, L. & Wang, Y. Glutamate stimulates glutamate receptor interacting protein 1 degradation by ubiquitin-proteasome system to regulate surface expression of GluR2. Neuroscience 145, 100–109 (2007).

    Article  CAS  PubMed  Google Scholar 

  39. Wyneken, U. et al. Kainate-induced seizures alter protein composition and N-methyl-D-aspartate receptor function of rat forebrain postsynaptic densities. Neuroscience 102, 65–74 (2001).

    Article  CAS  PubMed  Google Scholar 

  40. Giorgi, C. & Moore, M.J. The nuclear nurture and cytoplasmic nature of localized mRNPs. Semin. Cell Dev. Biol. 18, 186–193 (2007).

    Article  CAS  PubMed  Google Scholar 

  41. Besse, F. & Ephrussi, A. Translational control of localized mRNAs: restricting protein synthesis in space and time. Nat. Rev. Mol. Cell Biol. 9, 971–980 (2008).

    Article  CAS  PubMed  Google Scholar 

  42. Chen, L. A global comparison between nuclear and cytosolic transcriptomes reveals differential compartmentalization of alternative transcript isoforms. Nucleic Acids Res. 38, 1086–1097 (2010).

    Article  CAS  PubMed  Google Scholar 

  43. Muddashetty, R.S., Kelic, S., Gross, C., Xu, M. & Bassell, G.J. Dysregulated metabotropic glutamate receptor–dependent translation of AMPA receptor and postsynaptic density–95 mRNAs at synapses in a mouse model of fragile X syndrome. J. Neurosci. 27, 5338–5348 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Zalfa, F. et al. A new function for the fragile X mental retardation protein in regulation of PSD-95 mRNA stability. Nat. Neurosci. 10, 578–587 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Giorgi, C. et al. The EJC factor eIF4AIII modulates synaptic strength and neuronal protein expression. Cell 130, 179–191 (2007).

    Article  CAS  PubMed  Google Scholar 

  46. Chen, Z., Gore, B.B., Long, H., Ma, L. & Tessier-Lavigne, M. Alternative splicing of the Robo3 axon guidance receptor governs the midline switch from attraction to repulsion. Neuron 58, 325–332 (2008).

    Article  CAS  PubMed  Google Scholar 

  47. Black, D.L. & Zipursky, S.L. To cross or not to cross: alternatively spliced forms of the Robo3 receptor regulate discrete steps in axonal midline crossing. Neuron 58, 297–298 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Calarco, J.A. et al. Regulation of vertebrate nervous system alternative splicing and development by an SR-related protein. Cell 138, 898–910 (2009).

    Article  CAS  PubMed  Google Scholar 

  49. Zheng, S. et al. NMDA-induced neuronal survival is mediated through nuclear factor I-A in mice. J. Clin. Invest. 120, 2446–2456 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Qin, X.F., An, D.S., Chen, I.S. & Baltimore, D. Inhibiting HIV-1 infection in human T cells by lentiviral-mediated delivery of small interfering RNA against CCR5. Proc. Natl. Acad. Sci. USA 100, 183–188 (2003).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank J. Baraban and E. Anderson for thoughtful suggestions on the manuscript, and K. Martin, L. Zipursky, W. Yang and members of the Black laboratory for helpful discussion. We thank S. Sharma for the His-tagged PTBP1 recombinant proteins, and A. Han and S. Sharma for help with the EMSA experiments. We thank Q. Lin for help with Imaris software. This work was supported in part by grants from the US National Institutes of Health (RO1 GM 49662 to D.L.B., R01 MH60919 to T.J.O. and NIH F32 MH84562 to E.E.G.). D.L.B. is an Investigator of the Howard Hughes Medical Institute.

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S.Z. and D.L.B. designed the studies. E.E.G. and T.J.O. designed and performed the electrophysiological experiments. G.C. cloned and tested the shRNAs to knockdown PTBP1 and PTBP2. S.Z. performed all of the experiments. B.T.P. provided the Upf2loxP/loxP mice. S.Z., T.J.O. and D.L.B. wrote the paper.

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Correspondence to Douglas L Black.

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Zheng, S., Gray, E., Chawla, G. et al. PSD-95 is post-transcriptionally repressed during early neural development by PTBP1 and PTBP2. Nat Neurosci 15, 381–388 (2012). https://doi.org/10.1038/nn.3026

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