Abstract

Mutations in AUTS2 are associated with autism, intellectual disability, and microcephaly. AUTS2 is expressed in the brain and interacts with polycomb proteins, yet it is still unclear how mutations in AUTS2 lead to neurodevelopmental phenotypes. Here we report that when neuronal differentiation is initiated, there is a shift in expression from a long isoform to a short AUTS2 isoform. Yeast two-hybrid screen identified the splicing factor SF3B1 as an interactor of both isoforms, whereas the polycomb group proteins, PCGF3 and PCGF5, were found to interact exclusively with the long AUTS2 isoform. Reporter assays showed that the first exons of the long AUTS2 isoform function as a transcription repressor, but the part that consist of the short isoform acts as a transcriptional activator, both influenced by the cellular context. The expression levels of PCGF3 influenced the ability of the long AUTS2 isoform to activate or repress transcription. Mouse embryonic stem cells (mESCs) with heterozygote mutations in Auts2 had an increase in cell death during in vitro corticogenesis, which was significantly rescued by overexpressing the human AUTS2 transcripts. mESCs with a truncated AUTS2 protein (missing exons 12–20) showed premature neuronal differentiation, whereas cells overexpressing AUTS2, especially the long transcript, showed increase in expression of pluripotency markers and delayed differentiation. Taken together, our data suggest that the precise expression of AUTS2 isoforms is essential for regulating transcription and the timing of neuronal differentiation.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Additional information

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

References

  1. 1.

    Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, Willsey AJ, et al. De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature. 2012;485:237–41.

  2. 2.

    Hamdan FF, Srour M, Capo-Chichi J-M, Daoud H, Nassif C, Patry L, et al. De novo mutations in moderate or severe intellectual disability. PLoS Genet. 2014;10:e1004772.

  3. 3.

    Ben-David E, Shifman S. Combined analysis of exome sequencing points toward a major role for transcription regulation during brain development in autism. Mol Psychiatry. 2013;18:1054–6.

  4. 4.

    Pinto D, Delaby E, Merico D, Barbosa M, Merikangas A, Klei L, et al. Convergence of genes and cellular pathways dysregulated in autism spectrum disorders. Am J Hum Genet. 2014;94:677–94.

  5. 5.

    Ronan JL, Wu W, Crabtree GR. From neural development to cognition: unexpected roles for chromatin. Nat Rev Genet. 2013;14:347–59.

  6. 6.

    Suliman R, Ben-David E, Shifman S. Chromatin regulators, phenotypic robustness, and autism risk. Front Genet. 2014;5:81.

  7. 7.

    De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Ercument Cicek A, et al. Synaptic, transcriptional and chromatin genes disrupted in autism. Nature. 2014;515:209–15.

  8. 8.

    Ernst C. Proliferation and differentiation deficits are a major convergence point for neurodevelopmental disorders. Trends Neurosci. 2016;39:290–9.

  9. 9.

    Casanova EL, Casanova MF. Genetics studies indicate that neural induction and early neuronal maturation are disturbed in autism. Front Cell Neurosci. 2014;8:397.

  10. 10.

    Kaushik G, Zarbalis KS. Prenatal neurogenesis in autism spectrum disorders. Front Chem. 2016;4:12. https://doi.org/10.3389/fchem.2016.00012.

  11. 11.

    Packer A. Neocortical neurogenesis and the etiology of autism spectrum disorder. Neurosci Biobehav Rev. 2016;64:185–95.

  12. 12.

    Fromer M, Pocklington AJ, Kavanagh DH, Williams HJ, Dwyer S, Gormley P, et al. De novo mutations in schizophrenia implicate synaptic networks. Nature. 2014;506:179–84.

  13. 13.

    Shohat S, Ben-David E, Shifman S. Varying intolerance of gene pathways to mutational classes explain genetic convergence across neuropsychiatric disorders. Cell Rep. 2017;18:2217–27.

  14. 14.

    Zhu X, Need AC, Petrovski S, Goldstein DB. One gene, many neuropsychiatric disorders: lessons from Mendelian diseases. Nat Neurosci. 2014;17:773–81.

  15. 15.

    Sultana R, Yu C-E, Yu J, Munson J, Chen D, Hua W, et al. Identification of a novel gene on chromosome 7q11. 2 interrupted by a translocation breakpoint in a pair of autistic twins. Genomics. 2002;80:129–34.

  16. 16.

    Kalscheuer VM, FitzPatrick D, Tommerup N, Bugge M, Niebuhr E, Neumann LM, et al. Mutations in autism susceptibility candidate 2 (AUTS2) in patients with mental retardation. Hum Genet. 2007;121:501–9.

  17. 17.

    Huang X-L, Zou YS, Maher TA, Newton S, Milunsky JM. A de novo balanced translocation breakpoint truncating the autism susceptibility candidate 2 (AUTS2) gene in a patient with autism. Am J Med Genet Part A. 2010;152:2112–4.

  18. 18.

    Ben-David E, Granot-Hershkovitz E, Monderer-Rothkoff G, Lerer E, Levi S, Yaari M, et al. Identification of a functional rare variant in autism using genome-wide screen for monoallelic expression. Hum Mol Genet. 2011;20:3632–41.

  19. 19.

    Elia J, Gai X, Xie HM, Perin JC, Geiger E, Glessner JT, et al. Rare structural variants found in attention-deficit hyperactivity disorder are preferentially associated with neurodevelopmental genes. Mol Psychiatry. 2009;15:637–46.

  20. 20.

    Mefford HC, Muhle H, Ostertag P, von Spiczak S, Buysse K, Baker C, et al. Genome-wide copy number variation in epilepsy: novel susceptibility loci in idiopathic generalized and focal epilepsies. PLoS Genet. 2010;6:e1000962.

  21. 21.

    Amarillo IE, Li WL, Li X, Vilain E, Kantarci S. De novo single exon deletion of AUTS2 in a patient with speech and language disorder: a review of disrupted AUTS2 and further evidence for its role in neurodevelopmental disorders. Am J Med Genet A. 2014;164A:958–65.

  22. 22.

    Beunders G, Voorhoeve E, Golzio C, Pardo LM, Rosenfeld Ja, Talkowski ME, et al. Exonic deletions in AUTS2 cause a syndromic form of intellectual disability and suggest a critical role for the C terminus. Am J Hum Genet. 2013;92:210–20.

  23. 23.

    Bedogni F, Hodge RD, Nelson BR, Frederick EA, Shiba N, Daza RA, et al. Autism susceptibility candidate 2(Auts2) encodes a nuclear protein expressed in developing brain regions implicated in autism neuropathology. Gene Expr Patterns. 2010;10:9–15.

  24. 24.

    Oksenberg N, Stevison L, Wall JD, Ahituv N. Function and regulation of AUTS2, a gene implicated in autism and human evolution. PLoS Genet. 2013;9:e1003221.

  25. 25.

    Hori K, Nagai T, Shan W, Sakamoto A, Taya S, Hashimoto R, et al. Cytoskeletal regulation by AUTS2 in neuronal migration and neuritogenesis. Cell Rep. 2014;9:2166–79.

  26. 26.

    Gao Z, Lee P, Stafford JM, von Schimmelmann M, Schaefer A, Reinberg D. An AUTS2–Polycomb complex activates gene expression in the CNS. Nature. 2014;516:349–54.

  27. 27.

    Gao Z, Zhang J, Bonasio R, Strino F, Sawai A, Parisi F, et al. PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. Mol Cell. 2012;45:344–56.

  28. 28.

    Oksenberg N, Haliburton GDE, Eckalbar WL, Oren I, Nishizaki S, Murphy K, et al. Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes. Transl Psychiatry. 2014;4:e431.

  29. 29.

    Gaspard N, Bouschet T, Herpoel A, Naeije G, van den Ameele J, Vanderhaeghen P. Generation of cortical neurons from mouse embryonic stem cells. Nat Protoc. 2009;4:1454–63.

  30. 30.

    Gaspard N, Bouschet T, Hourez R, Dimidschstein J, Naeije G, van den Ameele J, et al. An intrinsic mechanism of corticogenesis from embryonic stem cells. Nature. 2008;455:351–7.

  31. 31.

    Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. Genome engineering using the CRISPR-Cas9 system. Nat Protoc. 2013;8:2281–308.

  32. 32.

    Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods. 2012;9:215–6.

  33. 33.

    Ge H, Liu Z, Church GM, Vidal M. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet. 2001;29:482–6.

  34. 34.

    Jansen R, Greenbaum D, Gerstein M. Relating whole-genome expression data with protein-protein interactions. Genome Res. 2002;12:37–46.

  35. 35.

    Deane CM, Salwiński Ł, Xenarios I, Eisenberg D. Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics. 2002;1:349–56.

  36. 36.

    Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, et al. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science. 2003;302:449–53.

  37. 37.

    Chen J, Xu H, Aronow BJ, Jegga AG. Improved human disease candidate gene prioritization using mouse phenotype. BMC Bioinformatics. 2007;8:392.

  38. 38.

    Isono K, Mizutani-Koseki Y, Komori T, Schmidt-Zachmann MS, Koseki H. Mammalian polycomb-mediated repression of Hox genes requires the essential spliceosomal protein Sf3b1. Genes Dev. 2005;19:536–41.

  39. 39.

    Kfir N, Lev-Maor G, Glaich O, Alajem A, Datta A, Sze SK, et al. SF3B1 association with chromatin determines splicing outcomes. Cell Rep. 2015;11:618–29.

  40. 40.

    Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 2006;125:315–26.

  41. 41.

    Harikumar A, Meshorer E Chromatin remodeling and bivalent histone modifications in embryonic stem cells. EMBO Rep. 2015;16:1609–19.

  42. 42.

    Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 2007;448:553–60.

  43. 43.

    Endoh M, Endo TA, Endoh T, Isono K, Sharif J, Ohara O, et al. Histone H2A mono-ubiquitination is a crucial step to mediate PRC1-dependent repression of developmental genes to maintain ES cell identity. PLoS Genet. 2012;8:e1002774.

  44. 44.

    Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet. 2008;4:e1000242.

  45. 45.

    McEvilly RJ, de Diaz MO, Schonemann MD, Hooshmand F, Rosenfeld MG. Transcriptional regulation of cortical neuron migration by POU domain factors. Science. 2002;295:1528–32.

  46. 46.

    Brennaman LH, Zhang X, Guan H, Triplett JW, Brown A, Demyanenko GP, et al. Polysialylated NCAM and ephrinA/EphA regulate synaptic development of GABAergic interneurons in prefrontal cortex. Cereb Cortex. 2013;23:162–77.

  47. 47.

    Nishikimi M, Oishi K, Tabata H, Torii K, Nakajima K. Segregation and pathfinding of callosal axons through EphA3 signaling. J Neurosci. 2011;31:16251–60.

  48. 48.

    Sado T, Nakajima N, Tada M, Takagi N. A novel mesoderm-specific cDNA isolated from a mouse embryonal carcinoma cell line (embryonal carcinoma cell/cDNA/in situ hybridization/mesoderm/mouse embryo). Dev Growth Differ. 1993;35:551–60.

  49. 49.

    Martin BL, Kimelman D. Brachyury establishes the embryonic mesodermal progenitor niche. Genes Dev. 2010;24:2778–83.

  50. 50.

    Bedogni F, Hodge RD, Elsen GE, Nelson BR, Daza RAM, Beyer RP, et al. Tbr1 regulates regional and laminar identity of postmitotic neurons in developing neocortex. Proc Natl Acad Sci USA. 2010;107:13129–34.

  51. 51.

    Edupuganti RR, Harikumar A, Aaronson Y, Biran A, Sailaja BS, Nissim-Rafinia M, et al. Alternative SET/TAFI promoters regulate embryonic stem cell differentiation. Stem Cell Reports. 2017;9:1291–303.

  52. 52.

    Oksenberg N, Ahituv N. The role of AUTS2 in neurodevelopment and human evolution. Trends Genet. 2013;29:600–8.

  53. 53.

    Vierbuchen T, Ostermeier A, Pang ZP, Kokubu Y, Südhof TC, Wernig M. Direct conversion of fibroblasts to functional neurons by defined factors. Nature. 2010;463:1035–41.

Download references

Acknowledgements

This research was supported by German-Israeli Foundation for Scientific Research and Development (GIF) (grant number 2224/2009 to SS), by the Israel Science Foundation (grant numbers 688/12 to SS, 575/17 to SS and 1140/17 to EM), and supported in part by ‘Investissements dʼAvenir’ program (Labex Biopsy, ANR-11-IDEX-0004-02 to MG) and Fondation Lejeune (to MG).

Author information

Affiliations

  1. Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel

    • Galya Monderer-Rothkoff
    • , Nitzan Tal
    • , Marina Risman
    • , Odem Shani
    • , Malka Nissim-Rafinia
    • , Laura Malki-Feldman
    • , Eran Meshorer
    •  & Sagiv Shifman
  2. Inserm, UMR-S839, Sorbonne Universités, Pierre et Marie Curie Université Paris 06, Institut du Fer à Moulin, Paris, 75005, France

    • Vera Medvedeva
    •  & Matthias Groszer

Authors

  1. Search for Galya Monderer-Rothkoff in:

  2. Search for Nitzan Tal in:

  3. Search for Marina Risman in:

  4. Search for Odem Shani in:

  5. Search for Malka Nissim-Rafinia in:

  6. Search for Laura Malki-Feldman in:

  7. Search for Vera Medvedeva in:

  8. Search for Matthias Groszer in:

  9. Search for Eran Meshorer in:

  10. Search for Sagiv Shifman in:

Conflict of interest

The authors declare that they have no conflict of interest.

Corresponding author

Correspondence to Sagiv Shifman.

Supplementary information

About this article

Publication history

Received

Revised

Accepted

Published

DOI

https://doi.org/10.1038/s41380-019-0409-1