A molecular brake that modulates spliceosome pausing at detained introns contributes to neurodegeneration
Dawei Meng, Qian Zheng, Xue Zhang, Xuejiao Piao, Li Luo, Yichang Jia
A molecular brake that modulates spliceosome pausing at detained introns contributes to neurodegeneration
Emerging evidence suggests that intron-detaining transcripts (IDTs) are a nucleus-detained and polyadenylated mRNA pool for cell to quickly and effectively respond to environmental stimuli and stress. However, the underlying mechanisms of detained intron (DI) splicing are still largely unknown. Here, we suggest that post-transcriptional DI splicing is paused at the Bact state, an active spliceosome but not catalytically primed, which depends on Smad Nuclear Interacting Protein 1 (SNIP1) and RNPS1 (a serine-rich RNA binding protein) interaction. RNPS1 and Bact components preferentially dock at DIs and the RNPS1 docking is sufficient to trigger spliceosome pausing. Haploinsufficiency of Snip1 attenuates neurodegeneration and globally rescues IDT accumulation caused by a previously reported mutant U2 snRNA, a basal spliceosomal component. Snip1 conditional knockout in the cerebellum decreases DI splicing efficiency and causes neurodegeneration. Therefore, we suggest that SNIP1 and RNPS1 form a molecular brake to promote spliceosome pausing, and that its misregulation contributes to neurodegeneration.
SNIP1 / RNPS1 / spliceosome / detained intron / neurodegeneration
[1] |
Adusumalli S, Ngian ZK, Lin WQ, et al. Increased intron retention is a post-transcriptional signature associated with progressive aging and Alzheimer’s disease. Aging Cell 2019;18: e12928.
CrossRef
Google scholar
|
[2] |
Anders S, Reyes A, Huber, W. Detecting differential usage of exons from RNA-seq data. Genome Res 2012;22:2008–2017.
CrossRef
Google scholar
|
[3] |
Aparicio-Prat E, Arnan C, Sala I, et al. DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs. BMC Genomics 2015;16:846.
CrossRef
Google scholar
|
[4] |
Athar A, Fullgrabe A, George N, et al. ArrayExpress update—from bulk to single-cell expression data. Nucleic Acids Res 2019;47:D711–D715.
CrossRef
Google scholar
|
[5] |
Bao P, Will CL, Urlaub H, et al. The RES complex is required for efficient transformation of the precatalytic B spliceosome into an activated B(act) complex. Genes Dev 2017;31:2416–2429.
CrossRef
Google scholar
|
[6] |
Bertram K, Agafonov DE, Dybkov O, et al. Cryo-EM structure of a pre-catalytic human spliceosome primed for activation. Cell 2017;170: 701–713.
CrossRef
Google scholar
|
[7] |
Bessonov S, Anokhina M, Will CL, et al. Isolation of an active step I spliceosome and composition of its RNP core. Nature 2008;452:846–850.
CrossRef
Google scholar
|
[8] |
Blazquez L, Emmett W, Faraway R, et al. Exon junction complex shapes the transcriptome by repressing recursive splicing. Mol Cell 2018;72:496–509.
CrossRef
Google scholar
|
[9] |
Boehm V, Britto-Borges T, Steckelberg AL. et al. Exon junction complexes suppress spurious splice sites to safeguard transcriptome integrity. Mol Cell 2018;72:482–495.
CrossRef
Google scholar
|
[10] |
Boelz S, Neu-Yilik G, Gehring NH, et al. A chemiluminescence-based reporter system to monitor nonsense-mediated mRNA decay. Biochem Biophys Res Commun 2006;349:186–191.
CrossRef
Google scholar
|
[11] |
Boutz PL, Bhutkar A, Sharp PA. Detained introns are a novel, wide-spread class of post-transcriptionally spliced introns. Genes Dev 2015;29:63–80.
CrossRef
Google scholar
|
[12] |
Bracken CP, Wall SJ, Barre B, et al. Regulation of cyclin D1 RNA stability by SNIP1. Cancer Res 2008;68:7621–7628.
CrossRef
Google scholar
|
[13] |
Braunschweig U, Barbosa-Morais NL, Pan Q. et al. Widespread intron retention in mammals functionally tunes transcriptomes. Genome Res 2014;24:1774–1786.
CrossRef
Google scholar
|
[14] |
Chen R.-Z, Cheng X, Tan Y. et al. An ENU-induced mutation in Twist1 transactivation domain causes hindlimb polydactyly with complete penetrance and dominant-negatively impairs E2A-dependent transcription. Sci Rep 2020;10:1–12.
CrossRef
Google scholar
|
[15] |
Consortium EP. An integrated encyclopedia of DNA elements in the human genome. Nature 2012;489:57.
CrossRef
Google scholar
|
[16] |
Darzacq X, Shav-Tal Y, de Turris V, et al. In vivo dynamics of RNA polymerase II transcription. Nat Struct Mol Biol 2007;14:796–806.
CrossRef
Google scholar
|
[17] |
Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013;29:15–21.
CrossRef
Google scholar
|
[18] |
Durocher D, Jackson SP. The FHA domain. FEBS Lett 2002;513:58–66.
CrossRef
Google scholar
|
[19] |
Dziembowski A, Ventura AP, Rutz B, et al. Proteomic analysis identifies a new complex required for nuclear pre-mRNA retention and splicing. EMBO J 2004;23:4847–4856.
CrossRef
Google scholar
|
[20] |
Fabrizio P, Dannenberg J, Dube P, et al. The evolutionarily conserved core design of the catalytic activation step of the yeast spliceosome. Mol Cell 2009;36:593–608.
CrossRef
Google scholar
|
[21] |
Fernandez JP, Moreno-Mateos MA, Gohr A, et al. RES complex is associated with intron definition and required for zebrafish early embryogenesis. PLoS Genet 2018;14:e1007473.
CrossRef
Google scholar
|
[22] |
Frankiw L, Majumdar D, Burns C, et al. BUD13 promotes a type I interferon response by countering intron retention in Irf7. Mol Cell 2019;73:803–814.
CrossRef
Google scholar
|
[23] |
Gehring NH, Kunz JB, Neu-Yilik G, et al. Exon-junction complex components specify distinct routes of nonsense-mediated mRNA decay with differential cofactor requirements. Mol Cell 2005;20:65–75.
CrossRef
Google scholar
|
[24] |
Gill J, Park Y, McGinnis JP. et al. Regulated intron removal integrates motivational state and experience. Cell 2017;169:836–848.
CrossRef
Google scholar
|
[25] |
Girard C, Will CL, Peng J, et al. Post-transcriptional spliceosomes are retained in nuclear speckles until splicing completion. Nat Commun 2012;3:994.
CrossRef
Google scholar
|
[26] |
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;72:510–524.
CrossRef
Google scholar
|
[27] |
Gottschalk A, Bartels C, Neubauer G, et al. A novel yeast U2 snRNP protein, Snu17p, is required for the first catalytic step of splicing and for progression of spliceosome assembly. Mol Cell Biol 2001;21:3037–3046.
CrossRef
Google scholar
|
[28] |
Haselbach D, Komarov I, Agafonov DE, et al. Structure and conformational dynamics of the human spliceosomal B(act) complex. Cell 2018;172:454–464.
CrossRef
Google scholar
|
[29] |
Hauer C, Sieber J, Schwarzl T, et al. Exon junction complexes show a distributional bias toward alternatively spliced mRNAs and against mRNAs coding for ribosomal proteins. Cell Rep 2016;16:1588–1603.
CrossRef
Google scholar
|
[30] |
Hayashi R, Handler D, Ish-Horowicz D, et al. The exon junction complex is required for definition and excision of neighboring introns in Drosophila. Genes Dev 2014;28:1772–1785.
CrossRef
Google scholar
|
[31] |
Hsu PD, Scott DA, Weinstein JA, et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 2013;31: 827–832.
CrossRef
Google scholar
|
[32] |
Hwang HW, Wentzel EA, Mendell JT. A hexanucleotide element directs microRNA nuclear import. Science 2007;315:97–100.
CrossRef
Google scholar
|
[33] |
Jacob AG, Smith CWJ. Intron retention as a component of regulated gene expression programs. Hum Genet 2017;136:1043–1057.
CrossRef
Google scholar
|
[34] |
Jia Y, Mu JC, Ackerman SL. Mutation of a U2 snRNA gene causes global disruption of alternative splicing and neurodegeneration. Cell 2012;148:296–308.
CrossRef
Google scholar
|
[35] |
Keren H, Lev-Maor G, Ast G. Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet 2010;11:345–355.
CrossRef
Google scholar
|
[36] |
Kim RH, Flanders KC, Reffey SB, et al. SNIP1 inhibits NF-κB signaling by competing for its binding to the C/H1 domain of CBP/p300 transcriptional co-activators. J Biol Chem 2001;276:46297–46304.
CrossRef
Google scholar
|
[37] |
Kim D, Paggi JM, Park C, et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 2019;37:907–915.
CrossRef
Google scholar
|
[38] |
Kim RH, Wang D, Tsang M, et al. A novel smad nuclear interacting protein, SNIP1, suppresses p300-dependent TGF-β signal transduction. Genes Dev 2000;14:1605–1616.
CrossRef
Google scholar
|
[39] |
Lander ES, Linton LM, Birren B, et al. Initial sequencing and analysis of the human genome. Nature 2001;409:860–921.
CrossRef
Google scholar
|
[40] |
Lardelli RM, Thompson JX, Yates JR., 3rd, et al. Release of SF3 from the intron branchpoint activates the first step of pre-mRNA splicing. RNA 2010;16:516–528.
CrossRef
Google scholar
|
[41] |
Le Hir H, Izaurralde E, Maquat LE, et al. The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exonexon junctions. EMBO J 2000;19:6860–6869.
CrossRef
Google scholar
|
[42] |
Le Hir H, Sauliere J, Wang Z. The exon junction complex as a node of post-transcriptional networks. Nat Rev Mol Cell Biol 2016;17:41–54.
CrossRef
Google scholar
|
[43] |
Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics 2009;25:2078–2079.
CrossRef
Google scholar
|
[44] |
Li C, Lin RI, Lai MC, et al. Nuclear Pnn/DRS protein binds to spliced mRNPs and participates in mRNA processing and export via interaction with RNPS1. Mol Cell Biol 2003;23:7363–7376.
CrossRef
Google scholar
|
[45] |
Lizen B, Claus M, Jeannotte L, et al. Perinatal induction of Cre recombination with tamoxifen. Transgenic Res 2015;24:1065–1077.
CrossRef
Google scholar
|
[46] |
Lovci MT, Ghanem D, Marr H, et al. Rbfox proteins regulate alter-native mRNA splicing through evolutionarily conserved RNA bridges. Nat Struct Mol Biol 2013;20:1434–1442.
CrossRef
Google scholar
|
[47] |
Luco RF, Pan Q, Tominaga K, et al. Regulation of alternative splicing by histone modifications. Science 2010;327:996–1000.
CrossRef
Google scholar
|
[48] |
Lykke-Andersen J, Shu MD, Steitz JA. Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1. Science 2001;293:1836–1839.
CrossRef
Google scholar
|
[49] |
Malone CD, Mestdagh C, Akhtar J, et al. The exon junction complex controls transposable element activity by ensuring faithful splicing of the piwi transcript. Genes Dev 2014;28:1786–1799.
CrossRef
Google scholar
|
[50] |
Maquat LE. Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics. Nat Rev Mol Cell Biol 2004;5:89–99.
CrossRef
Google scholar
|
[51] |
Mauger O, Lemoine F, Scheiffele P. Targeted intron retention and excision for rapid gene regulation in response to neuronal activity. Neuron 2016;92:1266–1278.
CrossRef
Google scholar
|
[52] |
Mayeda A, Badolato J, Kobayashi R, et al. Purification and characterization of human RNPS1: a general activator of pre-mRNA splicing. EMBO J 1999;18:4560–4570.
CrossRef
Google scholar
|
[53] |
McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome research 2010;20:1297–1303.
CrossRef
Google scholar
|
[54] |
Mi H, Muruganujan A, Casagrande JT, et al. Large-scale gene function analysis with the PANTHER classification system. Nat Protoc 2013;8:1551–1566.
CrossRef
Google scholar
|
[55] |
Murachelli AG, Ebert J, Basquin C, et al. The structure of the ASAP core complex reveals the existence of a Pinin-containing PSAP complex. Nat Struct Mol Biol 2012;19:378–386.
CrossRef
Google scholar
|
[56] |
Naro C, Jolly A, Di Persio S, et al. An orchestrated intron retention program in meiosis controls timely usage of transcripts during germ cell differentiation. Dev Cell 2017;41:82–93.
CrossRef
Google scholar
|
[57] |
Nilsen TW, Graveley BR. Expansion of the eukaryotic proteome by alternative splicing. Nature 2010;463:457–463.
CrossRef
Google scholar
|
[58] |
Ninomiya K, Kataoka N, Hagiwara M. Stress-responsive maturation of Clk1/4 pre-mRNAs promotes phosphorylation of SR splicing factor. J Cell Biol 2011;195:27–40.
CrossRef
Google scholar
|
[59] |
Ohrt T, Prior M, Dannenberg J, et al. Prp2-mediated protein rearrangements at the catalytic core of the spliceosome as revealed by dcFCCS. RNA 2012;18:1244–1256.
CrossRef
Google scholar
|
[60] |
Padgett RA, Grabowski PJ, Konarska MM, et al. Splicing of messenger RNA precursors. Annu Rev Biochem 1986;55:1119–1150.
CrossRef
Google scholar
|
[61] |
Pan Q, Shai O, Lee LJ, et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008;40:1413–1415.
CrossRef
Google scholar
|
[62] |
Park SK, Zhou X, Pendleton KE, et al. A conserved splicing silencer dynamically regulates O-GlcNAc transferase intron retention and O-GlcNAc homeostasis. Cell Rep 2017;20:1088–1099.
CrossRef
Google scholar
|
[63] |
Pendleton KE, Chen B, Liu K, et al. The U6 snRNA m(6)A methyltransferase METTL16 regulates SAM synthetase intron retention. Cell 2017;169:824–835.
CrossRef
Google scholar
|
[64] |
Peron SP, Freeman J, Iyer V, et al. A cellular resolution map of barrel cortex activity during tactile behavior. Neuron 2015;86:783–799.
CrossRef
Google scholar
|
[65] |
Picelli S, Bjorklund AK, Faridani OR, et al. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods 2013;10:1096–1098.
CrossRef
Google scholar
|
[66] |
Picelli S, Faridani OR, Björklund ÅK, et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 2014;9:171–181.
CrossRef
Google scholar
|
[67] |
Pitulescu ME, Schmidt I, Benedito R, et al. Inducible gene targeting in the neonatal vasculature and analysis of retinal angiogenesis in mice. Nat Protoc 2010;5:1518–1534.
CrossRef
Google scholar
|
[68] |
Pohlkamp T, Steller L, May P, et al. Generation and characterization of an Nse-CreERT2 transgenic line suitable for inducible gene manipulation in cerebellar granule cells. PLoS One 2014;9:e100384.
CrossRef
Google scholar
|
[69] |
Popp MW, Maquat LE. Organizing principles of mammalian nonsense-mediated mRNA decay. Annu Rev Genet 2013;47:139–165.
CrossRef
Google scholar
|
[70] |
Quinlan AR. BEDTools: The Swiss-Army tool for genome feature analysis. Curr Protoc Bioinformatics 2014;47:11.12.1–11.12.34.
CrossRef
Google scholar
|
[71] |
Ran FA, Hsu PD, Wright J, et al. Genome engineering using the CRISPR-Cas9 system. Nat Protoc 2013;8:2281–2308.
CrossRef
Google scholar
|
[72] |
Reichert VL, Le Hir H, Jurica MS, et al. 5’ exon interactions within the human spliceosome establish a framework for exon junction complex structure and assembly. Genes Dev 2002;16:2778–2791.
CrossRef
Google scholar
|
[73] |
Rinn JL, Kertesz M, Wang JK. et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007; 129:1311–1323.
CrossRef
Google scholar
|
[74] |
Sakashita E, Tatsumi S, Werner D, et al. Human RNPS1 and its associated factors: a versatile alternative pre-mRNA splicing regulator in vivo. Mol Cell Biol 2004;24:1174–1187.
CrossRef
Google scholar
|
[75] |
Salinger AP, Justice MJ. Mouse mutagenesis using N-ethyl-N-nitrosourea (ENU). Cold Spring Harbor Protocols 2008, 2008;3:pdb. prot4985.
CrossRef
Google scholar
|
[76] |
Schneider C, Agafonov DE, Schmitzova J, et al. Dynamic contacts of U2, RES, Cwc25, Prp8 and Prp45 proteins with the pre-mRNA branch-site and 3’ splice site during catalytic activation and step 1 catalysis in yeast spliceosomes. PLoS Genet 2015;11:e1005539.
CrossRef
Google scholar
|
[77] |
Schwerk C, Prasad J, Degenhardt K, et al. ASAP, a novel protein complex involved in RNA processing and apoptosis. Mol Cell Biol 2003;23:2981–2990.
CrossRef
Google scholar
|
[78] |
Shalem O, Sanjana NE, Hartenian E, et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 2014;343:84–87.
CrossRef
Google scholar
|
[79] |
Shi Y. Mechanistic insights into precursor messenger RNA splicing by the spliceosome. Nat Rev Mol Cell Biol 2017;18:655.
CrossRef
Google scholar
|
[80] |
Singh J, Padgett RA. Rates of in situ transcription and splicing in large human genes. Nat Struct Mol Biol 2009;16:1128–1133.
CrossRef
Google scholar
|
[81] |
Tan ZW, Fei G, Paulo JA, et al. O-GlcNAc regulates gene expression by controlling detained intron splicing. Nucleic Acids Res 2020;48:5656–5669.
CrossRef
Google scholar
|
[82] |
Tange TO, Shibuya T, Jurica MS, et al. Biochemical analysis of the EJC reveals two new factors and a stable tetrameric protein core. RNA 2005;11:1869–1883.
CrossRef
Google scholar
|
[83] |
Tennyson CN, Klamut HJ, Worton RG. The human dystrophin gene requires 16 hours to be transcribed and is cotranscriptionally spliced. Nat Genet 1995;9:184–190.
CrossRef
Google scholar
|
[84] |
Townsend C, Leelaram MN, Agafonov DE, et al. Mechanism of protein- guided folding of the active site U2/U6 RNA during spliceosome activation. Science 2020;370.
CrossRef
Google scholar
|
[85] |
Trembley JH, Tatsumi S, Sakashita E, et al. Activation of pre-mRNA splicing by human RNPS1 is regulated by CK2 phosphorylation. Mol Cell Biol 2005;25:1446–1457.
CrossRef
Google scholar
|
[86] |
Ullrich S, Guigo R. Dynamic changes in intron retention are tightly associated with regulation of splicing factors and proliferative activity during B-cell development. Nucleic Acids Res 2020;48:1327–1340.
CrossRef
Google scholar
|
[87] |
Van Nostrand EL, Pratt GA, Shishkin AA, et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 2016;13:508–514.
CrossRef
Google scholar
|
[88] |
Van Nostrand EL, Freese P, Pratt GA, et al. A large-scale binding and functional map of human RNA-binding proteins. Nature 2020a;583:711–719.
CrossRef
Google scholar
|
[89] |
Van Nostrand EL, Pratt GA, Yee BA, et al. Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins. Genome Biol 2020b;21:90.
CrossRef
Google scholar
|
[90] |
Venkatesan BM, Bashir R. Nanopore sensors for nucleic acid analysis. Nat Nanotechnol 2011;6:615–624.
CrossRef
Google scholar
|
[91] |
Wahl MC, Will CL, Luhrmann R. The spliceosome: design principles of a dynamic RNP machine. Cell 2009;136:701–718.
CrossRef
Google scholar
|
[92] |
Wan R, Bai R, Yan C, et al. Structures of the catalytically activated yeast spliceosome reveal the mechanism of branching. Cell 2019;177:339–351.
CrossRef
Google scholar
|
[93] |
Wang Q, Conlon EG, Manley JL, et al. Widespread intron retention impairs protein homeostasis in C9orf72 ALS brains. Genome Res 2020;30:1705–1715.
CrossRef
Google scholar
|
[94] |
Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 2010;38:e164–e164.
CrossRef
Google scholar
|
[95] |
Wang ET, Sandberg R, Luo S, et al. Alternative isoform regulation in human tissue transcriptomes. Nature 2008;456:470–476.
CrossRef
Google scholar
|
[96] |
Wilkinson ME, Charenton C, Nagai K. RNA splicing by the spliceosome. Annu Rev Biochem 2020;89:359–388.
CrossRef
Google scholar
|
[97] |
Wong JJ, Ritchie W, Ebner OA, et al. Orchestrated intron retention regulates normal granulocyte differentiation. Cell 2013;154:583–595.
CrossRef
Google scholar
|
[98] |
Wysoczanski P, Schneider C, Xiang S, et al. Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex. Nat Struct Mol Biol 2014;21:911–918.
CrossRef
Google scholar
|
[99] |
Xing Z, Lin A, Li C, et al. lncRNA directs cooperative epigenetic regulation downstream of chemokine signals. Cell 2014;159:1110–1125.
CrossRef
Google scholar
|
[100] |
Yan C, Wan R, Bai R, et al. Structure of a yeast activated spliceosome at 3.5 Å resolution. Science 2016;353:904–911.
CrossRef
Google scholar
|
[101] |
Yap K, Lim ZQ, et al. Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention. Genes Dev 2012;26:1209–1223.
CrossRef
Google scholar
|
[102] |
Zhan X, Yan C, Zhang X, et al. Structure of a human catalytic step I spliceosome. Science 2018;359:537–545.
CrossRef
Google scholar
|
[103] |
Zhang J, Lee D, Dhiman V, et al. An integrative ENCODE resource for cancer genomics. Nat Commun 2020;11:1–11.
CrossRef
Google scholar
|
[104] |
Zhang X, Yan C, Zhan X, et al. Structure of the human activated spliceosome in three conformational states. Cell Res 2018;28:307–322.
CrossRef
Google scholar
|
/
〈 | 〉 |