Using microarrays to facilitate positional cloning: Identification of tomosyn as an inhibitor of neurosecretion

PLoS Genetics

Volumn 1, Issue 1, 2005, Pages 0006-0016

  Dybbs, Michael ^a,b   Ngai, John ^b   Kaplan, Joshua M ^a  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 33644745585     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0010002     Document Type: Article

References (69)

1. Haffter P, Granato M, Brand M, Mullins MC, Hammerschmidt M, et al. (1996) The identification of genes with unique and essential functions in the development of the zebrafish, Danio rerio. Development 123: 1-36.
2. Driever W, Solnica-Krezel L, Schier AF, Neuhauss SC, Malicki J, et al. (1996) A genetic screen for mutations affecting embryogenesis in zebrafish. Development 123: 37-46.
3. Zarbalis K, May SR, Shen Y, Ekker M, Rubenstein JL, et al. (2004) A focused and efficient genetic screening strategy in the mouse: Identification of mutations that disrupt cortical development. PLoS Biol 2: DOI: 10.1371/journal.pbio.0020219
4. O'Brien TP, Frankel WN (2004) Moving forward with chemical mutagenesis in the mouse. J Physiol 554: 13-21.
5. Nadeau JH, Balling R, Barsh G, Beier D, Brown SD, et al. (2001) Sequence interpretation. Functional annotation of mouse genome sequences. Science 291: 1251-1255.
6. Bessereau JL, Wright A, Williams DC, Schuske K, Davis MW, et al. (2001) Mobilization of a Drosophila transposon in the Caenorhabditis elegans germ line. Nature 413: 70-74.
7. Cooley L, Kelley R, Spradling A (1988) Insertional mutagenesis of the Drosophila genome with single P elements. Science 239: 1121-1128.
8. Gaiano N, Amsterdam A, Kawakami K, Allende M, Becker T, et al. (1996) Insertional mutagenesis and rapid cloning of essential genes in zebrafish. Nature 383: 829-832.
9. Breindl M, Harbers K, Jaenisch R (1984) Retrovirus-induced lethal mutation in collagen I gene of mice is associated with an altered chromatin structure. Cell 38: 9-16.
10. Korswagen HC, Durbin RM, Smits MT, Plasterk RH (1996) Transposon Tc1-derived, sequence-tagged sites in Caenorhabditis elegans as markers for gene mapping. Proc Natl Acad Sci U S A 93: 14680-14685.
11. Jansen G, Hazendonk E, Thijssen KL, Plasterk RH (1997) Reverse genetics by chemical mutagenesis in Caenorhabditis elegans. Nat Genet 17: 119-121.
12. Rong YS, Golic KG (2000) Gene targeting by homologous recombination in Drosophila. Science 288: 2013-2018.
13. Bradley A, Zheng B, Liu P (1998) Thirteen years of manipulating the mouse genome: A personal history. Int J Dev Biol 42: 943-950.
14. Stemple DL (2004) TILLING-A high-throughput harvest for functional genomics. Nat Rev Genet 5: 145-150.
15. McCallum CM, Comai L, Greene EA, Henikoff S (2000) Targeting induced local lesions IN genomes (TILLING) for plant functional genomics. Plant Physiol 123: 439-442.
16. Hentze MW, Kulozik AE (1999) A perfect message: RNA surveillance and nonsense-mediated decay. Cell 96: 307-310.
17. Mango SE (2001) Stop making nonSense: The C. elegans smg genes. Trends Genet 17: 646-653.
18. Wilusz CJ, Wang W, Peltz SW (2001) Curbing the nonsense: The activation and regulation of mRNA surveillance. Genes Dev 15: 2781-2785.
19. Huusko P, Ponciano-Jackson D, Wolf M, Kiefer JA, Azorsa DO, et al. (2004) Nonsense-mediated decay microarray analysis identifies mutations of EPHB2 in human prostate cancer. Nat Genet 36: 979-983.
20. Noensie EN, Dietz HC (2001) A strategy for disease gene identification through nonsense-mediated mRNA decay inhibition. Nat Biotechnol 19: 434-439.
21. Frischmeyer PA, Dietz HC (1999) Nonsense-mediated mRNA decay in health and disease. Hum Mol Genet 8: 1893-1900.
22. Mendell JT, Dietz HC (2001) When the message goes awry: Disease-producing mutations that influence mRNA content and performance. Cell 107: 411-414.
23. Raser JM, O'Shea EK (2004) Control of stochasticity in eukaryotic gene expression. Science 304: 1811-1814.
24. Fraser HB, Hirsh AE, Giaever G, Kumm J, Eisen MB (2004) Noise minimization in eukaryotic gene expression. PLoS Biol 2: DOI: 10.1371/ journal.pbio.0020137
25. Brem RB, Yvert G, Clinton R, Kruglyak L (2002) Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755.
26. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, et al. (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297-302.
27. Kim SK, Lund J, Kiraly M, Duke K, Jiang M, et al. (2001) A gene expression map for Caenorhabditis elegans. Science 293: 2087-2092.
28. Zhang Y, Ma C, Delohery T, Nasipak B, Foat BC, et al. (2002) Identification of genes expressed in C. elegans touch receptor neurons. Nature 418: 331-335.
29. Way JC, Chalfie M (1988) Mec-3, a homeobox-containing gene that specifies differentiation of the touch receptor neurons in C. elegans. Cell 54: 5-16.
30. Xue D, Tu Y, Chalfie M (1993) Cooperative interactions between the Caenorhabditis elegans homeoproteins UNC-86 and MEC-3. Science 261: 1324-1328.
31. Cui X, Churchill GA (2003) Statistical tests for differential expression in cDNA microarray experiments. Genome Biol 4: 210.
32. Way JC, Chalfie M (1989) The mec-3 gene of Caenorhabditis elegans requires its own product for maintained expression and is expressed in three neuronal cell types. Genes Dev 3: 1823-1833.
33. Reiner DJ, Newton EM, Tian H, Thomas JH (1999) Diverse behavioural defects caused by mutations in Caenorhabditis elegans unc-43 CaM kinase II. Nature 402: 199-203.
34. Sagasti A, Hisamoto N, Hyodo J, Tanaka-Hino M, Matsumoto K, et al. (2001) The CaMKII UNC-43 activates the MAPKKK NSY-1 to execute a lateral signaling decision required for asymmetric olfactory neuron fates. Cell 105: 221-232.
35. Maxwell PH, Wiesener MS, Chang GW, Clifford SC, Vaux EC, et al. (1999) The tumour suppressor protein VHL targets hypoxia-inducible factors for oxygen-dependent proteolysis. Nature 399: 271-275.
36. Epstein AC, Gleadle JM, McNeill LA, Hewitson KS, O'Rourke J, et al. (2001) C. elegans EGL-9 and mammalian homologs define a family of dioxygenases that regulate HIF by prolyl hydroxylation. Cell 107: 43-54.
37. Jaakkola P, Mole DR, Tian YM, Wilson MI, Gielbert J, et al. (2001) Targeting of HIF-alpha to the von Hippel-Lindau ubiquitylation complex by O2-regulated prolyl hydroxylation. Science 292: 468-472.
38. Ivan M, Kondo K, Yang H, Kim W, Valiando J, et al. (2001) HIFalpha targeted for VHL-mediated destruction by proline hydroxylation: Implications for O2 sensing. Science 292: 464-468.
39. Trent C, Tsuing N, Horvitz HR (1983) Egg-laying defective mutants of the nematode Caenorhabditis elegans. Genetics 104: 619-647.
40. Avery L (1993) The genetics of feeding in Caenorhabditis elegans. Genetics 133: 897-917.
41. Miller KG, Alfonso A, Nguyen M, Crowell JA, Johnson CD, et al. (1996) A genetic selection for Caenorhabditis elegans synaptic transmission mutants. Proc Natl Acad Sci U S A 93: 12593-12598.
42. Nonet ML (1999) Studying mutants that affect neurotransmitter release in C. elegans. In: Bellen H editor. Neurotransmitter release. New York: Oxford University Press. pp. 265-303
43. Nguyen M, Alfonso A, Johnson CD, Rand JB (1995) Caenorhabditis elegans mutants resistant to inhibitors of acetylcholinesterase. Genetics 140: 527- 535.
44. Nonet ML, Grundahl K, Meyer BJ, Rand JB (1993) Synaptic function is impaired but not eliminated in C. elegans mutants lacking synaptotagmin. Cell 73: 1291-1305.
45. Lackner MR, Nurrish SJ, Kaplan JM (1999) Facilitation of synaptic transmission by EGL-30 Gqalpha and EGL-8 PLCbeta: DAG binding to UNC-13 is required to stimulate acetylcholine release. Neuron 24: 335-346.
46. Nurrish S, Segalat L, Kaplan JM (1999) Serotonin inhibition of synaptic transmission: Galpha(0) decreases the abundance of UNC-13 at release sites. Neuron 24: 231-242.
47. van der Linden AM, Simmer F, Cuppen E, Plasterk RH (2001) The G-protein beta-subunit GPB-2 in Caenorhabditis elegans regulates the G(o)al-pha-G(q)alpha signaling network through interactions with the regulator of G-protein signaling proteins EGL-10 and EAT-16. Genetics 158: 221-235.
48. Wang ZW, Saifee O, Nonet ML, Salkoff L (2001) SLO-1 potassium channels control quantal content of neurotransmitter release at the C. elegans neuromuscular junction. Neuron 32: 867-881.
49. Masuda ES, Huang BC, Fisher JM, Luo Y, Scheller RH (1998) Tomosyn binds t-SNARE proteins via a VAMP-like coiled coil. Neuron 21: 479-480.
50. Fujita Y, Shirataki H, Sakisaka T, Asakura T, Ohya T, et al. (1998) Tomosyn: A syntaxin-1-binding protein that forms a novel complex in the neurotransmitter release process. Neuron 20: 905-915.
51. Hatsuzawa K, Lang T, Fasshauer D, Bruns D, Jahn R (2003) The R-SNARE motif of tomosyn forms SNARE core complexes with syntaxin 1 and SNAP-25 and down-regulates exocytosis. J Biol Chem 278: 31159-31166.
52. Yizhar O, Matti U, Melamed R, Hagalili Y, Bruns D, et al. (2004) Tomosyn inhibits priming of large dense-core vesicles in a calcium-dependent manner. Proc Natl Acad Sci U S A 101: 2578-2583.
53. Nishimura MT, Stein M, Hou BH, Vogel JP, Edwards H, et al. (2003) Loss of a callose synthase results in salicylic acid-dependent disease resistance. Science 301: 969-972.
54. Sicinski P, Geng Y, Ryder-Cook AS, Barnard EA, Darlison MG, et al. (1989) The molecular basis of muscular dystrophy in the mdx mouse: A point mutation. Science 244: 1578-1580.
55. Tseng BS, Zhao P, Pattison JS, Gordon SE, Granchelli JA, et al. (2002) Regenerated mdx mouse skeletal muscle shows differential mRNA expression. J Appl Physiol 93: 537-545.
56. Roy PJ, Stuart JM, Lund J, Kim SK (2002) Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 418: 975-979.
57. Frischmeyer PA, van Hoof A, O'Donnell K, Guerrerio AL, Parker R, et al. (2002) An mRNA surveillance mechanism that eliminates transcripts lacking termination codons. Science 295: 2258-2261.
58. van Hoof A, Frischmeyer PA, Dietz HC, Parker R (2002) Exosome-mediated recognition and degradation of mRNAs lacking a termination codon. Science 295: 2262-2264.
59. Wickens M, Anderson P, Jackson RJ (1997) Life and death in the cytoplasm: Messages from the 39 end. Curr Opin Genet Dev 7: 220-232.
60. Lykke-Andersen J (2001) MRNA quality control: Marking the message for life or death. Curr Biol 11: R88-R91.
61. Singh G, Lykke-Andersen J (2003) New insights into the formation of active nonsense-mediated decay complexes. Trends Biochem Sci 28: 464-466.
62. Wagner E, Lykke-Andersen J (2002) MRNA surveillance: The perfect persist. J Cell Sci 115: 3033-3038.
63. Culbertson MR (1999) RNA surveillance. Unforeseen consequences for gene expression, inherited genetic disorders and cancer. Trends Genet 15: 74-80.
64. Nagy E, Maquat LE (1998) A rule for termination-codon position within intron-containing genes: When nonsense affects RNA abundance. Trends Biochem Sci 23: 198-199.
65. Glazier AM, Nadeau JH, Aitman TJ (2002) Finding genes that underlie complex traits. Science 298: 2345-2349.
66. Korstanje R, Paigen B (2002) From QTL to gene: The harvest begins. Nat Genet 31: 235-236.
67. Harries LW, Hattersley AT, Ellard S (2004) Messenger RNA transcripts of the hepatocyte nuclear factor-1alpha gene containing premature termination codons are subject to nonsense-mediated decay. Diabetes 53: 500-504.
68. Perrin-Vidoz L, Sinilnikova OM, Stoppa-Lyonnet D, Lenoir GM, Mazoyer S (2002) The nonsense-mediated mRNA decay pathway triggers degradation of most BRCA1 mRNAs bearing premature termination codons. Hum Mol Genet 11: 2805-2814.
69. Murphy CT, McCarroll SA, Bargmann CI, Fraser A, Kamath RS, et al. (2003) Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans. Nature 424: 277-283.