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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References
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).
Sheng, M. & Hoogenraad, C.C. The postsynaptic architecture of excitatory synapses: a more quantitative view. Annu. Rev. Biochem. 76, 823–847 (2007).
Migaud, M. et al. Enhanced long-term potentiation and impaired learning in mice with mutant postsynaptic density-95 protein. Nature 396, 433–439 (1998).
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).
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).
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).
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).
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).
Béïque, J.C. et al. Synapse-specific regulation of AMPA receptor function by PSD-95. Proc. Natl. Acad. Sci. USA 103, 19535–19540 (2006).
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).
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).
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).
Chang, Y.F., Imam, J.S. & Wilkinson, M.F. The nonsense-mediated decay RNA surveillance pathway. Annu. Rev. Biochem. 76, 51–74 (2007).
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).
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).
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).
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).
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).
Hyvonen, M.T. et al. Polyamine-regulated unproductive splicing and translation of spermidine/spermine N1-acetyltransferase. RNA 12, 1569–1582 (2006).
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).
Chen, L. & Zheng, S. Identify alternative splicing events based on position-specific evolutionary conservation. PLoS ONE 3, e2806 (2008).
Sorek, R. & Ast, G. Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. Genome Res. 13, 1631–1637 (2003).
Sugnet, C.W. et al. Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLOS Comput. Biol. 2, e4 (2006).
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).
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).
Spellman, R. et al. Regulation of alternative splicing by PTB and associated factors. Biochem. Soc. Trans. 33, 457–460 (2005).
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).
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).
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).
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).
Sans, N. et al. A developmental change in NMDA receptor–associated proteins at hippocampal synapses. J. Neurosci. 20, 1260–1271 (2000).
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).
Iwasato, T. et al. Dorsal telencephalon–specific expression of Cre recombinase in PAC transgenic mice. Genesis 38, 130–138 (2004).
Chen, L. et al. Stargazin regulates synaptic targeting of AMPA receptors by two distinct mechanisms. Nature 408, 936–943 (2000).
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).
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).
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).
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).
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).
Giorgi, C. & Moore, M.J. The nuclear nurture and cytoplasmic nature of localized mRNPs. Semin. Cell Dev. Biol. 18, 186–193 (2007).
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).
Chen, L. A global comparison between nuclear and cytosolic transcriptomes reveals differential compartmentalization of alternative transcript isoforms. Nucleic Acids Res. 38, 1086–1097 (2010).
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).
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).
Giorgi, C. et al. The EJC factor eIF4AIII modulates synaptic strength and neuronal protein expression. Cell 130, 179–191 (2007).
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).
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).
Calarco, J.A. et al. Regulation of vertebrate nervous system alternative splicing and development by an SR-related protein. Cell 138, 898–910 (2009).
Zheng, S. et al. NMDA-induced neuronal survival is mediated through nuclear factor I-A in mice. J. Clin. Invest. 120, 2446–2456 (2010).
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).
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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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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DOI: https://doi.org/10.1038/nn.3026
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