Caenorhabditis elegans PTR/PTCHD PTR-18 promotes the clearance of extracellular hedgehog-related protein via endocytosis

English version

Autoři: Hirohisa Chiyoda ^aff001; Masahiko Kume ^aff001; Carla Cadena del Castillo ^aff002; Kenji Kontani ^aff001; Anne Spang ^aff002; Toshiaki Katada ^aff001; Masamitsu Fukuyama ^aff001
Působiště autorů: Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan ^aff001; Biozentrum, University of Basel, Basel, Switzerland ^aff002
Vyšlo v časopise: Caenorhabditis elegans PTR/PTCHD PTR-18 promotes the clearance of extracellular hedgehog-related protein via endocytosis. PLoS Genet 17(4): e1009457. doi:10.1371/journal.pgen.1009457
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1009457

Souhrn

Spatiotemporal restriction of signaling plays a critical role in animal development and tissue homeostasis. All stem and progenitor cells in newly hatched C. elegans larvae are quiescent and capable of suspending their development until sufficient food is supplied. Here, we show that ptr-18, which encodes the evolutionarily conserved patched-related (PTR)/patched domain-containing (PTCHD) protein, temporally restricts the availability of extracellular hedgehog-related protein to establish the capacity of progenitor cells to maintain quiescence. We found that neural progenitor cells exit from quiescence in ptr-18 mutant larvae even when hatched under starved conditions. This unwanted reactivation depended on the activity of a specific set of hedgehog-related grl genes including grl-7. Unexpectedly, neither PTR-18 nor GRL-7 were expressed in newly hatched wild-type larvae. Instead, at the late embryonic stage, both PTR-18 and GRL-7 proteins were first localized around the apical membrane of hypodermal and neural progenitor cells and subsequently targeted for lysosomal degradation before hatching. Loss of ptr-18 caused a significant delay in GRL-7 clearance, causing this protein to be retained in the extracellular space in newly hatched ptr-18 mutant larvae. Furthermore, the putative transporter activity of PTR-18 was shown to be required for the appropriate function of the protein. These findings not only uncover a previously undescribed role of PTR/PTCHD in the clearance of extracellular hedgehog-related proteins via endocytosis-mediated degradation but also illustrate that failure to temporally restrict intercellular signaling during embryogenesis can subsequently compromise post-embryonic progenitor cell function.

Klíčová slova:

Caenorhabditis elegans – Embryos – Hedgehog signaling – Larvae – Lysosomes – Molting – Reporter genes – Stem cells

Zdroje

1. Hong Y, Roy R, Ambros V. Developmental regulation of a cyclin-dependent kinase inhibitor controls postembryonic cell cycle progression in Caenorhabditis elegans. Development. 1998;125: 3585–3597. 9716524

2. Baugh LR, Sternberg PW. DAF-16/FOXO regulates transcription of cki-1/Cip/Kip and repression of lin-4 during C. elegans L1 arrest. Curr Biol. 2006;16: 780–785. doi: 10.1016/j.cub.2006.03.021 16631585

3. Fukuyama M, Rougvie AE, Rothman JH. C. elegans DAF-18/PTEN mediates nutrient-dependent arrest of cell cycle and growth in the germline. Curr Biol. 2006;16: 773–779. doi: 10.1016/j.cub.2006.02.073 16631584

4. Zheng S, Qu Z, Zanetti M, Lam B, Chin-Sang I. C. elegans PTEN and AMPK block neuroblast divisions by inhibiting a BMP-insulin-PP2A-MAPK pathway. Development. 2018;145: dev166876. doi: 10.1242/dev.166876 30487179

5. Baugh LR. To grow or not to grow: nutritional control of development during Caenorhabditis elegans L1 arrest. Genetics. 2013;194: 539–555. doi: 10.1534/genetics.113.150847 23824969

6. Fukuyama M, Kontani K, Katada T, Rougvie AE. The C. elegans hypodermis couples progenitor cell quiescence to the dietary state. Curr Biol. 2015;25: 1241–1248. doi: 10.1016/j.cub.2015.03.016 25891400

7. Kasuga H, Fukuyama M, Kitazawa A, Kontani K, Katada T. The microRNA miR-235 couples blast-cell quiescence to the nutritional state. Nature. 2013;497: 503–506. doi: 10.1038/nature12117 23644454

8. Kume M, Chiyoda H, Kontani K, Katada T, Fukuyama M. Hedgehog-related genes regulate reactivation of quiescent neural progenitors in Caenorhabditis elegans. Biochemical and Biophysical Research Communications. 2019;520: 532–537. doi: 10.1016/j.bbrc.2019.10.045 31615656

9. Aspöck G, Kagoshima H, Niklaus G, Bürglin TR. Caenorhabditis elegans has scores of hedgehog-related genes: sequence and expression analysis. Genome Res. 1999;9: 909–923. doi: 10.1101/gr.9.10.909 10523520

10. Bürglin TR, Kuwabara PE. Homologs of the Hh signalling network in C. elegans. WormBook. 2006;: 1–14. doi: 10.1895/wormbook.1.76.1 18050469

11. Kuwabara PE, Lee MH, Schedl T, Jefferis GS. A C. elegans patched gene, ptc-1, functions in germ-line cytokinesis. Genes Dev. 2000;14: 1933–1944. 10921907

12. Zugasti O, Rajan J, Kuwabara PE. The function and expansion of the Patchedand Hedgehog-related homologs in C. elegans. Genome Res. 2005;15: 1402–1410. doi: 10.1101/gr.3935405 16204193

13. Soloviev A, Gallagher J, Marnef A, Kuwabara PE. C. elegans patched-3 is an essential gene implicated in osmoregulation and requiring an intact permease transporter domain. Dev Biol. 2011;351: 242–253. doi: 10.1016/j.ydbio.2010.12.035 21215260

14. Frand AR, Russel S, Ruvkun G. Functional genomic analysis of C. elegans molting. PLoS Biol. 2005;3: e312. doi: 10.1371/journal.pbio.0030312 16122351

15. Johnson RL, Scott MP. Control of Cell Growth and Fate by patched Genes. Cold Spring Harb Symp Quant Biol. 1997;62: 205–215. doi: 10.1101/SQB.1997.062.01.026 9598353

16. Carstea ED, Carstea ED, Morris JA, Morris JA, Coleman KG, Coleman KG, et al. Niemann-Pick C1 disease gene: homology to mediators of cholesterol homeostasis. Science. 1997;277: 228–231. doi: 10.1126/science.277.5323.228 9211849

17. Loftus SK, Morris JA, Carstea ED, Gu JZ, Cummings C, Brown A, et al. Murine Model of Niemann-Pick C Disease: Mutation in a Cholesterol Homeostasis Gene. Science. 1997;277: 232–235. doi: 10.1126/science.277.5323.232 9211850

18. Burke R, Nellen D, Bellotto M, Hafen E, Senti KA, Dickson BJ, et al. Dispatched, a novel sterol-sensing domain protein dedicated to the release of cholesterol-modified hedgehog from signaling cells. Cell. 1999;99: 803–815. doi: 10.1016/s0092-8674(00)81677-3 10619433

19. Kuwabara PE, Labouesse M. The sterol-sensing domain: multiple families, a unique role? Trends in Genetics. 2002;18: 193–201. doi: 10.1016/s0168-9525(02)02640-9 11932020

20. Chang T-Y, Chang CCY, Ohgami N, Yamauchi Y. Cholesterol sensing, trafficking, and esterification. Annu Rev Cell Dev Biol. 2006;22: 129–157. doi: 10.1146/annurev.cellbio.22.010305.104656 16753029

21. Tseng TT, Gratwick KS, Kollman J, Park D, Nies DH, Goffeau A, et al. The RND permease superfamily: an ancient, ubiquitous and diverse family that includes human disease and development proteins. J Mol Microbiol Biotechnol. 1999;1: 107–125. 10941792

22. Saier MH, Tam R, Reizer A, Reizer J. Two novel families of bacterial membrane proteins concerned with nodulation, cell division and transport. Molecular Microbiology. 1994;11: 841–847. doi: 10.1111/j.1365-2958.1994.tb00362.x 8022262

23. Goldberg M, Pribyl T, Juhnke S, Nies DH. Energetics and topology of CzcA, a cation/proton antiporter of the resistance-nodulation-cell division protein family. J Biol Chem. 1999;274: 26065–26070. doi: 10.1074/jbc.274.37.26065 10473554

24. Guan L, Nakae T. Identification of Essential Charged Residues in Transmembrane Segments of the Multidrug Transporter MexB ofPseudomonas aeruginosa. J Bacteriol. 2001;183: 1734–1739. doi: 10.1128/JB.183.5.1734–1739.2001

25. del Castillo CEC, Hannich JT, Kaech A, Chiyoda H, Fukuyama M, Faergeman NJ, et al. Patched regulates lipid homeostasis by controlling cellular cholesterol levels. bioRxiv. 2019;7: 816256. doi: 10.1101/816256

26. Ma Y, Erkner A, Gong R, Yao S, Taipale J, Basler K, et al. Hedgehog-Mediated Patterning of the Mammalian Embryo Requires Transporter-like Function of Dispatched. Cell. 2002;111: 63–75. doi: 10.1016/s0092-8674(02)00977-7 12372301

27. Taipale J, Cooper MK, Maiti T, Beachy PA. Patched acts catalytically to suppress the activity of Smoothened. Nature. 2002;418: 892–897. doi: 10.1038/nature00989 12192414

28. Marshall CR, Noor A, Vincent JB, Lionel AC, Feuk L, Skaug J, et al. Structural variation of chromosomes in autism spectrum disorder. Am J Hum Genet. 2008;82: 477–488. doi: 10.1016/j.ajhg.2007.12.009 18252227

29. Noor A, Whibley A, Marshall CR, Gianakopoulos PJ, Piton A, Carson AR, et al. Disruption at the PTCHD1 Locus on Xp22.11 in Autism spectrum disorder and intellectual disability. Sci Transl Med. 2010;2: 49ra68–49ra68. doi: 10.1126/scitranslmed.3001267 20844286

30. Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R, et al. Functional impact of global rare copy number variation in autism spectrum disorders. Nature. 2010;466: 368–372. doi: 10.1038/nature09146 20531469

31. Whibley AC, Plagnol V, Tarpey PS, Abidi F, Fullston T, Choma MK, et al. Fine-scale survey of X chromosome copy number variants and indels underlying intellectual disability. Am J Hum Genet. 2010;87: 173–188. doi: 10.1016/j.ajhg.2010.06.017 20655035

32. Filges I, Röthlisberger B, Blattner A, Boesch N, Demougin P, Wenzel F, et al. Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism. Clin Genet. 2011;79: 79–85. doi: 10.1111/j.1399-0004.2010.01590.x 21091464

33. Chaudhry A, Noor A, Degagne B, Baker K, Bok LA, Brady AF, et al. Phenotypic spectrum associated with PTCHD1 deletions and truncating mutations includes intellectual disability and autism spectrum disorder. Clin Genet. 2015; 88: 224–233. doi: 10.1111/cge.12482 25131214

34. Torrico B, Fernàndez-Castillo N, Hervás A, Milà M, Salgado M, Rueda I, et al. Contribution of common and rare variants of the PTCHD1 gene to autism spectrum disorders and intellectual disability. Eur J Hum Genet. 2015;23: 1694–1701. doi: 10.1038/ejhg.2015.37 25782667

35. Wells MF, Wimmer RD, Schmitt LI, Feng G, Halassa MM. Thalamic reticular impairment underlies attention deficit in Ptchd1Y/- mice. Nature. 2016;532: 58–63. doi: 10.1038/nature17427 27007844

36. Bolatto C, Parada C, Revello F, Zuñiga A, Cabrera P, Cambiazo V. Spatial and temporal distribution of Patched-related protein in the Drosophila embryo. Gene Expression Patterns. 2015;19: 120–128. doi: 10.1016/j.gep.2015.10.002 26506022

37. Perens EA, Shaham S. C. elegans daf-6 encodes a patched-related protein required for lumen formation. Dev Cell. 2005;8: 893–906. doi: 10.1016/j.devcel.2005.03.009 15935778

38. Oikonomou G, Perens EA, Lu Y, Watanabe S, Jorgensen EM, Shaham S. Opposing activities of LIT-1/NLK and DAF-6/patched-related direct sensory compartment morphogenesis in C. elegans. PLoS Biol. 2011;9: e1001121. doi: 10.1371/journal.pbio.1001121 21857800

39. Wallace SW, Singhvi A, Liang Y, Lu Y, Shaham S. PROS-1/Prospero Is a Major Regulator of the Glia-Specific Secretome Controlling Sensory-Neuron Shape and Function in C. elegans. Cell Reports. 2016;15: 550–562. doi: 10.1016/j.celrep.2016.03.051 27068465

40. Wang W, Perens EA, Oikonomou G, Lu Y, Shaham S. IGDB-2, an Ig/FNIII protein, binds the ion channel LGC-34 and controls sensory compartment morphogenesis in C. elegans. Developmental Biology. 2017; 430: 105–112.

41. Lin C-CJ, Wang MC. Microbial metabolites regulate host lipid metabolism through NR5A–Hedgehog signalling. Nat Cell Biol. 2017;19: 550–557. doi: 10.1038/ncb3515 28436966

42. Templeman NM, Cota V, Keyes W, Kaletsky R, Murphy CT. CREB Non-autonomously Controls Reproductive Aging through Hedgehog/Patched Signaling. Dev Cell. 2020;54: 92–105.e5. doi: 10.1016/j.devcel.2020.05.023 32544391

43. Sulston JE. Post-embryonic development in the ventral cord of Caenorhabditis elegans. Philos Trans R Soc Lond, B, Biol Sci. 1976;275: 287–297. doi: 10.1098/rstb.1976.0084 8804

44. Hao L, Johnsen R, Lauter G, Baillie D, Bürglin TR. Comprehensive analysis of gene expression patterns of hedgehog-related genes. BMC Genomics. 2006;7: 280. doi: 10.1186/1471-2164-7-280 17076889

45. Gilleard JS, Barry JD, Johnstone IL. cis regulatory requirements for hypodermal cell-specific expression of the Caenorhabditis elegans cuticle collagen gene dpy-7. Mol Cell Biol. 1997;17: 2301–2311. doi: 10.1128/mcb.17.4.2301 9121480

46. Johnson AD, Fitzsimmons D, Hagman J, Chamberlin HM. EGL-38 Pax regulates the ovo-related gene lin-48 during Caenorhabditis elegans organ development. Development. Oxford University Press for The Company of Biologists Limited; 2001;128: 2857–2865.

47. Parry JM, Sundaram MV. A non-cell-autonomous role for Ras signaling in C. elegans neuroblast delamination. Development. 2014;141: 4279–4284. doi: 10.1242/dev.112045 25371363

48. Doonan R, Hatzold J, Raut S, Conradt B, Alfonso A. HLH-3 is a C. elegans Achaete/Scute protein required for differentiation of the hermaphrodite-specific motor neurons. Mechanisms of Development. 2008;125: 883–893. doi: 10.1016/j.mod.2008.06.002 18586090

49. Wei X, Potter CJ, Luo L, Shen K. Controlling gene expression with the Q repressible binary expression system in Caenorhabditis elegans. Nature Methods. 2012;9: 391–395. doi: 10.1038/nmeth.1929 22406855

50. Page A. The cuticle. WormBook. 2007. doi: 10.1895/wormbook.1.138.1 18050497

51. McMahon L, Muriel JM, Roberts B, Quinn M, Johnstone IL. Two Sets of Interacting Collagens Form Functionally Distinct Substructures within a Caenorhabditis elegans Extracellular Matrix. Mol Biol Cell. 2003;14: 1366–1378. doi: 10.1091/mbc.e02-08-0479 12686594

52. Grant B, Hirsh D. Receptor-mediated Endocytosis in the Caenorhabditis elegans Oocyte. Kimble J, editor. Mol Biol Cell. 1999;10: 4311–4326. doi: 10.1091/mbc.10.12.4311 10588660

53. Chen CC-H, Schweinsberg PJ, Vashist S, Mareiniss DP, Lambie EJ, Grant BD. RAB-10 Is Required for Endocytic Recycling in the Caenorhabditis elegans Intestine. Mol Biol Cell. 2006;17: 1286–1297. doi: 10.1091/mbc.e05-08-0787 16394106

54. Treusch S, Knuth S, Slaugenhaupt SA, Goldin E, Grant BD, Fares H. Caenorhabditis elegans functional orthologue of human protein h-mucolipin-1 is required for lysosome biogenesis. Proceedings of the National Academy of Sciences. 2004;101: 4483–4488. doi: 10.1073/pnas.0400709101 15070744

55. Shinoda H, Shannon M, Nagai T. Fluorescent Proteins for Investigating Biological Events in Acidic Environments. IJMS. 2018;19: 1548. doi: 10.3390/ijms19061548 29789517

56. Krogh A, Larsson B, Heijne von G, Sonnhammer ELL. Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. Journal of Molecular Biology. 2001;305: 567–580. doi: 10.1006/jmbi.2000.4315 11152613

57. Weiss LE, Milenkovic L, Yoon J, Stearns T, Moerner WE. Motional dynamics of single Patched1 molecules in cilia are controlled by Hedgehog and cholesterol. Proceedings of the National Academy of Sciences. 2019;116: 5550–5557. doi: 10.1073/pnas.1816747116 30819883

58. Myers BR, Neahring L, Zhang Y, Roberts KJ, Beachy PA. Rapid, direct activity assays for Smoothened reveal Hedgehog pathway regulation by membrane cholesterol and extracellular sodium. Proc Natl Acad Sci USA. 2017;114: E11141–E11150. doi: 10.1073/pnas.1717891115 29229834

59. Bidet M, Joubert O, Lacombe B, Ciantar M, Nehmé R, Mollat P, et al. The Hedgehog Receptor Patched Is Involved in Cholesterol Transport. Johannes L, editor. PLoS ONE. 2011;6: e23834. doi: 10.1371/journal.pone.0023834 21931618

60. Chen Y, Struhl G. Dual Roles for Patched in Sequestering and Transducing Hedgehog. Cell. 1996;87: 553–563. doi: 10.1016/s0092-8674(00)81374-4 8898207

61. Incardona JP, Lee JH, Robertson CP, Enga K, Kapur RP, Roelink H. Receptor-mediated endocytosis of soluble and membrane-tethered Sonic hedgehog by Patched-1. Proc Natl Acad Sci USA. 2000;97: 12044–12049. doi: 10.1073/pnas.220251997 11027307

62. Briscoe J, Chen Y, Jessell TM, Struhl G. A hedgehog-insensitive form of patched provides evidence for direct long-range morphogen activity of sonic hedgehog in the neural tube. Mol Cell. 2001;7: 1279–1291. doi: 10.1016/s1097-2765(01)00271-4 11430830

63. Torroja C, Gorfinkiel N, Guerrero I. Patched controls the Hedgehog gradient by endocytosis in a dynamin-dependent manner, but this internalization does not play a major role in signal transduction. Development. 2004;131: 2395–2408. doi: 10.1242/dev.01102 15102702

64. Fra AM, Locati M, Otero K, Sironi M, Signorelli P, Massardi ML, et al. Cutting Edge: Scavenging of Inflammatory CC Chemokines by the Promiscuous Putatively Silent Chemokine Receptor D6. The Journal of Immunology. 2003;170: 2279–2282. doi: 10.4049/jimmunol.170.5.2279 12594248

65. Weber M, Blair E, Simpson CV, O’Hara M, Blackburn PE, Rot A, et al. The Chemokine Receptor D6 Constitutively Traffics to and from the Cell Surface to Internalize and Degrade Chemokines. Mol Biol Cell. 2004;15: 2492–2508. doi: 10.1091/mbc.e03-09-0634 15004236

66. Jamieson T, Cook DN, Nibbs RJB, Rot A, Nixon C, Mclean P, et al. The chemokine receptor D6 limits the inflammatory response in vivo. Nat Immunol. 2005;6: 403–411. doi: 10.1038/ni1182 15750596

67. Pastenes L, Ibáñez F, Bolatto C, Pavéz L, Cambiazo V. Molecular characterization of a novel patched-related protein in Apis mellifera and Drosophila melanogaster. Arch Insect Biochem Physiol. 2008;68: 156–170. doi: 10.1002/arch.20245 18563713

68. Oikonomou G, Perens EA, Lu Y, Shaham S. Some, but not all, retromer components promote morphogenesis of C. elegans sensory compartments. Dev Biol. 2012;362: 42–49. doi: 10.1016/j.ydbio.2011.11.009 22138055

69. Oikonomou G, Shaham S. On the morphogenesis of glial compartments in the sensory organs of Caenorhabditis elegans. Worm. 2014;1: 51–55. doi: 10.4161/worm.19343 24058823

70. Singhal A, Shaham S. Infrared laser-induced gene expression for tracking development and function of single C. elegans embryonic neurons. Nature Communications. 2017;8: 14100. doi: 10.1038/ncomms14100 28098184

71. Hendriks G-J, Gaidatzis D, Aeschimann F, Großhans H. Extensive oscillatory gene expression during C. elegans larval development. Mol Cell. 2014;53: 380–392. doi: 10.1016/j.molcel.2013.12.013 24440504

72. Bürglin TR. Warthog and groundhog, novel families related to hedgehog. Curr Biol. 1996;6: 1047–1050. doi: 10.1016/s0960-9822(02)70659-3 8805384

73. Marigo V, Davey RA, Zuo Y, Cunningham JM, Tabin CJ. Biochemical evidence that patched is the Hedgehog receptor. Nature. 1996;384: 176–179. doi: 10.1038/384176a0 8906794

74. Stone DM, Hynes M, Armanini M, Swanson TA, Gu Q, Johnson RL, et al. The tumour-suppressor gene patched encodes a candidate receptor for Sonic hedgehog. Nature. 1996;384: 129–134. doi: 10.1038/384129a0 8906787

75. Chung JH, Larsen AR, Chen E, Bunz F. A PTCH1 homolog transcriptionally activated by p53 suppresses Hedgehog signaling. J Biol Chem. 2014;289: 33020–33031. doi: 10.1074/jbc.M114.597203 25296753

76. Ung DC, Iacono G, Méziane H, Blanchard E, Papon M-A, Selten M, et al. Ptchd1 deficiency induces excitatory synaptic and cognitive dysfunctions in mouse. Mol Psychiatry. 2018;23: 1356–1367. doi: 10.1038/mp.2017.39 28416808

77. Tora D, Gomez AM, Michaud J-F, Yam PT, Charron F, Scheiffele P. Cellular Functions of the Autism Risk Factor PTCHD1 in Mice. Journal of Neuroscience. 2017;37: 11993–12005. doi: 10.1523/JNEUROSCI.1393-17.2017 29118110

78. Chuang P-T, McMahon AP. Vertebrate Hedgehog signalling modulated by induction of a Hedgehog-binding protein. Nature. 1999;397: 617–621. doi: 10.1038/17611 10050855

79. Chuang P-T, Kawcak T, McMahon AP. Feedback control of mammalian Hedgehog signaling by the Hedgehog-binding protein, Hip1, modulates Fgf signaling during branching morphogenesis of the lung. Genes Dev. 2003;17: 342–347. doi: 10.1101/gad.1026303 12569124

80. Bishop B, Aricescu AR, Harlos K, O’Callaghan CA, Jones EY, Siebold C. Structural insights into hedgehog ligand sequestration by the human hedgehog-interacting protein HHIP. Nat Struct Mol Biol. 2009;16: 1–8. doi: 10.1038/nsmb0109-1 19125164

81. Bosanac I, Maun HR, Scales SJ, Wen X, Lingel A, Bazan JF, et al. The structure of SHH in complex with HHIP reveals a recognition role for the Shh pseudo active site in signaling. Nat Struct Mol Biol. 2009;16: 691–697. doi: 10.1038/nsmb.1632 19561609

82. Holtz AM, Peterson KA, Nishi Y, Morin S, Song JY, Charron F, et al. Essential role for ligand-dependent feedback antagonism of vertebrate hedgehog signaling by PTCH1, PTCH2 and HHIP1 during neural patterning. Development. 2013;140: 3423–3434. doi: 10.1242/dev.095083 23900540

83. Hao L, Mukherjee K, Liegeois S, Baillie D, Labouesse M, Bürglin TR. The hedgehog-related gene qua-1 is required for molting in Caenorhabditis elegans. Dev Dyn. 2006;235: 1469–1481. doi: 10.1002/dvdy.20721 16502424

84. Kostrouchova M, Krause M, Kostrouch Z, Rall JE. CHR3: a Caenorhabditis elegans orphan nuclear hormone receptor required for proper epidermal development and molting. Development. 1998;125: 1617–1626. 9521900

85. Kostrouchova M, Krause M, Kostrouch Z, Rall JE. Nuclear hormone receptor CHR3 is a critical regulator of all four larval molts of the nematode Caenorhabditis elegans. Proceedings of the National Academy of Sciences. 2001;98: 7360–7365. doi: 10.1073/pnas.131171898 11416209

86. Kouns NA, Nakielna J, Behensky F, Krause MW, Kostrouch Z, Kostrouchova M. NHR-23 dependent collagen and hedgehog-related genes required for molting. Biochem Biophys Res Commun. 2011;413: 515–520. doi: 10.1016/j.bbrc.2011.08.124 21910973

87. Lažetić V, Fay DS. Molting in C. elegans. Worm. 2017;6: e1330246. doi: 10.1080/21624054.2017.1330246 28702275

88. Lewis JA, Fleming JT. Basic Culture Methods. Methods in Cell Biology. 1995;48: 3–29. doi: 10.1016/S0091-679X(08)61381-3 8531730

89. Dickinson DJ, Pani AM, Heppert JK, Higgins CD, Goldstein B. Streamlined Genome Engineering with a Self-Excising Drug Selection Cassette. Genetics. 2015;200: 1035–1049. doi: 10.1534/genetics.115.178335 26044593

90. Friedland AE, Tzur YB, Esvelt KM, Colaiácovo MP, Church GM, Calarco JA. Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods. 2013;10: 741–743. doi: 10.1038/nmeth.2532 23817069

91. Tursun B, Cochella L, Carrera I, Hobert O. A toolkit and robust pipeline for the generation of fosmid-based reporter genes in C. elegans. Hart AC, editor. PLoS ONE. 2009;4: e4625. doi: 10.1371/journal.pone.0004625 19259264

92. Mello CC, Kramer JM, Stinchcomb D, Ambros V. Efficient gene transfer in C.elegans: Extrachromosomal maintenance and integration of transforming sequences. EMBO J. 1991;10: 3959–3970. 1935914

93. Dokshin GA, Ghanta KS, Piscopo KM, Mello CC. Robust Genome Editing with Short Single-Stranded and Long, Partially Single-Stranded DNA Donors in Caenorhabditis elegans. Genetics. 2018;210: 781–787. doi: 10.1534/genetics.118.301532 30213854

94. Miller DM, Shakes DC. Chapter 16 Immunofluorescence Microscopy. Methods in Cell Biology. 1995;48: 365–394. doi: 10.1016/S0091-679X(08)61396-5 8531735

95. Kawasaki I, Shim Y-H, Kirchner J, Kaminker J, Wood WB, Strome S. PGL-1, a Predicted RNA-Binding Component of Germ Granules, Is Essential for Fertility in C. elegans. Cell. 1998;94: 635–645. doi: 10.1016/s0092-8674(00)81605-0 9741628

96. Sulston JE, Hodgkin J. Methods. In: Wood WB, editor. The nematode Caenorhabditis elegans. Cold Spring Harbor Laboratory Press; 1987. pp. 587–606.

97. Kondo T, Hirohashi S. Application of highly sensitive fluorescent dyes (CyDye DIGE Fluor saturation dyes) to laser microdissection and two-dimensional difference gel electrophoresis (2D-DIGE) for cancer proteomics. Nat Protoc. 2007;1: 2940–2956. doi: 10.1038/nprot.2006.421 17406554

98. Reboul J, Vaglio P, Rual J-F, Lamesch P, Martinez M, Armstrong CM, et al. C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat Genet. 2003;34: 35–41. doi: 10.1038/ng1140 12679813

99. Kamath RS, Martinez-Campos M, Zipperlen P, Fraser AG, Ahringer J. Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegans. Genome Biology 2015 16:1. doi: 10.1186/gb-2000-2-1-research0002 11178279

100. Timmons L, Fire A. Specific interference by ingested dsRNA. Nature. 1998;395: 854–854. doi: 10.1038/27579 9804418

101. Fukuyama M, Sakuma K, Park R, Kasuga H, Nagaya R, Atsumi Y, et al. C. elegans AMPKs promote survival and arrest germline development during nutrient stress. Biol Open. 2012;1: 929–936. doi: 10.1242/bio.2012836 23213370

102. Harfe BD, Gomes AV, Kenyon C, Liu J, Krause M, Fire A. Analysis of a Caenorhabditis elegans Twist homolog identifies conserved and divergent aspects of mesodermal patterning. Genes Dev. 1998;12: 2623–2635. doi: 10.1101/gad.12.16.2623 9716413

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