A Drosophila model of Pontocerebellar Hypoplasia reveals a critical role for the RNA exosome in neurons
Autoři:
Derrick J. Morton aff001; Binta Jalloh aff002; Lily Kim aff001; Isaac Kremsky aff001; Rishi J. Nair aff001; Khuong B. Nguyen aff001; J. Christopher Rounds aff002; Maria C. Sterrett aff001; Brianna Brown aff003; Thalia Le aff001; Maya C. Karkare aff001; Kathryn D. McGaughey aff001; Shaoyi Sheng aff001; Sara W. Leung aff001; Milo B. Fasken aff001; Kenneth H. Moberg aff003; Anita H. Corbett aff001
Působiště autorů:
Department of Biology, RRC 1021, Emory University, NE, Atlanta, Georgia, United States of America
aff001; Genetics and Molecular Biology Graduate Program, Emory University, NE, Atlanta, Georgia, United States of America
aff002; Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, United States of America
aff003; Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, NE, Atlanta, Georgia, United States of America
aff004
Vyšlo v časopise:
A Drosophila model of Pontocerebellar Hypoplasia reveals a critical role for the RNA exosome in neurons. PLoS Genet 16(7): e32767. doi:10.1371/journal.pgen.1008901
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pgen.1008901
Souhrn
The RNA exosome is an evolutionarily-conserved ribonuclease complex critically important for precise processing and/or complete degradation of a variety of cellular RNAs. The recent discovery that mutations in genes encoding structural RNA exosome subunits cause tissue-specific diseases makes defining the role of this complex within specific tissues critically important. Mutations in the RNA exosome component 3 (EXOSC3) gene cause Pontocerebellar Hypoplasia Type 1b (PCH1b), an autosomal recessive neurologic disorder. The majority of disease-linked mutations are missense mutations that alter evolutionarily-conserved regions of EXOSC3. The tissue-specific defects caused by these amino acid changes in EXOSC3 are challenging to understand based on current models of RNA exosome function with only limited analysis of the complex in any multicellular model in vivo. The goal of this study is to provide insight into how mutations in EXOSC3 impact the function of the RNA exosome. To assess the tissue-specific roles and requirements for the Drosophila ortholog of EXOSC3 termed Rrp40, we utilized tissue-specific RNAi drivers. Depletion of Rrp40 in different tissues reveals a general requirement for Rrp40 in the development of many tissues including the brain, but also highlight an age-dependent requirement for Rrp40 in neurons. To assess the functional consequences of the specific amino acid substitutions in EXOSC3 that cause PCH1b, we used CRISPR/Cas9 gene editing technology to generate flies that model this RNA exosome-linked disease. These flies show reduced viability; however, the surviving animals exhibit a spectrum of behavioral and morphological phenotypes. RNA-seq analysis of these Drosophila Rrp40 mutants reveals increases in the steady-state levels of specific mRNAs and ncRNAs, some of which are central to neuronal function. In particular, Arc1 mRNA, which encodes a key regulator of synaptic plasticity, is increased in the Drosophila Rrp40 mutants. Taken together, this study defines a requirement for the RNA exosome in specific tissues/cell types and provides insight into how defects in RNA exosome function caused by specific amino acid substitutions that occur in PCH1b can contribute to neuronal dysfunction.
Klíčová slova:
Amino acid substitution – Drosophila melanogaster – Exosomes – Neurons – Phenotypes – RNA interference – RNA structure – Small nucleolar RNA
Zdroje
1. Mitchell P, Petfalski E, Shevchenko A, Mann M, Tollervey D. The exosome: a conserved eukaryotic RNA processing complex containing multiple 3'—>5' exoribonucleases. Cell. 1997;91(4):457–66. doi: 10.1016/s0092-8674(00)80432-8 9390555.
2. Allmang C, Petfalski E, Podtelejnikov A, Mann M, Tollervey D, Mitchell P. The yeast exosome and human PM-Scl are related complexes of 3' —> 5' exonucleases. Genes Dev. 1999;13(16):2148–58. doi: 10.1101/gad.13.16.2148 10465791.
3. Boczonadi V, Muller JS, Pyle A, Munkley J, Dor T, Quartararo J, et al. EXOSC8 mutations alter mRNA metabolism and cause hypomyelination with spinal muscular atrophy and cerebellar hypoplasia. Nat Commun. 2014;5:4287. Epub 2014/07/06. doi: 10.1038/ncomms5287 24989451; PubMed Central PMCID: PMC4102769.
4. Gerstberger S, Hafner M, Ascano M, Tuschl T. Evolutionary conservation and expression of human RNA-binding proteins and their role in human genetic disease. Adv Exp Med Biol. 2014;825:1–55. Epub 2014/09/10. doi: 10.1007/978-1-4939-1221-6_1 25201102; PubMed Central PMCID: PMC4180674.
5. Di Donato N, Neuhann T, Kahlert AK, Klink B, Hackmann K, Neuhann I, et al. Mutations in EXOSC2 are associated with a novel syndrome characterised by retinitis pigmentosa, progressive hearing loss, premature ageing, short stature, mild intellectual disability and distinctive gestalt. J Med Genet. 2016;53(6):419–25. Epub 2016/02/05. doi: 10.1136/jmedgenet-2015-103511 26843489.
6. Wan J, Yourshaw M, Mamsa H, Rudnik-Schoneborn S, Menezes MP, Hong JE, et al. Mutations in the RNA exosome component gene EXOSC3 cause pontocerebellar hypoplasia and spinal motor neuron degeneration. Nat Genet. 2012;44(6):704–8. Epub 2012/05/01. doi: 10.1038/ng.2254 22544365; PubMed Central PMCID: PMC3366034.
7. Mitchell P, Petfalski E, Tollervey D. The 3' end of yeast 5.8S rRNA is generated by an exonuclease processing mechanism. Genes Dev. 1996;10(4):502–13. Epub 1996/02/15. doi: 10.1101/gad.10.4.502 8600032.
8. Liu Q, Greimann JC, Lima CD. Reconstitution, activities, and structure of the eukaryotic RNA exosome. Cell. 2006;127(6):1223–37. Epub 2006/12/19. doi: 10.1016/j.cell.2006.10.037 17174896.
9. Makino DL, Conti E. Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement. Acta Crystallogr D Biol Crystallogr. 2013;69(Pt 11):2226–35. Epub 2013/11/06. doi: 10.1107/S0907444913011438 24189234; PubMed Central PMCID: PMC3817696.
10. Briggs MW, Burkard KT, Butler JS. Rrp6p, the yeast homologue of the human PM-Scl 100-kDa autoantigen, is essential for efficient 5.8 S rRNA 3' end formation. J Biol Chem. 1998;273(21):13255–63. Epub 1998/05/28. doi: 10.1074/jbc.273.21.13255 9582370.
11. Hou D, Ruiz M, Andrulis ED. The ribonuclease Dis3 is an essential regulator of the developmental transcriptome. BMC Genomics. 2012;13:359. Epub 2012/08/03. doi: 10.1186/1471-2164-13-359 22853036; PubMed Central PMCID: PMC3434026.
12. Lim SJ, Boyle PJ, Chinen M, Dale RK, Lei EP. Genome-wide localization of exosome components to active promoters and chromatin insulators in Drosophila. Nucleic acids research. 2013;41(5):2963–80. doi: 10.1093/nar/gkt037 23358822; PubMed Central PMCID: PMC3597698.
13. Yang X, Bayat V, DiDonato N, Zhao Y, Zarnegar B, Siprashvili Z, et al. Genetic and genomic studies of pathogenic EXOSC2 mutations in the newly described disease SHRF implicate the autophagy pathway in disease pathogenesis. Hum Mol Genet. 2019. Epub 2019/10/20. doi: 10.1093/hmg/ddz251 31628467.
14. Pefanis E, Wang J, Rothschild G, Lim J, Chao J, Rabadan R, et al. Noncoding RNA transcription targets AID to divergently transcribed loci in B cells. Nature. 2014;514(7522):389–93. Epub 2014/08/15. doi: 10.1038/nature13580 25119026; PubMed Central PMCID: PMC4372240.
15. Fasken MB, Morton DJ, Kuiper EG, Jones SK, Leung SW, Corbett AH. The RNA Exosome and Human Disease. Methods Mol Biol. 2020;2062:3–33. Epub 2019/11/27. doi: 10.1007/978-1-4939-9822-7_1 31768969.
16. Morton DJ, Kuiper EG, Jones SK, Leung SW, Corbett AH, Fasken MB. The RNA exosome and RNA exosome-linked disease. RNA. 2018;24(2):127–42. Epub 2017/11/03. doi: 10.1261/rna.064626.117 29093021; PubMed Central PMCID: PMC5769741.
17. Muller JS, Giunta M, Horvath R. Exosomal Protein Deficiencies: How Abnormal RNA Metabolism Results in Childhood-Onset Neurological Diseases. J Neuromuscul Dis. 2015;2(Suppl 2):S31–S7. Epub 2015/01/01. doi: 10.3233/JND-150086 27127732; PubMed Central PMCID: PMC4845884.
18. Wan J, Yourshaw M, Mamsa H, Rudnik-Schoneborn S, Menezes MP, Hong JE, et al. Mutations in the RNA exosome component gene EXOSC3 cause pontocerebellar hypoplasia and spinal motor neuron degeneration. Nat Genet. 2012;44(6):704–8. Epub 2012/05/01. doi: 10.1038/ng.2254 22544365; PubMed Central PMCID: PMC3366034.
19. Eggens VR, Barth PG, Niermeijer JM, Berg JN, Darin N, Dixit A, et al. EXOSC3 mutations in pontocerebellar hypoplasia type 1: novel mutations and genotype-phenotype correlations. Orphanet J Rare Dis. 2014;9(1):23. Epub 2014/02/15. doi: 10.1186/1750-1172-9-23 24524299; PubMed Central PMCID: PMC3928094.
20. Rudnik-Schoneborn S, Senderek J, Jen JC, Houge G, Seeman P, Puchmajerova A, et al. Pontocerebellar hypoplasia type 1: clinical spectrum and relevance of EXOSC3 mutations. Neurology. 2013;80(5):438–46. Epub 2013/01/04. doi: 10.1212/WNL.0b013e31827f0f66 23284067; PubMed Central PMCID: PMC3590055.
21. Halevy A, Lerer I, Cohen R, Kornreich L, Shuper A, Gamliel M, et al. Novel EXOSC3 mutation causes complicated hereditary spastic paraplegia. J Neurol. 2014;261(11):2165–9. Epub 2014/08/26. doi: 10.1007/s00415-014-7457-x 25149867.
22. Zanni G, Scotton C, Passarelli C, Fang M, Barresi S, Dallapiccola B, et al. Exome sequencing in a family with intellectual disability, early onset spasticity, and cerebellar atrophy detects a novel mutation in EXOSC3. Neurogenetics. 2013;14(3–4):247–50. Epub 2013/08/27. doi: 10.1007/s10048-013-0371-z 23975261.
23. van Dijk T, Baas F, Barth PG, Poll-The BT. What's new in pontocerebellar hypoplasia? An update on genes and subtypes. Orphanet J Rare Dis. 2018;13(1):92. Epub 2018/06/16. doi: 10.1186/s13023-018-0826-2 29903031; PubMed Central PMCID: PMC6003036.
24. Fasken MB, Losh JS, Leung SW, Brutus S, Avin B, Vaught JC, et al. Insight into the RNA Exosome Complex Through Modeling Pontocerebellar Hypoplasia Type 1b Disease Mutations in Yeast. Genetics. 2017;205(1):221–37. Epub 2016/10/27. doi: 10.1534/genetics.116.195917 27777260; PubMed Central PMCID: PMC5223504.
25. Gillespie A, Gabunilas J, Jen JC, Chanfreau GF. Mutations of EXOSC3/Rrp40p associated with neurological diseases impact ribosomal RNA processing functions of the exosome in S. cerevisiae. RNA. 2017;23(4):466–72. Epub 2017/01/06. doi: 10.1261/rna.060004.116 28053271; PubMed Central PMCID: PMC5340910.
26. de Belle JS, Heisenberg M. Associative odor learning in Drosophila abolished by chemical ablation of mushroom bodies. Science. 1994;263(5147):692–5. Epub 1994/02/04. doi: 10.1126/science.8303280 8303280.
27. Armstrong JD, de Belle JS, Wang Z, Kaiser K. Metamorphosis of the mushroom bodies; large-scale rearrangements of the neural substrates for associative learning and memory in Drosophila. Learn Mem. 1998;5(1–2):102–14. Epub 1999/08/24. 10454375; PubMed Central PMCID: PMC311269.
28. Lee T, Lee A, Luo L. Development of the Drosophila mushroom bodies: sequential generation of three distinct types of neurons from a neuroblast. Development. 1999;126(18):4065–76. Epub 1999/08/24. 10457015.
29. Crittenden JR, Skoulakis EM, Han KA, Kalderon D, Davis RL. Tripartite mushroom body architecture revealed by antigenic markers. Learn Mem. 1998;5(1–2):38–51. Epub 1999/08/24. 10454371; PubMed Central PMCID: PMC311260.
30. Fushima K, Tsujimura H. Precise control of fasciclin II expression is required for adult mushroom body development in Drosophila. Dev Growth Differ. 2007;49(3):215–27. Epub 2007/03/31. doi: 10.1111/j.1440-169X.2007.00922.x 17394600.
31. Zhang YQ, Bailey AM, Matthies HJ, Renden RB, Smith MA, Speese SD, et al. Drosophila fragile X-related gene regulates the MAP1B homolog Futsch to control synaptic structure and function. Cell. 2001;107(5):591–603. Epub 2001/12/06. doi: 10.1016/s0092-8674(01)00589-x 11733059.
32. Zinder JC, Lima CD. Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors. Genes Dev. 2017;31(2):88–100. Epub 2017/02/17. doi: 10.1101/gad.294769.116 28202538; PubMed Central PMCID: PMC5322736.
33. Belair C, Sim S, Kim KY, Tanaka Y, Park IH, and, et al. The RNA exosome nuclease complex regulates human embryonic stem cell differentiation. J Cell Biol. 2019. Epub 2019/07/17. doi: 10.1083/jcb.201811148 31308215.
34. Mistry DS, Chen Y, Sen GL. Progenitor function in self-renewing human epidermis is maintained by the exosome. Cell Stem Cell. 2012;11(1):127–35. Epub 2012/07/10. doi: 10.1016/j.stem.2012.04.022 22770246; PubMed Central PMCID: PMC3392610.
35. McIver SC, Kang YA, DeVilbiss AW, O'Driscoll CA, Ouellette JN, Pope NJ, et al. The exosome complex establishes a barricade to erythroid maturation. Blood. 2014;124(14):2285–97. Epub 2014/08/15. doi: 10.1182/blood-2014-04-571083 25115889; PubMed Central PMCID: PMC4183988.
36. Kiss DL, Andrulis ED. Genome-wide analysis reveals distinct substrate specificities of Rrp6, Dis3, and core exosome subunits. RNA. 2010;16(4):781–91. Epub 2010/02/27. doi: 10.1261/rna.1906710 20185544; PubMed Central PMCID: PMC2844625.
37. Biancheri R, Cassandrini D, Pinto F, Trovato R, Di Rocco M, Mirabelli-Badenier M, et al. EXOSC3 mutations in isolated cerebellar hypoplasia and spinal anterior horn involvement. J Neurol. 2013;260(7):1866–70. Epub 2013/04/09. doi: 10.1007/s00415-013-6896-0 23564332.
38. Di Giovambattista AP, Jacome Querejeta I, Ventura Faci P, Rodriguez Martinez G, Ramos Fuentes F. [Familial EXOSC3-related pontocerebellar hypoplasia]. An Pediatr (Barc). 2017;86(5):284–6. Epub 2016/11/24. doi: 10.1016/j.anpedi.2016.09.011 27876572.
39. Eggens VR, Barth PG, Niermeijer JM, Berg JN, Darin N, Dixit A, et al. EXOSC3 mutations in pontocerebellar hypoplasia type 1: novel mutations and genotype-phenotype correlations. Orphanet J Rare Dis. 2014;9:23. Epub 2014/02/15. doi: 10.1186/1750-1172-9-23 24524299; PubMed Central PMCID: PMC3928094.
40. Bizzari S, Hamzeh AR, Mohamed M, Al-Ali MT, Bastaki F. Expanded PCH1D phenotype linked to EXOSC9 mutation. Eur J Med Genet. 2019. Epub 2019/01/29. doi: 10.1016/j.ejmg.2019.01.012 30690203.
41. Burns DT, Donkervoort S, Muller JS, Knierim E, Bharucha-Goebel D, Faqeih EA, et al. Variants in EXOSC9 Disrupt the RNA Exosome and Result in Cerebellar Atrophy with Spinal Motor Neuronopathy. Am J Hum Genet. 2018;102(5):858–73. Epub 2018/05/05. doi: 10.1016/j.ajhg.2018.03.011 29727687; PubMed Central PMCID: PMC5986733.
42. Howse PE. Brain structure and behavior in insects. Annu Rev Entomol. 1975;20:359–79. Epub 1975/01/01. doi: 10.1146/annurev.en.20.010175.002043 1090240.
43. Wasmuth EV, Zinder JC, Zattas D, Das M, Lima CD. Structure and reconstitution of yeast Mpp6-nuclear exosome complexes reveals that Mpp6 stimulates RNA decay and recruits the Mtr4 helicase. Elife. 2017;6. Epub 2017/07/26. doi: 10.7554/eLife.29062 28742025; PubMed Central PMCID: PMC5553935.
44. Falk S, Bonneau F, Ebert J, Kogel A, Conti E. Mpp6 Incorporation in the Nuclear Exosome Contributes to RNA Channeling through the Mtr4 Helicase. Cell Rep. 2017;20(10):2279–86. Epub 2017/09/07. doi: 10.1016/j.celrep.2017.08.033 28877463; PubMed Central PMCID: PMC5603729.
45. Lorentzen E, Dziembowski A, Lindner D, Seraphin B, Conti E. RNA channelling by the archaeal exosome. EMBO Rep. 2007;8(5):470–6. Epub 2007/03/24. doi: 10.1038/sj.embor.7400945 17380186; PubMed Central PMCID: PMC1866195.
46. Zinder JC, Wasmuth EV, Lima CD. Nuclear RNA Exosome at 3.1 A Reveals Substrate Specificities, RNA Paths, and Allosteric Inhibition of Rrp44/Dis3. Mol Cell. 2016;64(4):734–45. Epub 2016/11/08. doi: 10.1016/j.molcel.2016.09.038 27818140; PubMed Central PMCID: PMC5115963.
47. Ivanov I, Atkinson D, Litvinenko I, Angelova L, Andonova S, Mumdjiev H, et al. Pontocerebellar hypoplasia type 1 for the neuropediatrician: Genotype-phenotype correlations and diagnostic guidelines based on new cases and overview of the literature. Eur J Paediatr Neurol. 2018;22(4):674–81. Epub 2018/04/17. doi: 10.1016/j.ejpn.2018.03.011 29656927.
48. Schwabova J, Brozkova DS, Petrak B, Mojzisova M, Pavlickova K, Haberlova J, et al. Homozygous EXOSC3 mutation c.92G—>C, p.G31A is a founder mutation causing severe pontocerebellar hypoplasia type 1 among the Czech Roma. J Neurogenet. 2013;27(4):163–9. Epub 2013/07/26. doi: 10.3109/01677063.2013.814651 23883322.
49. Wu JS, Luo L. A protocol for dissecting Drosophila melanogaster brains for live imaging or immunostaining. Nat Protoc. 2006;1(4):2110–5. Epub 2007/05/10. doi: 10.1038/nprot.2006.336 17487202.
50. Grenningloh G, Rehm EJ, Goodman CS. Genetic analysis of growth cone guidance in Drosophila: fasciclin II functions as a neuronal recognition molecule. Cell. 1991;67(1):45–57. Epub 1991/10/04. doi: 10.1016/0092-8674(91)90571-f 1913818.
51. Gratz SJ, Wildonger J, Harrison MM, O'Connor-Giles KM. CRISPR/Cas9-mediated genome engineering and the promise of designer flies on demand. Fly (Austin). 2013;7(4):249–55. Epub 2013/10/04. doi: 10.4161/fly.26566 24088745; PubMed Central PMCID: PMC3896497.
52. Gratz SJ, Ukken FP, Rubinstein CD, Thiede G, Donohue LK, Cummings AM, et al. Highly specific and efficient CRISPR/Cas9-catalyzed homology-directed repair in Drosophila. Genetics. 2014;196(4):961–71. Epub 2014/01/31. doi: 10.1534/genetics.113.160713 24478335; PubMed Central PMCID: PMC3982687.
53. Bauer JH, Goupil S, Garber GB, Helfand SL. An accelerated assay for the identification of lifespan-extending interventions in Drosophila melanogaster. Proc Natl Acad Sci U S A. 2004;101(35):12980–5. Epub 2004/08/26. doi: 10.1073/pnas.0403493101 15328413; PubMed Central PMCID: PMC516504.
54. Pak C, Garshasbi M, Kahrizi K, Gross C, Apponi LH, Noto JJ, et al. Mutation of the conserved polyadenosine RNA binding protein, ZC3H14/dNab2, impairs neural function in Drosophila and humans. Proc Natl Acad Sci U S A. 2011;108(30):12390–5. Epub 2011/07/08. doi: 10.1073/pnas.1107103108 21734151; PubMed Central PMCID: PMC3145741.
55. Andrulis ED, Werner J, Nazarian A, Erdjument-Bromage H, Tempst P, Lis JT. The RNA processing exosome is linked to elongating RNA polymerase II in Drosophila. Nature. 2002;420(6917):837–41. Epub 2002/12/20. doi: 10.1038/nature01181 12490954.
56. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20. Epub 2014/04/04. doi: 10.1093/bioinformatics/btu170 24695404; PubMed Central PMCID: PMC4103590.
57. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–9. Epub 2012/03/06. doi: 10.1038/nmeth.1923 22388286; PubMed Central PMCID: PMC3322381.
58. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36. Epub 2013/04/27. doi: 10.1186/gb-2013-14-4-r36 23618408; PubMed Central PMCID: PMC4053844.
59. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. Epub 2014/12/18. doi: 10.1186/s13059-014-0550-8 25516281; PubMed Central PMCID: PMC4302049.
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