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A coding-independent function of an alternative Ube3a transcript during neuronal development


The E3 ubiquitin ligase Ube3a is an important regulator of activity-dependent synapse development and plasticity. Ube3a mutations cause Angelman syndrome and have been associated with autism spectrum disorders (ASD). However, the biological significance of alternative Ube3a transcripts generated in mammalian neurons remains unknown. We report here that Ube3a1 RNA, a transcript that encodes a truncated Ube3a protein lacking catalytic activity, prevents exuberant dendrite growth and promotes spine maturation in rat hippocampal neurons. Surprisingly, Ube3a1 RNA function was independent of its coding sequence but instead required a unique 3′ untranslated region and an intact microRNA pathway. Ube3a1 RNA knockdown increased activity of the plasticity-regulating miR-134, suggesting that Ube3a1 RNA acts as a dendritic competing endogenous RNA. Accordingly, the dendrite-growth-promoting effect of Ube3a1 RNA knockdown in vivo is abolished in mice lacking miR-134. Taken together, our results define a noncoding function of an alternative Ube3a transcript in dendritic protein synthesis, with potential implications for Angelman syndrome and ASD.

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Figure 1: Ube3a1 RNA is an activity-dependent, dendritic transcript in primary hippocampal neurons.
Figure 2: Ube3a1 RNA knockdown increases dendrite complexity and reduces dendritic spine volume and mEPSC amplitudes.
Figure 3: Ube3a1 function in dendritogenesis is coding-independent.
Figure 4: Ube3a1 function in dendritogenesis requires an intact microRNA pathway.
Figure 5: Ube3a1 RNA is a competing endogenous RNA for the miR379–410 cluster.
Figure 6: Ube3a1 function in vivo depends on miR379–410 miRNAs.

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  1. Ebert, D.H. & Greenberg, M.E. Activity-dependent neuronal signalling and autism spectrum disorder. Nature 493, 327–337 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Jiang, Y.H. et al. Mutation of the Angelman ubiquitin ligase in mice causes increased cytoplasmic p53 and deficits of contextual learning and long-term potentiation. Neuron 21, 799–811 (1998).

    CAS  PubMed  Google Scholar 

  3. Matsuura, T. et al. De novo truncating mutations in E6-AP ubiquitin-protein ligase gene (UBE3A) in Angelman syndrome. Nat. Genet. 15, 74–77 (1997).

    CAS  PubMed  Google Scholar 

  4. Glessner, J.T. et al. Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature 459, 569–573 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Sato, M. & Stryker, M.P. Genomic imprinting of experience-dependent cortical plasticity by the ubiquitin ligase gene Ube3a. Proc. Natl. Acad. Sci. USA 107, 5611–5616 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Yashiro, K. et al. Ube3a is required for experience-dependent maturation of the neocortex. Nat. Neurosci. 12, 777–783 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Wallace, M.L., Burette, A.C., Weinberg, R.J. & Philpot, B.D. Maternal loss of Ube3a produces an excitatory/inhibitory imbalance through neuron type-specific synaptic defects. Neuron 74, 793–800 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Dindot, S.V., Antalffy, B.A., Bhattacharjee, M.B. & Beaudet, A.L. The Angelman syndrome ubiquitin ligase localizes to the synapse and nucleus, and maternal deficiency results in abnormal dendritic spine morphology. Hum. Mol. Genet. 17, 111–118 (2008).

    CAS  PubMed  Google Scholar 

  9. Miao, S. et al. The Angelman syndrome protein Ube3a is required for polarized dendrite morphogenesis in pyramidal neurons. J. Neurosci. 33, 327–333 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Greer, P.L. et al. The Angelman Syndrome protein Ube3A regulates synapse development by ubiquitinating arc. Cell 140, 704–716 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Margolis, S.S. et al. EphB-mediated degradation of the RhoA GEF Ephexin5 relieves a developmental brake on excitatory synapse formation. Cell 143, 442–455 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Filipowicz, W., Bhattacharyya, S.N. & Sonenberg, N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat. Rev. Genet. 9, 102–114 (2008).

    CAS  PubMed  Google Scholar 

  13. Schratt, G. microRNAs at the synapse. Nat. Rev. Neurosci. 10, 842–849 (2009).

    CAS  PubMed  Google Scholar 

  14. McNeill, E. & Van Vactor, D. MicroRNAs shape the neuronal landscape. Neuron 75, 363–379 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Seitz, H. et al. A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain. Genome Res. 14, 1741–1748 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Fiore, R. et al. Mef2-mediated transcription of the miR379–410 cluster regulates activity-dependent dendritogenesis by fine-tuning Pumilio2 protein levels. EMBO J. 28, 697–710 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Schratt, G.M. et al. A brain-specific microRNA regulates dendritic spine development. Nature 439, 283–289 (2006).

    CAS  PubMed  Google Scholar 

  18. Gao, J. et al. A novel pathway regulates memory and plasticity via SIRT1 and miR-134. Nature 466, 1105–1109 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Jimenez-Mateos, E.M. et al. Silencing microRNA-134 produces neuroprotective and prolonged seizure-suppressive effects. Nat. Med. 18, 1087–1094 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Bicker, S. et al. The DEAH-box helicase DHX36 mediates dendritic localization of the neuronal precursor-microRNA-134. Genes Dev. 27, 991–996 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Huibregtse, J.M., Scheffner, M., Beaudenon, S. & Howley, P.M. A family of proteins structurally and functionally related to the E6-AP ubiquitin-protein ligase. Proc. Natl. Acad. Sci. USA 92, 2563–2567 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Yamamoto, Y., Huibregtse, J.M. & Howley, P.M. The human E6-AP gene (UBE3A) encodes three potential protein isoforms generated by differential splicing. Genomics 41, 263–266 (1997).

    CAS  PubMed  Google Scholar 

  23. Cooper, E.M., Hudson, A.W., Amos, J., Wagstaff, J. & Howley, P.M. Biochemical analysis of Angelman syndrome-associated mutations in the E3 ubiquitin ligase E6-associated protein. J. Biol. Chem. 279, 41208–41217 (2004).

    CAS  PubMed  Google Scholar 

  24. Landers, M. et al. Regulation of the large (approximately 1000 kb) imprinted murine Ube3a antisense transcript by alternative exons upstream of Snurf/Snrpn. Nucleic Acids Res. 32, 3480–3492 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Filonova, I., Trotter, J.H., Banko, J.L. & Weeber, E.J. Activity-dependent changes in MAPK activation in the Angelman Syndrome mouse model. Learn. Mem. 21, 98–104 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Martin, K.C. & Ephrussi, A. mRNA localization: gene expression in the spatial dimension. Cell 136, 719–730 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Steward, O., Wallace, C.S., Lyford, G.L. & Worley, P.F. Synaptic activation causes the mRNA for the IEG Arc to localize selectively near activated postsynaptic sites on dendrites. Neuron 21, 741–751 (1998).

    CAS  PubMed  Google Scholar 

  28. Gregory, R.I. et al. The Microprocessor complex mediates the genesis of microRNAs. Nature 432, 235–240 (2004).

    CAS  PubMed  Google Scholar 

  29. Meister, G. et al. Identification of novel argonaute-associated proteins. Curr. Biol. 15, 2149–2155 (2005).

    CAS  PubMed  Google Scholar 

  30. Tay, Y., Rinn, J. & Pandolfi, P.P. The multilayered complexity of ceRNA crosstalk and competition. Nature 505, 344–352 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Fone, K.C. & Porkess, M.V. Behavioural and neurochemical effects of post-weaning social isolation in rodents-relevance to developmental neuropsychiatric disorders. Neurosci. Biobehav. Rev. 32, 1087–1102 (2008).

    CAS  PubMed  Google Scholar 

  32. Tay, Y. et al. Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell 147, 344–357 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Denzler, R., Agarwal, V., Stefano, J., Bartel, D.P. & Stoffel, M. Assessing the ceRNA Hypothesis with Quantitative Measurements of miRNA and Target Abundance. Mol. Cell 54, 766–776 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Bosson, A.D., Zamudio, J.R. & Sharp, P.A. Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition. Mol. Cell 56, 347–359 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Mukaetova-Ladinska, E.B., Arnold, H., Jaros, E., Perry, R. & Perry, E. Depletion of MAP2 expression and laminar cytoarchitectonic changes in dorsolateral prefrontal cortex in adult autistic individuals. Neuropathol. Appl. Neurobiol. 30, 615–623 (2004).

    CAS  PubMed  Google Scholar 

  36. Raymond, G.V., Bauman, M.L. & Kemper, T.L. Hippocampus in autism: a Golgi analysis. Acta Neuropathol. 91, 117–119 (1996).

    CAS  PubMed  Google Scholar 

  37. Penzes, P., Cahill, M.E., Jones, K.A., VanLeeuwen, J.E. & Woolfrey, K.M. Dendritic spine pathology in neuropsychiatric disorders. Nat. Neurosci. 14, 285–293 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Hutsler, J.J. & Zhang, H. Increased dendritic spine densities on cortical projection neurons in autism spectrum disorders. Brain Res. 1309, 83–94 (2010).

    CAS  PubMed  Google Scholar 

  39. Sanders, S.J. et al. Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism. Neuron 70, 863–885 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Bevins, R.A. & Besheer, J. Object recognition in rats and mice: a one-trial non-matching-to-sample learning task to study 'recognition memory'. Nat. Protoc. 1, 1306–1311 (2006).

    PubMed  Google Scholar 

  41. Poon, M.M., Choi, S.H., Jamieson, C.A., Geschwind, D.H. & Martin, K.C. Identification of process-localized mRNAs from cultured rodent hippocampal neurons. J. Neurosci. 26, 13390–13399 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Christensen, M., Larsen, L.A., Kauppinen, S. & Schratt, G. Recombinant adeno-associated virus-mediated microRNA delivery into the postnatal mouse brain reveals a role for miR-134 in dendritogenesis in vivo. Front. Neural Circuits 3, 16 (2010).

    PubMed  PubMed Central  Google Scholar 

  43. Shevtsova, Z., Malik, J.M., Michel, U., Bahr, M. & Kugler, S. Promoters and serotypes: targeting of adeno-associated virus vectors for gene transfer in the rat central nervous system in vitro and in vivo. Exp. Physiol. 90, 53–59 (2005).

    CAS  PubMed  Google Scholar 

  44. Zolotukhin, S. et al. Recombinant adeno-associated virus purification using novel methods improves infectious titer and yield. Gene Ther. 6, 973–985 (1999).

    CAS  PubMed  Google Scholar 

  45. Siegel, G. et al. A functional screen implicates microRNA-138-dependent regulation of the depalmitoylation enzyme APT1 in dendritic spine morphogenesis. Nat. Cell Biol. 11, 705–716 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Schratt, G.M., Nigh, E.A., Chen, W.G., Hu, L. & Greenberg, M.E. BDNF regulates the translation of a select group of mRNAs by a mammalian target of rapamycin-phosphatidylinositol 3-kinase-dependent pathway during neuronal development. J. Neurosci. 24, 7366–7377 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).

    CAS  PubMed  Google Scholar 

  48. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    PubMed  PubMed Central  Google Scholar 

  49. Thorvaldsdóttir, H., Robinson, J.T. & Mesirov, J.P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14, 178–192 (2013).

    PubMed  Google Scholar 

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We acknowledge technical assistance of U. Beck, E. Becker, R. Gondrum, G. Jarosch, H. Kaiser and H. Rippberger. This work was funded by grants from the European Research Council (Starting Grant “Neuromir”), the European Union FP7 (“EpimiRNA”), the Deutsche Forschungsgemeinschaft (DFG) (SFB593, FOR2107: SCHR 1136/3-1) and the Universitätsklinikum Gießen-Marburg to G.S., the DFG (FOR2107) to R.S. (SCHW 559/14-1) and M.W. (WO 1732/4-1) and the Von Behring-Röntgen-Foundation (62-0004) to S.B.

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Authors and Affiliations



J.V. performed most experiments (dendritogenesis, luciferase assays, western blots, rAAV injections, strand-specific qPCR) and analyzed the data. G.S. designed the study, supervised the project and wrote the manuscript. S.B. performed FISH, compartmentalized culture and synaptosome assays. A.A.-A. performed and analyzed patch-clamp recordings. M.L. and R.F. established and characterized the miR379–410 knockout colony. S.S. cloned and validated the Drosha shRNA construct. T.W. performed dendritogenesis assays and generated Ube3a constructs. R.S. and M.W. designed and supervised the rat behavioral studies. D.S. performed juvenile social isolation studies in rats. F.M. and C.D. analyzed deep sequencing data.

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Correspondence to Gerhard Schratt.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 Ube3a1 RNA expression analysis by RNA sequencing.

a) Genomic view (UCSC genome browser) of the murine Ube3a locus including alternative Ube3a transcripts. The region surrounding the Ube3a1 3’UTR is boxed. Note the presence of sequence reads in the aggregate RNA-seq exon coverage panel at the genomic location of the Ube3a1 3’UTR. b) Representation of sequence reads at the location of the Ube3a1 3’UTR (boxed region in a) from rat hippocampal neurons according to ribo-minus RNA sequencing. The position of Ube3a exons 9-11, intron 11 and the UTR1 is indicated. c) Strand-specific qPCR analysis of 3’UTR1 or intron11 containing transcripts in either antisense (as) or sense orientation.

Supplementary Figure 2 Developmental expression of Ube3a1 RNA.

qPCR analysis of Ube3a1 RNA (a), Limk1 mRNA (b) Ube3a2/3 mRNA (c) expression from developing primary rat hippocampal neurons. Values are presented relative to expression at 3 DIV. N=3-5. *p<0.05, **p<0.01, ***p<0.001 (T-test).

Supplementary Figure 3 Subcellular expression of Ube3a1 RNA

a) Representative immunofluorescence analysis of cell body (upper panel) or process (lower panel) compartments from standard (left panel) or FUDR-treated (right panel) compartmentalized hippocampal neuron cultures, stained with anti-GFAP (green), anti-MAP2 (red) or Hoechst (blue). Scale bar = 50 μm. b) qPCR analysis of Ube3a1 and Ube3a2/3 with RNA from cell bodies and processes of compartmentalized hippocampal neuron cultures. Bar graphs represent the average ratio of Ube3a1 to Ube3a2/3 RNA levels from three independent preparations ± SD. c) qPCR analysis of indicated RNAs in rat P15 forebrain synaptosomes. Values are presented relative to a whole forebrain control sample. d) Conventional RT-PCR analysis of P15 whole rat forebrain (WB) and synaptosomes (SY) with primers directed against the indicated transcripts.

Supplementary Figure 4 Ube3a protein expression and knockdown validation.

a) Different fractions from a rat P15 forebrain synaptosome preparation were used for Western blotting with a monoclonal mouse anti-Ube3a antibody (Becton Dickinson) which recognizes aa. 501-712 of mouse Ube3a. Marker lane indicates 100 kD. Sup: supernatant; Pel: pellet; Syn: synaptosomes. b) HEK293 cells were transfected with the indicated constructs and analyzed for the expression of GFP-Ube3a-fusion proteins by Western blotting using the anti-Ube3a antibody described in a). c) Primary rat hippocampal neurons (13-18 DIV) were co-transfected with GFP-Ube3a-fusion constructs and dsRed and analyzed by confocal microscopy. Scale bar = 50 μm. d) HEK293 cells were co-transfected with GFP-Ube3a-fusion and indicated shRNA constructs. Expression was assessed by Western blotting using an anti-GFP antibody and an anti-Actin antibody as a loading control. e) Primary rat hippocampal neurons (10-18 DIV) were infected with rAAV expressing the indicated shRNA constructs. Expression of endogenous Ube3a protein was measured by Western blotting using an anti-Ube3a antibody that recognizes the common Ube3a N-terminus. anti-ß-actin Western served as a loading control. f) qRT-PCR analysis of indicated RNAs from hippocampal neurons infected with rAAV-Ube3a1-shRNA or rAAV-control-shRNA. Values were normalized to Gapdh expression and are presented as the ratio of Ube3a1 vs. control shRNA infected neurons ± SD. N=4 (ANOVA p=0.015323; *p<0.05 (post-hoc T-test).

Supplementary Figure 5 Regulation of dendritogenesis by GFP-Ube3a1 and GFP-Ube3a2.

a) qPCR analysis of GFP RNA expression in primary cortical neurons that had been nucleofected with the indicated GFP-Ube3a-fusion constructs. Values are presented as 40-ct and are representative for multiple independent experiments. b) Representative images of primary hippocampal neurons (DIV 13 - 18) transfected with the indicated shRNA and Ube3a1 expression constructs. c) Representative images of primary hippocampal neurons (DIV 7 - 10) transfected with the indicated expression vectors and treated with BDNF (40 ng/ml) for 48 hours prior to fixation. Scale bar = 50 μm. d) Quantification of dendrite complexity in neurons transfected with the indicated GFP expression plasmids. Values are presented relative to GFP-only transfected neurons. n=3.

Supplementary Figure 6 The Ube3a1 coding sequence (cds) is not involved in dendritogenesis.

a) anti-GFP Western blot with lysates from HEK293 cells transfected with the indicated GFP-Ube3a-fusion constructs. b) Quantification of dendrite complexity in neurons transfected with the indicated shRNA and Ube3a1 expression constructs. Values are presented relative to control shRNA transfected neurons. N=3. n.s.: not significant.

Supplementary Figure 7 Full-length blots related to Figure 4a.

a) GFP-Drosha. b) GFP. c) beta-Actin. Boxes indicate regions of the blot presented in Fig. 4a. Additional band in a) represents overexposed GFP signal.

Supplementary Figure 8 Ube3a1 ceRNA function.

a) Schematic representation of rat 3’UTRs for known miR-134 target mRNAs. Putative binding sites predicted by TargetScan ( for miR-134, miR-485 and miR-758 are marked by colored circles. The total number of additional miR379-410 seed matches is indicated. UTRs are not drawn to scale. b) Luciferase assay in primary hippocampal neurons co-transfected with Creb1-luc reporters and indicated shRNAs. Values are relative to reporter expression under basal conditions. N=7 (Creb1-luc). N=4 (Creb1-m134-luc). **p<0.01 (T-test).

Supplementary Figure 9 Quantitative PCR of miR-134 target mRNAs in neuronal cell bodies and dendrites.

a-c) Standard curves with indicated amounts of plasmids containing Pum2 (a), Limk1 (b) and Ube3a1 (c) sequence. The slope of a regression curve based on measured Ct-values is indicated in each diagram. d) Calculated RNA molecules per ng total RNA isolated from either the cell body or dendrite compartment of FUDR-treated hippocampal neurons (DIV 18) cultured on filter insets. Results from three independent experiments ± SD are shown.

Supplementary Figure 10 Full-length blots related to Figure 5f.

a) Limk1. b) Creb1. c) Pum2. d) Tubulin. Boxes indicate regions of blot presented in Fig. 5f. Membranes were cut after blotting to simultaneously probe for proteins running at different molecular weights.

Supplementary Figure 11 Genotyping and validation of miR379-410−/− mice.

a) Genotyping PCR of miR379/410−/− (KO) and wild-type (WT) mice using the indicated primer pairs. b) qPCR analysis of pre-miR-134 expression in wild-type (wt; n=7) and miR379/410−/− mice (ko; n=7). **p<0.01.

Supplementary Figure 12 Normal cortical layering in miR379-410/ (ko) mice.

Coronal brain sections (80 mm, single hemisphere) of 8-weeks old wildtype (a), miR379-410+/− (b) or miR379-410−/− (ko; c, d) mice stained with nuclear Hoechst dye. The positions of cortical layers I-VI are indicated in the higher magnification images (right panels). No differences were observed in the general organization of the cerebral cortex or hippocampus.

Supplementary Figure 13 Model for the ceRNA function of Ube3a1 during dendritic development.

During normal activity-dependent neuronal development, Ube3a1 RNA levels steadily increase, resulting in the sequestration of dendritic miRNAs from the miR379-410 cluster, including miR-134 and miR-485. This releases protein-coding targets of these miRNAs, such as Limk1 and Pum2 mRNA, from translational repression, thereby leading to enhanced local synthesis of Limk1 and Pum2, which in turn promotes spine growth and inhibits dendrite elaboration, respectively. In conditions of Ube3a1 RNA deficiency, spine growth is suppressed whereas the brake on dendrite elaboration is loosened.

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Valluy, J., Bicker, S., Aksoy-Aksel, A. et al. A coding-independent function of an alternative Ube3a transcript during neuronal development. Nat Neurosci 18, 666–673 (2015).

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