Neurophysiological Defects and Neuronal Gene Deregulation in Mutants
miR-124 is conserved in sequence and neuronal expression across the animal kingdom and is predicted to have hundreds of mRNA targets. Diverse defects in neural development and function were reported from miR-124 antisense studies in vertebrates, but a nematode knockout of mir-124 surprisingly lacked detectable phenotypes. To provide genetic insight from Drosophila, we deleted its single mir-124 locus and found that it is dispensable for gross aspects of neural specification and differentiation. On the other hand, we detected a variety of mutant phenotypes that were rescuable by a mir-124 genomic transgene, including short lifespan, increased dendrite variation, impaired larval locomotion, and aberrant synaptic release at the NMJ. These phenotypes reflect extensive requirements of miR-124 even under optimal culture conditions. Comparison of the transcriptomes of cells from wild-type and mir-124 mutant animals, purified on the basis of mir-124 promoter activity, revealed broad upregulation of direct miR-124 targets. However, in contrast to the proposed mutual exclusion model for miR-124 function, its functional targets were relatively highly expressed in miR-124–expressing cells and were not enriched in genes annotated with epidermal expression. A notable aspect of the direct miR-124 network was coordinate targeting of five positive components in the retrograde BMP signaling pathway, whose activation in neurons increases synaptic release at the NMJ, similar to mir-124 mutants. Derepression of the direct miR-124 target network also had many secondary effects, including over-activity of other post-transcriptional repressors and a net incomplete transition from a neuroblast to a neuronal gene expression signature. Altogether, these studies demonstrate complex consequences of miR-124 loss on neural gene expression and neurophysiology.
Vyšlo v časopise:
Neurophysiological Defects and Neuronal Gene Deregulation in Mutants. PLoS Genet 8(2): e32767. doi:10.1371/journal.pgen.1002515
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1002515
Souhrn
miR-124 is conserved in sequence and neuronal expression across the animal kingdom and is predicted to have hundreds of mRNA targets. Diverse defects in neural development and function were reported from miR-124 antisense studies in vertebrates, but a nematode knockout of mir-124 surprisingly lacked detectable phenotypes. To provide genetic insight from Drosophila, we deleted its single mir-124 locus and found that it is dispensable for gross aspects of neural specification and differentiation. On the other hand, we detected a variety of mutant phenotypes that were rescuable by a mir-124 genomic transgene, including short lifespan, increased dendrite variation, impaired larval locomotion, and aberrant synaptic release at the NMJ. These phenotypes reflect extensive requirements of miR-124 even under optimal culture conditions. Comparison of the transcriptomes of cells from wild-type and mir-124 mutant animals, purified on the basis of mir-124 promoter activity, revealed broad upregulation of direct miR-124 targets. However, in contrast to the proposed mutual exclusion model for miR-124 function, its functional targets were relatively highly expressed in miR-124–expressing cells and were not enriched in genes annotated with epidermal expression. A notable aspect of the direct miR-124 network was coordinate targeting of five positive components in the retrograde BMP signaling pathway, whose activation in neurons increases synaptic release at the NMJ, similar to mir-124 mutants. Derepression of the direct miR-124 target network also had many secondary effects, including over-activity of other post-transcriptional repressors and a net incomplete transition from a neuroblast to a neuronal gene expression signature. Altogether, these studies demonstrate complex consequences of miR-124 loss on neural gene expression and neurophysiology.
Zdroje
1. LaiEC 2002 microRNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation. Nat Genet 30 363 364
2. DoenchJGSharpPA 2004 Specificity of microRNA target selection in translational repression. Genes Dev 18 504 511
3. BrenneckeJStarkARussellRBCohenSM 2005 Principles of MicroRNA-Target Recognition. PLoS Biol 3 e85 doi:10.1371/journal.pbio.0030085
4. LewisBPBurgeCBBartelDP 2005 Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120 15 20
5. FriedmanRCFarhKKBurgeCBBartelDP 2009 Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19 92 105
6. StarkALinMFKheradpourPPedersenJSPartsL 2007 Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450 219 232
7. BartelDP 2009 MicroRNAs: target recognition and regulatory functions. Cell 136 215 233
8. AboobakerAATomancakPPatelNRubinGMLaiEC 2005 Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development. Proc Natl Acad Sci U S A 102 18017 18022
9. ClarkAMGoldsteinLDTevlinMTavareSShahamS 2010 The microRNA miR-124 controls gene expression in the sensory nervous system of Caenorhabditis elegans. Nucleic Acids Res 38 3780 3793
10. RajasethupathyPFiumaraFSheridanRBetelDPuthanveettilSV 2009 Characterization of small RNAs in aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREB. Neuron 63 803 817
11. Lagos-QuintanaMRauhutRYalcinAMeyerJLendeckelW 2002 Identification of tissue-specific microRNAs from mouse. Curr Biol 12 735 739
12. LandgrafPRusuMSheridanRSewerAIovinoN 2007 A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing. Cell 129 1401 1414
13. WienholdsEKloostermanWPMiskaEAlvarez-SaavedraEBerezikovE 2005 MicroRNA expression in zebrafish embryonic development. Science 309 310 311
14. LimLPLauNCGarrett-EngelePGrimsonASchelterJM 2005 Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433 769 773
15. StarkABrenneckeJBushatiNRussellRBCohenSM 2005 Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3′UTR evolution. Cell 123 1133 1146
16. KarginovFVConacoCXuanZSchmidtBHParkerJS 2007 A biochemical approach to identifying microRNA targets. Proc Natl Acad Sci U S A 104 19291 19296
17. HendricksonDGHoganDJHerschlagDFerrellJEBrownPO 2008 Systematic identification of mRNAs recruited to argonaute 2 by specific microRNAs and corresponding changes in transcript abundance. PLoS ONE 3 e2126 doi:10.1371/journal.pone.0002126
18. WangWXWilfredBRHuYStrombergAJNelsonPT 2010 Anti-Argonaute RIP-Chip shows that miRNA transfections alter global patterns of mRNA recruitment to microribonucleoprotein complexes. Rna 16 394 404
19. HendricksonDGHoganDJMcCulloughHLMyersJWHerschlagD 2009 Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol 7 e1000238 doi:10.1371/journal.pbio.1000238
20. ChiSWZangJBMeleADarnellRB 2009 Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460 479 486
21. VisvanathanJLeeSLeeBLeeJWLeeSK 2007 The microRNA miR-124 antagonizes the anti-neural REST/SCP1 pathway during embryonic CNS development. Genes Dev 21 744 749
22. CaoXPfaffSLGageFH 2007 A functional study of miR-124 in the developing neural tube. Genes Dev 21 531 536
23. MakeyevEVZhangJCarrascoMAManiatisT 2007 The MicroRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing. Mol Cell 27 435 448
24. ChengLCPastranaETavazoieMDoetschF 2009 miR-124 regulates adult neurogenesis in the subventricular zone stem cell niche. Nat Neurosci 12 399 408
25. MaioranoNAMallamaciA 2009 Promotion of embryonic cortico-cerebral neuronogenesis by miR-124. Neural Dev 4 40
26. YuJYChungKHDeoMThompsonRCTurnerDL 2008 MicroRNA miR-124 regulates neurite outgrowth during neuronal differentiation. Exp Cell Res 314 2618 2633
27. YooASStaahlBTChenLCrabtreeGR 2009 MicroRNA-mediated switching of chromatin-remodelling complexes in neural development. Nature 460 642 646
28. LiuKLiuYMoWQiuRWangX 2011 MiR-124 regulates early neurogenesis in the optic vesicle and forebrain, targeting NeuroD1. Nucleic Acids Res 39 2869 2879
29. MiskaEAAlvarez-SaavedraEAbbottALLauNCHellmanAB 2007 Most Caenorhabditis elegans microRNAs Are Individually Not Essential for Development or Viability. PLoS Genet 3 e215 doi:10.1371/journal.pgen.0030215
30. RubyJGStarkAJohnstonWKKellisMBartelDP 2007 Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res 17 1850 1864
31. XuXLLiYWangFGaoFB 2008 The steady-state level of the nervous-system-specific microRNA-124a is regulated by dFMR1 in Drosophila. J Neurosci 28 11883 11889
32. BerezikovERobineNSamsonovaAWestholmJONaqviA 2011 Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res 21 203 215
33. RobinsHLiYPadgettRW 2005 Incorporating structure to predict microRNA targets. Proc Natl Acad Sci U S A 102 4006 4009
34. SweeneySTDavisGW 2002 Unrestricted synaptic growth in spinster-a late endosomal protein implicated in TGF-beta-mediated synaptic growth regulation. Neuron 36 403 416
35. ShkumatavaAStarkASiveHBartelDP 2009 Coherent but overlapping expression of microRNAs and their targets during vertebrate development. Genes Dev 23 466 481
36. MuPHanYCBetelDYaoESquatritoM 2009 Genetic dissection of the miR-17∼92 cluster of microRNAs in Myc-induced B-cell lymphomas. Genes Dev 23 2806 2811
37. BaekDVillenJShinCCamargoFDGygiSP 2008 The impact of microRNAs on protein output. Nature 455 64 71
38. JohnnidisJBHarrisMHWheelerRTStehling-SunSLamMH 2008 Regulation of progenitor cell proliferation and granulocyte function by microRNA-223. Nature
39. SelbachMSchwanhausserBThierfelderNFangZKhaninR 2008 Widespread changes in protein synthesis induced by microRNAs. Nature 455 58 63
40. JinZBHirokawaGGuiLTakahashiROsakadaF 2009 Targeted deletion of miR-182, an abundant retinal microRNA. Mol Vis 15 523 533
41. BetelDKoppalAAgiusPSanderCLeslieC 2010 Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol 11 R90
42. RheadBKarolchikDKuhnRMHinrichsASZweigAS 2010 The UCSC Genome Browser database: update 2010. Nucleic Acids Res 38 D613 619
43. TomancakPBermanBPBeatonAWeiszmannRKwanE 2007 Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol 8 R145
44. BayatVJaiswalMBellenHJ 2011 The BMP signaling pathway at the Drosophila neuromuscular junction and its links to neurodegenerative diseases. Curr Opin Neurobiol 21 182 188
45. GrimsonAFarhKKJohnstonWKGarrett-EngelePLimLP 2007 MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27 91 105
46. LaiECTamBRubinGM 2005 Pervasive regulation of Drosophila Notch target genes by GY-box-, Brd-box-, and K-box-class microRNAs. Genes Dev 19 1067 1080
47. StarkABrenneckeJRussellRBCohenSM 2003 Identification of Drosophila MicroRNA Targets. PLoS Biol 1 e60 doi:10.1371/journal.pbio.0000060
48. BallRWWarren-PaquinMTsurudomeKLiaoEHElazzouziF 2010 Retrograde BMP signaling controls synaptic growth at the NMJ by regulating trio expression in motor neurons. Neuron 66 536 549
49. McCabeBDHomSAberleHFetterRDMarquesG 2004 Highwire regulates presynaptic BMP signaling essential for synaptic growth. Neuron 41 891 905
50. SoodPKrekAZavolanMMacinoGRajewskyN 2006 Cell-type-specific signatures of microRNAs on target mRNA expression. Proc Natl Acad Sci U S A 103 2746 2751
51. TylerDMOkamuraKChungWJHagenJWBerezikovE 2008 Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci. Genes Dev 22 26 36
52. GerberAPLuschnigSKrasnowMABrownPOHerschlagD 2006 Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster. Proc Natl Acad Sci U S A 103 4487 4492
53. DubnauJChiangAGradyLBarditchJGossweilerS 2003 The staufen/pumilio pathway is involved in Drosophila long-term memory. Curr Biol 13 286 296
54. YeBPetritschCClarkIEGavisERJanLY 2004 Nanos and Pumilio are essential for dendrite morphogenesis in Drosophila peripheral neurons. Curr Biol 14 314 321
55. SchweersBAWaltersKJSternM 2002 The Drosophila melanogaster translational repressor pumilio regulates neuronal excitability. Genetics 161 1177 1185
56. CarneyTDMillerMRRobinsonKJBayraktarOAOsterhoutJA 2012 Functional genomics identifies neural stem cell sub-type expression profiles and genes regulating neuroblast homeostasis. Dev Biol 361 137 146
57. SmibertPLaiEC 2008 Lessons from microRNA mutants in worms, flies and mice. Cell Cycle 7
58. LiXCassidyJJReinkeCAFischboeckSCarthewRW 2009 A microRNA imparts robustness against environmental fluctuation during development. Cell 137 273 282
59. BrennerJLJasiewiczKLFahleyAFKempBJAbbottAL 2010 Loss of individual microRNAs causes mutant phenotypes in sensitized genetic backgrounds in C. elegans. Curr Biol 20 1321 1325
60. GaoFB 2010 Context-dependent functions of specific microRNAs in neuronal development. Neural Dev 5 25
61. LaiECBurksCPosakonyJW 1998 The K box, a conserved 3′ UTR sequence motif, negatively regulates accumulation of Enhancer of split Complex transcripts. Development 125 4077 4088
62. LaiECPosakonyJW 1997 The Bearded box, a novel 3′ UTR sequence motif, mediates negative post-transcriptional regulation of Bearded and Enhancer of split Complex gene expression. Development 124 4847 4856
63. RajewskyNSocciND 2004 Computational identification of microRNA targets. Dev Biol 267 529 535
64. SmibertPLaiEC 2010 A view from Drosophila: multiple biological functions for individual microRNAs. Semin Cell Dev Biol 21 745 753
65. BushatiNStarkABrenneckeJCohenSM 2008 Temporal Reciprocity of miRNAs and Their Targets during the Maternal-to-Zygotic Transition in Drosophila. Curr Biol 18 501 506
66. KarresJSHilgersVCarreraITreismanJCohenSM 2007 The conserved microRNA miR-8 tunes atrophin levels to prevent neurodegeneration in Drosophila. Cell 131 136 145
67. AmbrosV 2011 MicroRNAs and developmental timing. Curr Opin Genet Dev 21
68. DavalosAGoedekeLSmibertPRamirezCMWarrierNP 2011 miR-33a/b contribute to the regulation of fatty acid metabolism and insulin signaling. Proc Natl Acad Sci U S A 108 9232 9237
69. FlyntASLaiEC 2008 Biological principles of microRNA-mediated regulation: shared themes amid diversity. Nat Rev Genet 9 831 842
70. BartelDPChenCZ 2004 Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat Genet 5 396 400
71. KhanAABetelDMillerMLSanderCLeslieCS 2009 Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol 27 549 555
72. GraveleyBRBrooksANCarlsonJWDuffMOLandolinJM 2011 The developmental transcriptome of Drosophila melanogaster. Nature
73. GongWJGolicKG 2003 Ends-out, or replacement, gene targeting in Drosophila. Proc Natl Acad Sci U S A 100 2556 2561
74. VenkenKJCarlsonJWSchulzeKLPanHHeY 2009 Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster. Nat Methods 6 431 434
75. BaroloSCastroBPosakonyJW 2004 New Drosophila transgenic reporters: insulated P-element vectors expressing fast-maturing RFP. Biotechniques 36 436 440, 442
76. LoyaCMLuCSVan VactorDFulgaTA 2009 Transgenic microRNA inhibition with spatiotemporal specificity in intact organisms. Nat Methods 6 897 903
77. LouisMPiccinottiSVosshallLB 2008 High-resolution measurement of odor-driven behavior in Drosophila larvae. J Vis Exp
78. HutzingerRFeederleRMrazekJSchiefermeierNBalwierzPJ 2009 Expression and processing of a small nucleolar RNA from the Epstein-Barr virus genome. PLoS Pathog 5 e1000547 doi:10.1371/journal.ppat.1000547
79. SchusterCMDavisGWFetterRDGoodmanCS 1996 Genetic dissection of structural and functional components of synaptic plasticity. I. Fasciclin II controls synaptic stabilization and growth. Neuron 17 641 654
80. MerinoCPenneyJGonzalezMTsurudomeKMoujahidineM 2009 Nemo kinase interacts with Mad to coordinate synaptic growth at the Drosophila neuromuscular junction. J Cell Biol 185 713 725
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2012 Číslo 2
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
Najčítanejšie v tomto čísle
- Gene Expression and Stress Response Mediated by the Epigenetic Regulation of a Transposable Element Small RNA
- Contrasting Properties of Gene-Specific Regulatory, Coding, and Copy Number Mutations in : Frequency, Effects, and Dominance
- Homeobox Genes Critically Regulate Embryo Implantation by Controlling Paracrine Signaling between Uterine Stroma and Epithelium
- Nondisjunction of a Single Chromosome Leads to Breakage and Activation of DNA Damage Checkpoint in G2