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Research Paper

Neuronal-specific microexon splicing of TAF1 mRNA is directly regulated by SRRM4/nSR100

, , , ORCID Icon, , , , , , , , , , , & ORCID Icon show all
Pages 62-74 | Received 21 May 2019, Accepted 14 Aug 2019, Published online: 27 Sep 2019

References

  • Irimia M, Weatheritt RJ, Ellis JD, et al. A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell. 2014;159(7):1511–1523.
  • Raj B, Irimia M, Braunschweig U, et al. A global regulatory mechanism for activating an exon network required for neurogenesis. Mol Cell. 2014;56(1):90–103.
  • Quesnel-Vallieres M, Irimia M, Cordes SP, et al. Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development. Genes Dev. 2015;29(7):746–759.
  • Quesnel-Vallieres M, Dargaei Z, Irimia M, et al. Misregulation of an Activity-Dependent Splicing Network as a Common Mechanism Underlying Autism Spectrum Disorders. Mol Cell. 2016;64(6):1023–1034.
  • Burley SK, Roeder RG. Biochemistry and structural biology of transcription factor IID (TFIID). Annu Rev Biochem. 1996;65:769–799.
  • Makino S, Kaji R, Ando S, et al. Reduced neuron-specific expression of the TAF1 gene is associated with X-linked dystonia-parkinsonism. Am J Hum Genet. 2007;80(3):393–406.
  • O’Rawe JA, Wu Y, Dorfel MJ, et al. TAF1 Variants Are Associated with Dysmorphic Features, Intellectual Disability, and Neurological Manifestations. Am J Hum Genet. 2015;97(6):922–932.
  • Aneichyk T, Hendriks WT, Yadav R, et al. Dissecting the Causal Mechanism of X-Linked Dystonia-Parkinsonism by Integrating Genome and Transcriptome Assembly. Cell. 2018;172(5):897–909 e21.
  • Lee LV, Pascasio FM, Fuentes FD, et al. Torsion dystonia in Panay, Philippines. Adv Neurol. 1976;14:137–151.
  • Lee LV, Rivera C, Teleg RA, et al. The unique phenomenology of sex-linked dystonia parkinsonism (XDP, DYT3, “Lubag”). Int J Neurosci. 2011;121(Suppl 1):3–11.
  • Goto S, Kawarai T, Morigaki R, et al. Defects in the striatal neuropeptide Y system in X-linked dystonia-parkinsonism. Brain. 2013;136(Pt 5):1555–1567.
  • Goto S, Lee LV, Munoz EL, et al. Functional anatomy of the basal ganglia in X-linked recessive dystonia-parkinsonism. Ann Neurol. 2005;58(1):7–17.
  • Erben L, He MX, Laeremans A, et al. A Novel Ultrasensitive In Situ Hybridization Approach to Detect Short Sequences and Splice Variants with Cellular Resolution. Mol Neurobiol. 2017;55(7):6169–6181.
  • Hubbard KS, Gut IM, Lyman ME, et al. Longitudinal RNA sequencing of the deep transcriptome during neurogenesis of cortical glutamatergic neurons from murine ESCs. F1000Res. 2013;2:35.
  • Lotharius J, Falsig J, van Beek J, et al. Progressive degeneration of human mesencephalic neuron-derived cells triggered by dopamine-dependent oxidative stress is dependent on the mixed-lineage kinase pathway. J Neurosci. 2005;25(27):6329–6342.
  • Scholz D, Poltl D, Genewsky A, et al. Rapid, complete and large-scale generation of post-mitotic neurons from the human LUHMES cell line. J Neurochem. 2011;119(5):957–971.
  • Gonatopoulos-Pournatzis T, Wu M, Braunschweig U, et al. Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons. Mol Cell. 2018;72(3):510–24 e12.
  • Nolte D, Niemann S, Muller U. Specific sequence changes in multiple transcript system DYT3 are associated with X-linked dystonia parkinsonism. Proc Natl Acad Sci U S A. 2003;100(18):10347–10352.
  • Herzfeld T, Nolte D, Muller U. Structural and functional analysis of the human TAF1/DYT3 multiple transcript system. Mamm Genome. 2007;18(11):787–795.
  • Wahl MC, Will CL, Luhrmann R. The spliceosome: design principles of a dynamic RNP machine. Cell. 2009;136(4):701–718.
  • Daguenet E, Dujardin G, Valcarcel J. The pathogenicity of splicing defects: mechanistic insights into pre-mRNA processing inform novel therapeutic approaches. EMBO Rep. 2015;16(12):1640–1655.
  • Barbosa-Morais NL, Irimia M, Pan Q, et al. The evolutionary landscape of alternative splicing in vertebrate species. Science. 2012;338(6114):1587–1593.
  • Raj B, Blencowe BJ. Alternative Splicing in the Mammalian Nervous System: recent Insights into Mechanisms and Functional Roles. Neuron. 2015;87(1):14–27.
  • Vuong JK, Lin CH, Zhang M, et al. PTBP1 and PTBP2 Serve Both Specific and Redundant Functions in Neuronal Pre-mRNA Splicing. Cell Rep. 2016;17(10):2766–2775.
  • Muller F, Zaucker A, Tora L. Developmental regulation of transcription initiation: more than just changing the actors. Curr Opin Genet Dev. 2010;20(5):533–540.
  • Mal TK, Masutomi Y, Zheng L, et al. Structural and functional characterization on the interaction of yeast TFIID subunit TAF1 with TATA-binding protein. J Mol Biol. 2004;339(4):681–693.
  • Bhattacharya S, Lou X, Hwang P, et al. Structural and functional insight into TAF1-TAF7, a subcomplex of transcription factor II D. Proc Natl Acad Sci U S A. 2014;111(25):9103–9108.
  • Wang H, Curran EC, Hinds TR, et al. Crystal structure of a TAF1-TAF7 complex in human transcription factor IID reveals a promoter binding module. Cell Res. 2014;24(12):1433–1444.
  • Chalkley GE, Verrijzer CP. DNA binding site selection by RNA polymerase II TAFs: a TAF(II)250-TAF(II)150 complex recognizes the initiator. Embo J. 1999;18(17):4835–4845.
  • Louder RK, He Y, Lopez-Blanco JR, et al. Structure of promoter-bound TFIID and model of human pre-initiation complex assembly. Nature. 2016;531(7596):604–609.
  • Curran EC, Wang H, Hinds TR, et al. Zinc knuckle of TAF1 is a DNA binding module critical for TFIID promoter occupancy. Sci Rep. 2018;8(1):4630.
  • Chen X, Hiller M, Sancak Y, et al. Tissue-specific TAFs counteract Polycomb to turn on terminal differentiation. Science. 2005;310(5749):869–872.
  • Pointud JC, Mengus G, Brancorsini S, et al. The intracellular localisation of TAF7L, a paralogue of transcription factor TFIID subunit TAF7, is developmentally regulated during male germ-cell differentiation. J Cell Sci. 2003;116(Pt 9):1847–1858.
  • Wang PJ, Page DC. Functional substitution for TAF(II)250 by a retroposed homolog that is expressed in human spermatogenesis. Hum Mol Genet. 2002;11(19):2341–2346.
  • Herrera FJ, Yamaguchi T, Roelink H, et al. Core promoter factor TAF9B regulates neuronal gene expression. Elife. 2014;3:e02559.
  • Buljan M, Chalancon G, Eustermann S, et al. Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. Mol Cell. 2012;46(6):871–883.
  • Ellis JD, Barrios-Rodiles M, Colak R, et al. Tissue-specific alternative splicing remodels protein-protein interaction networks. Mol Cell. 2012;46(6):884–892.
  • Yang X, Coulombe-Huntington J, Kang S, et al. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. Cell. 2016;164(4):805–817.
  • Sako W, Morigaki R, Kaji R, et al. Identification and localization of a neuron-specific isoform of TAF1 in rat brain: implications for neuropathology of DYT3 dystonia. Neuroscience. 2011;189:100–107.
  • Ito N, Hendriks WT, Dhakal J, et al. Decreased N-TAF1 expression in X-linked dystonia-parkinsonism patient-specific neural stem cells. Dis Model Mech. 2016;9(4):451–462.
  • Rusconi F, Paganini L, Braida D, et al. LSD1 Neurospecific Alternative Splicing Controls Neuronal Excitability in Mouse Models of Epilepsy. Cereb Cortex. 2015;25(9):2729–2740.
  • Ohnishi T, Shirane M, Nakayama KI. SRRM4-dependent neuron-specific alternative splicing of protrudin transcripts regulates neurite outgrowth. Sci Rep. 2017;7:41130.
  • van Nuland R, Smits AH, Pallaki P, et al. Quantitative dissection and stoichiometry determination of the human SET1/MLL histone methyltransferase complexes. Mol Cell Biol. 2013;33(10):2067–2077.
  • Calarco JA, Superina S, O’Hanlon D, et al. Regulation of vertebrate nervous system alternative splicing and development by an SR-related protein. Cell. 2009;138(5):898–910.
  • Baymaz HI, Spruijt CG, Vermeulen M. Identifying nuclear protein-protein interactions using GFP affinity purification and SILAC-based quantitative mass spectrometry. Methods Mol Biol. 2014;1188:207–226.
  • Rappsilber J, Mann M, Ishihama Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc. 2007;2(8):1896–1906.
  • Smits AH, Jansen PW, Poser I, et al. Stoichiometry of chromatin-associated protein complexes revealed by label-free quantitative mass spectrometry-based proteomics. Nucleic Acids Res. 2013;41(1):e28.
  • Vizcaino JA, Csordas A, Del-Toro N, et al. 2016 update of the PRIDE database and its related tools. Nucleic Acids Res. 2016;44(22):11033.