A Genome-Wide RNAi Screen for Factors Involved in Neuronal Specification in
One of the central goals of developmental neurobiology is to describe and understand the multi-tiered molecular events that control the progression of a fertilized egg to a terminally differentiated neuron. In the nematode Caenorhabditis elegans, the progression from egg to terminally differentiated neuron has been visually traced by lineage analysis. For example, the two gustatory neurons ASEL and ASER, a bilaterally symmetric neuron pair that is functionally lateralized, are generated from a fertilized egg through an invariant sequence of 11 cellular cleavages that occur stereotypically along specific cleavage planes. Molecular events that occur along this developmental pathway are only superficially understood. We take here an unbiased, genome-wide approach to identify genes that may act at any stage to ensure the correct differentiation of ASEL. Screening a genome-wide RNAi library that knocks-down 18,179 genes (94% of the genome), we identified 245 genes that affect the development of the ASEL neuron, such that the neuron is either not generated, its fate is converted to that of another cell, or cells from other lineage branches now adopt ASEL fate. We analyze in detail two factors that we identify from this screen: (1) the proneural gene hlh-14, which we find to be bilaterally expressed in the ASEL/R lineages despite their asymmetric lineage origins and which we find is required to generate neurons from several lineage branches including the ASE neurons, and (2) the COMPASS histone methyltransferase complex, which we find to be a critical embryonic inducer of ASEL/R asymmetry, acting upstream of the previously identified miRNA lsy-6. Our study represents the first comprehensive, genome-wide analysis of a single neuronal cell fate decision. The results of this analysis provide a starting point for future studies that will eventually lead to a more complete understanding of how individual neuronal cell types are generated from a single-cell embryo.
Vyšlo v časopise:
A Genome-Wide RNAi Screen for Factors Involved in Neuronal Specification in. PLoS Genet 7(6): e32767. doi:10.1371/journal.pgen.1002109
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1002109
Souhrn
One of the central goals of developmental neurobiology is to describe and understand the multi-tiered molecular events that control the progression of a fertilized egg to a terminally differentiated neuron. In the nematode Caenorhabditis elegans, the progression from egg to terminally differentiated neuron has been visually traced by lineage analysis. For example, the two gustatory neurons ASEL and ASER, a bilaterally symmetric neuron pair that is functionally lateralized, are generated from a fertilized egg through an invariant sequence of 11 cellular cleavages that occur stereotypically along specific cleavage planes. Molecular events that occur along this developmental pathway are only superficially understood. We take here an unbiased, genome-wide approach to identify genes that may act at any stage to ensure the correct differentiation of ASEL. Screening a genome-wide RNAi library that knocks-down 18,179 genes (94% of the genome), we identified 245 genes that affect the development of the ASEL neuron, such that the neuron is either not generated, its fate is converted to that of another cell, or cells from other lineage branches now adopt ASEL fate. We analyze in detail two factors that we identify from this screen: (1) the proneural gene hlh-14, which we find to be bilaterally expressed in the ASEL/R lineages despite their asymmetric lineage origins and which we find is required to generate neurons from several lineage branches including the ASE neurons, and (2) the COMPASS histone methyltransferase complex, which we find to be a critical embryonic inducer of ASEL/R asymmetry, acting upstream of the previously identified miRNA lsy-6. Our study represents the first comprehensive, genome-wide analysis of a single neuronal cell fate decision. The results of this analysis provide a starting point for future studies that will eventually lead to a more complete understanding of how individual neuronal cell types are generated from a single-cell embryo.
Zdroje
1. BrennerS 1974 The genetics of Caenorhabditis elegans. Genetics 77 71 94
2. WoodWB 1988 The nematode Caenorhabditis elegans: Cold Spring Harbor Laboratory Press
3. HobertO 2010 Neurogenesis in the nematode Caenorhabditis elegans. WormBook 1 24
4. FireAXuSMontgomeryMKKostasSADriverSE 1998 Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans [see comments]. Nature 391 806 811
5. KamathRSAhringerJ 2003 Genome-wide RNAi screening in Caenorhabditis elegans. Methods 30 313 321
6. SulstonJESchierenbergEWhiteJGThomsonJN 1983 The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev Biol 100 64 119
7. BertrandVHobertO 2010 Lineage programming: navigating through transient regulatory states via binary decisions. Curr Opin Genet Dev
8. LinRHillRJPriessJR 1998 POP-1 and anterior-posterior fate decisions in C. elegans embryos. Cell 92 229 239
9. SulstonJE 1983 Neuronal cell lineages in the nematode Caenorhabditis elegans. Cold Spring Harb Symp Quant Biol 48 443 452
10. SchnabelRHutterHMoermanDSchnabelH 1997 Assessing normal embryogenesis in Caenorhabditis elegans using a 4D microscope: variability of development and regional specification. Dev Biol 184 234 265
11. OrtizCOFaumontSTakayamaJAhmedHKGoldsmithAD 2009 Lateralized gustatory behavior of C. elegans is controlled by specific receptor-type guanylyl cyclases. Curr Biol 19 996 1004
12. PooleRJHobertO 2006 Early embryonic programming of neuronal left/right asymmetry in C. elegans. Curr Biol 16 2279 2292
13. GoodKCioskRNanceJNevesAHillRJ 2004 The T-box transcription factors TBX-37 and TBX-38 link GLP-1/Notch signaling to mesoderm induction in C. elegans embryos. Development 131 1967 1978
14. JohnstonRJHobertO 2003 A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426 845 849
15. ChangSJohnstonRJJrHobertO 2003 A transcriptional regulatory cascade that controls left/right asymmetry in chemosensory neurons of C. elegans. Genes Dev 17 2123 2137
16. JohnstonRJJrChangSEtchbergerJFOrtizCOHobertO 2005 MicroRNAs acting in a double-negative feedback loop to control a neuronal cell fate decision. Proc Natl Acad Sci U S A 102 12449 12454
17. DidianoDCochellaLTursunBHobertO 2010 Neuron-type specific regulation of a 3′UTR through redundant and combinatorially acting cis-regulatory elements. RNA 16 349 363
18. SarinSO'Meara MMFlowersEBAntonioCPooleRJ 2007 Genetic Screens for Caenorhabditis elegans Mutants Defective in Left/Right Asymmetric Neuronal Fate Specification. Genetics 176 2109 2130
19. FireA 1999 RNA-triggered gene silencing. Trends Genet 15 358 363
20. SchmitzCKingePHutterH 2007 Axon guidance genes identified in a large-scale RNAi screen using the RNAi-hypersensitive Caenorhabditis elegans strain nre-1(hd20) lin-15b(hd126). Proc Natl Acad Sci U S A 104 834 839
21. KennedySWangDRuvkunG 2004 A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans. Nature 427 645 649
22. SimmerFMoormanCVan Der LindenAMKuijkEVan Den BerghePV 2003 Genome-Wide RNAi of C. elegans Using the Hypersensitive rrf-3 Strain Reveals Novel Gene Functions. PLoS Biol 1 e12 doi:10.1371/journal.pbio.0000012
23. KamathRSFraserAGDongYPoulinGDurbinR 2003 Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421 231 237
24. ZipperlenPFraserAGKamathRSMartinez-CamposMAhringerJ 2001 Roles for 147 embryonic lethal genes on C.elegans chromosome I identified by RNA interference and video microscopy. Embo J 20 3984 3992
25. CioskRDePalmaMPriessJR 2006 Translational regulators maintain totipotency in the Caenorhabditis elegans germline. Science 311 851 853
26. WattsJLEtemad-MoghadamBGuoSBoydLDraperBW 1996 par-6, a gene involved in the establishment of asymmetry in early C. elegans embryos, mediates the asymmetric localization of PAR-3. Development 122 3133 3140
27. UchidaONakanoHKogaMOhshimaY 2003 The C. elegans che-1 gene encodes a zinc finger transcription factor required for specification of the ASE chemosensory neurons. Development 130 1215 1224
28. FrankCABaumPDGarrigaG 2003 HLH-14 is a C. elegans achaete-scute protein that promotes neurogenesis through asymmetric cell division. Development 130 6507 6518
29. TursunBCochellaLCarreraIHobertO 2009 A toolkit and robust pipeline for the generation of fosmid-based reporter genes in C. elegans. PLoS ONE 4 e4625 doi:10.1371/journal.pone.0004625
30. TenneyKShilatifardA 2005 A COMPASS in the voyage of defining the role of trithorax/MLL-containing complexes: linking leukemogensis to covalent modifications of chromatin. J Cell Biochem 95 429 436
31. SimonetTDulermoRSchottSPalladinoF 2007 Antagonistic functions of SET-2/SET1 and HPL/HP1 proteins in C. elegans development. Dev Biol 312 367 383
32. XuLStromeS 2001 Depletion of a novel SET-domain protein enhances the sterility of mes-3 and mes-4 mutants of Caenorhabditis elegans. Genetics 159 1019 1029
33. O'MearaMMZhangFHobertO 2010 Maintenance of Neuronal Laterality in Caenorhabditis elegans Through MYST Histone Acetyltransferase Complex Components LSY-12, LSY-13 and LIN-49. Genetics
34. TavernaSDIlinSRogersRSTannyJCLavenderH 2006 Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs. Mol Cell 24 785 796
35. FlowersEBPooleRJTursunBBashllariEPe'erI 2010 The Groucho ortholog UNC-37interacts with the short Groucho-like protein LSY-22 to control developmental decisions in C. elegans. Development 137 1799 1805
36. ZhaoCEmmonsSW 1995 A transcription factor controlling development of peripheral sense organs in C. elegans. Nature 373 74 78
37. PortmanDSEmmonsSW 2000 The basic helix-loop-helix transcription factors LIN-32 and HLH-2 function together in multiple steps of a C. elegans neuronal sublineage. Development 127 5415 5426
38. SkeathJBCarrollSB 1994 The achaete-scute complex: generation of cellular pattern and fate within the Drosophila nervous system. The FASEB journal: official publication of the Federation of American Societies for Experimental Biology 8 714 721
39. BertrandNCastroDSGuillemotF 2002 Proneural genes and the specification of neural cell types. Nat Rev Neurosci 3 517 530
40. RossJMKalisAKMurphyMWZarkowerD 2005 The DM domain protein MAB-3 promotes sex-specific neurogenesis in C. elegans by regulating bHLH proteins. Developmental cell 8 881 892
41. NevesAPriessJR 2005 The REF-1 family of bHLH transcription factors pattern C. elegans embryos through Notch-dependent and Notch-independent pathways. Dev Cell 8 867 879
42. SawaH 2010 Specification of neurons through asymmetric cell divisions. Curr Opin Neurobiol 20 44 49
43. KalettaTSchnabelHSchnabelR 1997 Binary specification of the embryonic lineage in Caenorhabditis elegans. Nature 390 294 298
44. BertrandVHobertO 2009 Linking asymmetric cell division to the terminal differentiation program of postmitotic neurons in C. elegans. Dev Cell 16 563 575
45. MolinLMounseyAAslamSBauerPYoungJ 2000 Evolutionary conservation of redundancy between a diverged pair of forkhead transcription factor homologues. Development 127 4825 4835
46. MaduroMFMeneghiniMDBowermanBBroitman-MaduroGRothmanJH 2001 Restriction of mesendoderm to a single blastomere by the combined action of SKN-1 and a GSK-3beta homolog is mediated by MED-1 and -2 in C. elegans. Molecular cell 7 475 485
47. MaduroMFRothmanJH 2002 Making worm guts: the gene regulatory network of the Caenorhabditis elegans endoderm. Dev Biol 246 68 85
48. PocockRAhringerJMitschMMaxwellSWoollardA 2004 A regulatory network of T-box genes and the even-skipped homologue vab-7 controls patterning and morphogenesis in C. elegans. Development 131 2373 2385
49. LathamJADentSY 2007 Cross-regulation of histone modifications. Nat Struct Mol Biol 14 1017 1024
50. VezzoliABonadiesNAllenMDFreundSMSantiveriCM 2010 Molecular basis of histone H3K36me3 recognition by the PWWP domain of Brpf1. Nat Struct Mol Biol 17 617 619
51. MartinDGBaetzKShiXWalterKLMacDonaldVE 2006 The Yng1p plant homeodomain finger is a methyl-histone binding module that recognizes lysine 4-methylated histone H3. Mol Cell Biol 26 7871 7879
52. PenaPVDavrazouFShiXWalterKLVerkhushaVV 2006 Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2. Nature 442 100 103
53. SchnabelRPriessJR 1997 Specification of Cell Fates in the Early Embryo. RiddleDLBlumenthalTMeyerBJPriessJR Celegans II Cold Spring Harbor Cold Spring Harbor Laboratory Press 361 382
54. HodgkinJDoniachT 1997 Natural variation and copulatory plug formation in Caenorhabditis elegans. Genetics 146 149 164
55. TsalikELNiacarisTWenickASPauKAveryL 2003 LIM homeobox gene-dependent expression of biogenic amine receptors in restricted regions of the C. elegans nervous system. Dev Biol 263 81 102
56. LanjuinAVanHovenMKBargmannCIThompsonJKSenguptaP 2003 Otx/otd Homeobox Genes Specify Distinct Sensory Neuron Identities in C. elegans. Dev Cell 5 621 633
57. FlamesNHobertO 2009 Gene regulatory logic of dopamine neuron differentiation. Nature 458 885 889
58. MyersTRGreenwaldI 2005 lin-35 Rb acts in the major hypodermis to oppose ras-mediated vulval induction in C. elegans. Developmental cell 8 117 123
59. HobertO 2002 PCR fusion-based approach to create reporter gene constructs for expression analysis in transgenic C. elegans. Biotechniques 32 728 730
60. RualJFCeronJKorethJHaoTNicotAS 2004 Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res 14 2162 2168
61. KimJKGabelHWKamathRSTewariMPasquinelliA 2005 Functional genomic analysis of RNA interference in C. elegans. Science 308 1164 1167
62. EdelsteinAAmodajNHooverKValeRStuurmanN 2010 Computer Control of Microscopes Using µManager: John Wiley & Sons, Inc
63. SarinSPrabhuSO'MearaMMPe'erIHobertO 2008 Caenorhabditis elegans mutant allele identification by whole-genome sequencing. Nat Methods 5 865 867
64. BigelowHDoitsidouMSarinSHobertO 2009 MAQGene: software to facilitate C. elegans mutant genome sequence analysis. Nat Methods 6 549
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2011 Číslo 6
- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
Najčítanejšie v tomto čísle
- Statistical Inference on the Mechanisms of Genome Evolution
- Recurrent Chromosome 16p13.1 Duplications Are a Risk Factor for Aortic Dissections
- Chromosomal Macrodomains and Associated Proteins: Implications for DNA Organization and Replication in Gram Negative Bacteria
- Maps of Open Chromatin Guide the Functional Follow-Up of Genome-Wide Association Signals: Application to Hematological Traits