Aspöck, G., Kagoshima, H., Niklaus, G., and Bürglin, T.R. (1999). Caenorhabditis elegans has scores of hedgehog-related genes: sequence and expression analysis. Genome Res. 9, 909–923.
Baugh, L.R., and Sternberg, P.W. (2006). DAF-16/FOXO Regulates Transcription of cki-1/Cip/Kip and Repression of lin-4 during C. elegans L1 Arrest. Curr. Biol. 16, 780–785.
Baugh, L.R., DeModena, J., and Sternberg, P.W. (2009). RNA Pol II accumulates at promoters of growth genes during developmental arrest. Science (80-. ). 324, 92–94.
Bolatto, C., Parada, C., Revello, F., Zuñiga, A., Cabrera, P., and Cambiazo, V. (2015). Spatial and temporal distribution of Patched-related protein in the Drosophila embryo. Gene Expr. Patterns 19, 120–128.
Brenner, S. (1974). THE GENETICS OF CAENORHABDZTZS ELEGANS. Genetics 77, 71–94.
Bürglin, T.R., and Kuwabara, P.E. (2006). Homologs of the Hh signalling network in C. elegans. WormBook 1–14. Burke, R., Nellen, D., Bellotto, M., Hafen, E., Senti, K.A., Dickson, B.J., and Basler, K. (1999). Dispatched, a novel sterol-sensing domain protein dedicated to the release of cholesterol-modified Hedgehog from signaling cells. Cell 99, 803–815.
Carstea, E.D., Morris, J.A., Coleman, K.G., Loftus, S.K., Zhang, D., Cummings, C., Gu, J., Rosenfeld, M.A., Pavan, W.J., Krizman, D.B., et al. (1997). Niemann-Pick C1 disease gene: Homology to mediators of cholesterol homeostasis. Science (80-. ). 277, 228–231.
Chaudhry, A., Noor, A., Degagne, B., Baker, K., Bok, L.A., Brady, A.F., Chitayat, D., Chung, B.H., Cytrynbaum, C., Dyment, D., et al. (2015). Phenotypic spectrum associated with PTCHD1 deletions and truncating mutations includes intellectual disability and autism spectrum disorder. Clin. Genet. 88, 224–233.
Chen, Y., and Baugh, L.R. (2014). Ins-4 and daf-28 function redundantly to regulate C. elegans L1 arrest. Dev. Biol. 394, 314–326.
Chen, C.C.-H., Schweinsberg, P.J., Vashist, S., Mareiniss, D.P., Lambie, E.J., and Grant, and B.D. (2006). RAB-10 Is Required for Endocytic Recycling in the Caenorhabditis elegans Intestine. Mol. Biol. Cell 17, 1286–1297.
Cheung, T.H., and Rando, T.A. (2013). Molecular regulation of stem cell quiescence. Nat. Rev. Mol. Cell Biol. 14, 329– 340.
Choi, M.K., Son, S., Hong, M., Choi, M.S., Kwon, J.Y., and Lee, J. (2016). Maintenance of membrane integrity and permeability depends on a patched-related protein in Caenorhabditis elegans. Genetics 202, 1411–1420.
Chung, J.H., Larsen, A.R., Chen, E., and Bunz, F. (2014). A PTCH1 homolog transcriptionally activated by p53 suppresses hedgehog signaling. J. Biol. Chem. 289, 33020–33031.
D.M., S., M., H., M., A., T.A., S., Q., G., R.L., J., M.P., S., D., P., A., G., H., P., et al. (1996). The tumour-suppressor gene patched encodes a candidate receptor for Sonic hedgehog. Nature 384, 129–134.
D’Angelo, G., Matusek, T., Pizette, S., and Thérond, P.P. (2015). Endocytosis of hedgehog through dispatched regulates long-range signaling. Dev. Cell 32, 290–303.
Dickinson, D.J., Pani, A.M., Heppert, J.K., Higgins, C.D., and Goldstein, B. (2015). Streamlined genome engineering with a self-excising drug selection cassette. Genetics 200, 1035–1049.
Doonan, R., Hatzold, J., Raut, S., Conradt, B., and Alfonso, A. (2008). HLH-3 is a C. elegans Achaete/Scute protein required for differentiation of the hermaphrodite-specific motor neurons. Mech. Dev. 125, 883–893.
Duerr, J. (2006). Immunohistochemistry. WormBook 1–61.
Filges, I., Röthlisberger, B., Blattner, A., Boesch, N., Demougin, P., Wenzel, F., Huber, A.R., Heinimann, K., Weber, P., and Miny, P. (2011). Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism. Clin. Genet. 79, 79–85.
Forbes, A.J., Nakano, Y., Taylor, A.M., and Ingham, P.W. (1993). Genetic analysis of hedgehog signalling in the Drosophila embryo. Development 119, 115–124.
Fukuyama, M., Rougvie, A.E., and Rothman, J.H. (2006). C. elegans DAF-18/PTEN Mediates Nutrient-Dependent Arrest of Cell Cycle and Growth in the Germline. Curr. Biol. 16, 773–779.
Fukuyama, M., Kontani, K., Katada, T., and Rougvie, A.E. (2015). The C. Elegans hypodermis couples progenitor cell quiescence to the dietary state. Curr. Biol. 25, 1241–1248.
Gilleard, J.S., Barry, J.D., and Johnstone, I.L. (1997). cis regulatory requirements for hypodermal cell-specific expression of the Caenorhabditis elegans cuticle collagen gene dpy-7. Mol. Cell. Biol. 17, 2301–2311.
Grant, B., and Hirsh, D. (1999). Receptor-mediated endocytosis in the Caenorhabditis elegans oocyte. Mol. Biol. Cell 10, 4311–4326.
Hao, L., Johnsen, R., Lauter, G., Baillie, D., and Bürglin, T.R. (2006a). Comprehensive analysis of gene expression patterns of hedgehog-related genes. BMC Genomics 7.
Hao, L., Mukherjee, K., Liegeois, S., Baillie, D., Labouesse, M., and Bürglin, T.R. (2006b). The hedgehog-related gene qua-1 is required for molting in Caenorhabditis elegans. Dev. Dyn. 235, 1469–1481.
Hermann, G.J., Schroeder, L.K., Hieb, C.A., Kershner, A.M., Rabbitts, B.M., Grant, P.F.B.D., and Priess, and J.R. (2005). Genetic Analysis of Lysosomal Trafficking in Caenorhabditis elegans. Mol. Biol. Cell 16, 3273–3288.
Hong, Y., Roy, R., and Ambros, V. (1998). Developmental regulation of a cyclin-dependent kinase inhibitor controls postembryonic cell cycle progression in Caenorhabditis elegans. Development 125, 3585–3597.
Johnson, T.E., Mitchell, D.H., Kline, S., Kemal, R., and Foy, J. (1984). Arresting development arrests aging in the nematode Caenorhabditis elegans. Mech. Ageing Dev. 28, 23–40.
Kamath, R.S., Martinez-Campos, M., Zipperlen, P., Fraser, A.G., and Ahringer, J. (2000). Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegans Ravi S Kamath , Maruxa Martinez-Campos , Peder Zipperlen , Andrew G Fraser. Genome Biol. 2, 1–10.
Kaplan, R.E.W., Chen, Y., Moore, B.T., Jordan, J.M., Maxwell, C.S., Schindler, A.J., and Baugh, L.R. (2015). dbl-1/TGF-β and daf-12/NHR Signaling Mediate Cell-Nonautonomous Effects of daf-16/FOXO on Starvation-Induced Developmental Arrest. PLoS Genet. 11, 1–23.
Kasuga, H., Fukuyama, M., Kitazawa, A., Kontani, K., and Katada, T. (2013). The microRNA miR-235 couples blast-cell quiescence to the nutritional state. Nature 497, 503–506.
Katayama, H., Yamamoto, A., Mizushima, N., Yoshimori, T., and Miyawaki, A. (2008). GFP-like Proteins Stably Accumulate in Lysosomes. Cell Struct. Funct. 33, 1–12.
Kawasaki, I., Shim, Y.H., Kirchner, J., Kaminker, J., Wood, W.B., and Strome, S. (1998). PGL-1, a predicted RNA-binding component of germ granules, is essential for fertility in C. elegans. Cell 94, 635–645.
Krogh, A., Larsson, B., Von Heijne, G., and Sonnhammer, E.L.L. (2001). Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 305, 567–580.
Kume, M., Chiyoda, H., Kontani, K., Katada, T., and Fukuyama, M. (2019). Hedgehog-related genes regulate reactivation of quiescent neural progenitors in Caenorhabditis elegans. Biochem. Biophys. Res. Commun. 520, 532– 537.
Kuwabara, P.E., Lee, M.H., Schedl, T., and Jefferis, G.S. (2000). A C. elegans patched gene, ptc-1, functions in germ-line cytokinesis. Genes Dev. 14, 1933–1944.
Li, N., and Clevers, H. (2010). Coexistence of quiescent and active adult stem cells in mammals. Science (80-. ). 327, 542–545.
Lin, C.C.J., and Wang, M.C. (2017). Microbial metabolites regulate host lipid metabolism through NR5A-Hedgehog signalling. Nat. Cell Biol. 19, 550–557.
Loftus, S.K., Morris, J.A., Carstea, E.D., Gu, J.Z., Cummings, C., Brown, A., Ellison, J., Ohno, K., Rosenfeld, M.A., Tagle, D.A., et al. (1997). Murine model of Niemann-Pick C disease: Mutation in a cholesterol homeostasis gene. Science (80-. ). 277, 232–235.
Lu, X., Liu, S., and Kornberg, T.B. (2006). The C-terminal tail of the Hedgehog receptor Patched regulates both localization and turnover. Genes Dev. 20, 2539–2551.
Marigo, V., Davey, R.A., Zuo, Y., Cunningham, J.M., and Tabin, C.J. (1996). Biochemical evidence that patched is the hedgehog receptor. Nature 384, 176–179.
Marshall, C.R., Noor, A., Vincent, J.B., Lionel, A.C., Feuk, L., Skaug, J., Shago, M., Moessner, R., Pinto, D., Ren, Y., et al. (2008). Structural Variation of Chromosomes in Autism Spectrum Disorder. Am. J. Hum. Genet. 82, 477–488.
Matsumoto, A., Takeishi, S., Kanie, T., Susaki, E., Onoyama, I., Tateishi, Y., Nakayama, K., and Nakayama, K.I. (2011). P57 Is required for quiescence and maintenance of adult hematopoietic stem cells. Cell Stem Cell 9, 262–271. Mello, C.C., Kramer, J.M., Stinchcomb, D., and Ambros, V. (1991). Efficient gene transfer in C.elegans: extrachromosomal maintenance and integration of transforming sequences. EMBO J. 10, 3959–3970.
Noor, A., Whibley, A., Marshall, C.R., Gianakopoulos, P.J., Piton, A., Carson, A.R., Orlic-Milacic, M., Lionel, A.C., Sato, D., Pinto, D., et al. (2010). Disruption at the PTCHD1 locus on Xp22.11 in autism spectrum disorder and intellectual disability. Sci. Transl. Med. 2, 49ra68-49ra68.
Oikonomou, G., Perens, E.A., Lu, Y., and Shaham, S. (2012). Some, but not all, retromer components promote morphogenesis of C. elegans sensory compartments. Dev. Biol. 362, 42–49.
Parry, J.M., and Sundaram, M. V. (2014). A non-cell-autonomous role for Ras signaling in C. elegans neuroblast delamination. Development 141, 4279–4284.
PE, K., and M, L. (2002). The sterol-sensing domain: multiple families, a unique role? Trends Genet. 18, 193–201. Perens, E.A., and Shaham, S. (2005). C. elegans daf-6 encodes a patched-related protein required for lumen formation. Dev. Cell 8, 893–906.
Pinto, D., Pagnamenta, A.T., Klei, L., Anney, R., Merico, D., Regan, R., Conroy, J., Magalhaes, T.R., Correia, C., Abrahams, B.S., et al. (2010). Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466, 368–372.
Poteryaev, D., Fares, H., Bowerman, B., and Spang, A. (2007). Caenorhabditis elegans SAND-1 is essential for RAB-7 function in endosomal traffic. EMBO J. 26, 301–312.
Reboul, J., Vaglio, P., Rual, J.-F., Lamesch, P., Martinez, M., Armstrong, C.M., Li, S., Jacotot, L., Bertin, N., Janky, R., et al. (2003). C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat. Genet. 34, 35–41.
Rodgers, J.T., King, K.Y., Brett, J.O., Cromie, M.J., Charville, G.W., Maguire, K.K., Brunson, C., Mastey, N., Liu, L., Tsai, C.R., et al. (2014). MTORC1 controls the adaptive transition of quiescent stem cells from G 0 to G Alert. Nature 510, 393–396.
Rohlfing, A.K., Miteva, Y., Moronetti, L., He, L., and Lamitina, T. (2011). The Caenorhabditis elegans mucin-like protein OSM-8 negatively regulates osmosensitive physiology via the transmembrane protein PTR-23. PLoS Genet. 7. Soloviev, A., Gallagher, J., Marnef, A., and Kuwabara, P.E. (2011). C. elegans patched-3 is an essential gene implicated in osmoregulation and requiring an intact permease transporter domain. Dev. Biol. 351, 242–253.
Sulston, J.E. (1976). Post-embryonic development in the ventral cord of Caenorhabditis elegans. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 275, 287–297.
Sulston, J.E., and Horvitz, H.R. (1977). Post-embryonic Cell Lineages of the Nematode, Caenorhabditis elegans. Torrico, B., Fernàndez-Castillo, N., Hervás, A., Milà, M., Salgado, M., Rueda, I., Buitelaar, J.K., Rommelse, N., Oerlemans, A.M., Bralten, J., et al. (2015). Contribution of common and rare variants of the PTCHD1 gene to autism spectrum disorders and intellectual disability. Eur. J. Hum. Genet. 23, 1694–1701.
Treusch, S., Knuth, S., Slaugenhaupt, S.A., Goldin, E., Grant, B.D., and Fares, H. (2004). Caenorhabditis elegans functional orthologue of human protein h-mucolipin-1 is required for lysosome biogenesis. Proc. Natl. Acad. Sci. U. S. A. 101, 4483–4488.
Tseng, T.T., Gratwick, K.S., Kollman, J., Park, D., Nies, D.H., Goffeau, A., and Saier, M.H. (1999). The RND permease superfamily: an ancient, ubiquitous and diverse family that includes human disease and development proteins. J. Mol. Microbiol. Biotechnol. 1, 107–125.
Tursun, B., Cochella, L., Carrera, I., and Hobert, O. (2009). A Toolkit and Robust Pipeline for the Generation of Fosmid-Based Reporter Genes in C. elegans. PLoS One 4, e4625.
Ung, D.C., Iacono, G., Méziane, H., Blanchard, E., Papon, M.-A., Selten, M., van Rhijn, J.-R., Montjean, R., Rucci, J., Martin, S., et al. (2018). Ptchd1 deficiency induces excitatory synaptic and cognitive dysfunctions in mouse. Mol. Psychiatry 23, 1356–1367.
Wang, X., and Chamberlin, H.M. (2002). Multiple regulatory changes contribute to the evolution of the Caenorhabditis lin-48 ovo gene. Genes Dev. 16, 2345–2349.
Wei, X., Potter, C.J., Luo, L., and Shen, K. (2012). Controlling gene expression with the Q repressible binary expression system in Caenorhabditis elegans. Nat. Methods 9, 391–395.
Wells, M.F., Wimmer, R.D., Schmitt, L.I., Feng, G., and Halassa, M.M. (2016). Thalamic reticular impairment underlies attention deficit in Ptchd1 Y’mice. Nature 532, 58–63.
Wicks, S.R., Yeh, R.T., Gish, W.R., Waterston, R.H., and Plasterk, R.H.A. (2001). Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map. Nat. Genet. 28, 160–164.
Winnier, A.R., Meir, J.Y., Ross, J.M., Tavernarakis, N., Driscoll, M., Ishihara, T., Katsura, I., and Iii, D.M.M. (1999). UNC-4 / UNC-37-dependent repression of motor neuron-specific genes controls synaptic choice in Caenorhabditis elegans. 2774–2786.
Zhang, J., Grindley, J.C., Yin, T., Jayasinghe, S., He, X.C., Ross, J.T., Haug, J.S., Rupp, D., Porter-Westpfahl, K.S., Wiedemann, L.M., et al. (2006). PTEN maintains haematopoietic stem cells and acts in lineage choice and leukaemia prevention. Nature 441, 518–522.
Zheng, S., Qu, Z., Zanetti, M., Lam, B., and Chin-Sang, I. (2018). C. elegans PTEN and AMPK block neuroblast divisions by inhibiting a BMP-insulin-PP2A-MAPK pathway . Development 145, dev166876.
Zhong, Y., Gu, L.J., Sun, X.G., Yang, S.H., and Zhang, X.H. (2014). Comprehensive analysis of patched domain-containing genes reveals a unique evolutionary pattern. Genet. Mol. Res. 13, 7318–7331.
Zugasti, O., Rajan, J., and Kuwabara, P.E. (2005). The function and expansion of the Patched- and Hedgehog-related homologs in C. elegans. Genome Res. 15, 1402–1410.