Tandem inverted repeat system for selection of effective transgenic RNAi strains in Chlamydomonas

Plant Journal

Volumn 40, Issue 4, 2004, Pages 611-621

  Rohr, Jennifer ^a   Sarkar, Nandita ^a   Balenger, Susan ^b   Jeong, Byeong Ryool ^a   Cerutti, Heriberto ^a  

^a UNIVERSITY OF NEBRASKA   (United States)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Functional genomics; Inverted repeat transgene; Post transcriptional gene silencing; Reverse genetics; RNA interference

Indexed keywords

GENES; GENETIC ENGINEERING; MICROORGANISMS; MUTAGENESIS;

GENE SILENCING; INVERTED REPEAT (IR) TRANSGENES; REVERSE GENETICS;

RNA;

PROTOZOAL PROTEIN; RNA;

ANIMAL; ARTICLE; CHLAMYDOMONAS; GENE EXPRESSION REGULATION; GENETIC SELECTION; GENETICS; METABOLISM; MULTIGENE FAMILY; NUCLEOTIDE REPEAT; RNA INTERFERENCE; TRANSGENIC ORGANISM;

ANIMALS; CHLAMYDOMONAS; GENE EXPRESSION REGULATION; MULTIGENE FAMILY; ORGANISMS, GENETICALLY MODIFIED; PROTOZOAN PROTEINS; REPETITIVE SEQUENCES, NUCLEIC ACID; RNA; RNA INTERFERENCE; SELECTION (GENETICS);

GENES; GENETIC ENGINEERING; MICROBIOLOGY; MUTATION; NUCLEIC ACIDS;

ALGAE; CHLAMYDOMONAS; CHLAMYDOMONAS REINHARDTII; EUKARYOTA; FUNGI; METAZOA; PROTOZOA;

EID: 8444222059     PISSN: 09607412     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2004.02227.x     Document Type: Article

References (73)

1. Brown, A.E., Bugeon, L., Crisanti, A. and Catteruccia, F. (2003) Stable and heritable gene silencing in the malaria vector Anopheles stephensi. Nucleic Acids Res. 31, e85.
2. Brummelkamp, T.R., Bernards, R. and Agami, R. (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science, 19, 550-553.
3. Carmell, M.A., Zhang, L., Conklin, D.S., Hannon, G.J. and Rosenquist, T.A. (2003) Germline transmission of RNAi in mice. Nat. Struct. Biol. 10, 91-92.
4. Carninci, P., Nishiyama, Y., Westover, A., Itoh, M., Nagaoka, S., Sasaki, N., Okazaki, Y., Muramatsu, M. and Hayashizaki, Y. (1998) Thermostabilization and thermoactivation of thermolabile enzymes by trehalose and its application for the synthesis of full length cDNA. Proc. Natl Acad. Sci. USA, 95, 520-524.
5. Carrington, J.C. and Ambros, V. (2003) Role of microRNAs in plant and animal development. Science, 301, 336-338.
6. Cerutti, H. (2003) RNA interference: traveling in the cell and gaining functions? Trends Genet. 19, 39-46.
7. Chen, S., Hofius, D., Sonnewald, U. and Börnke, F. (2003) Temporal and spatial control of gene silencing in transgenic plants by inducible expression of double-stranded RNA. Plant J. 36, 731-740.
8. Chuang, C.F. and Meyerowitz, E.M. (2000) Specific and heritable genetic interference by double-stranded RNA in Arabidopsis thaliana. Proc. Natl Acad. Sci. USA, 97, 4985-4990.
9. Cutter, A.D., Payseur, B.A., Salcedo, T. et al. (2003) Molecular correlates of genes exhibiting RNAi phenotypes in Caenorhabditis elegans. Genome Res. 13, 2651-2657.
10. Dudley, N.R., Labbe, J.C. and Goldstein, B. (2002) Using RNA interference to identify genes required for RNA interference. Proc. Natl Acad. Sci. USA, 99, 4191-4196.
11. Dykxhoorn, D.M., Novina, C.D. and Sharp, P.A. (2003) Killing the messenger: short RNAs that silence gene expression. Nat. Rev. Mol. Cell Biol. 4, 457-467.
12. Fuhrmann, M., Stahlberg, A., Govorunova, E., Rank, S. and Hegemann, P. (2001) The abundant retinal protein of the Chlamydomonas eye is not the photoreceptor for phototaxis and photophobic responses. J. Cell Sci. 114, 3857-3863.
13. Goldschmidt-Clermont, M. and Rahire, M. (1986) Sequence, evolution and differential expression of the two genes encoding variant small subunits of ribulose bisphosphate carboxylase/oxygenase in Chlamydomonas reinhardtii. J. Mol. Biol. 191, 421-432.
14. Gonczy, P., Echeverri, C., Oegema, K. et al. (2000) Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature, 408, 331-336.
15. Gossele, V., Fache, I., Meulewaeter, F., Cornelissen, M. and Metzlaff, M. (2002) SVISS - a novel transient gene silencing system for gene function discovery and validation in tobacco plants. Plant J. 32, 859-866.
16. Greene, E.A., Codomo, C.A., Taylor, N.E. et al. (2003) Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis. Genetics, 164, 731-740.
17. Guo, H.-S., Fei, J.-F., Xie, Q. and Chua, N.H. (2003) A chemical-regulated inducible RNAi system in plants. Plant J. 34, 383-392.
18. Hamilton, A.J. and Baulcombe, D.C. (1999) A species of small antisense RNA in posttranscriptional gene silencing in plants. Science, 286, 950-952.
19. Han, Y., Griffiths, A., Li, H. and Grierson, D. (2004) The effect of endogenous mRNA levels on co-suppression in tomato. FEBS Lett. 563, 123-128.
20. Hanin, M. and Paszkowski, J. (2003) Plant genome modification by homologous recombination. Curr. Opin. Plant Biol. 6, 157-162.
21. Hannon, G.J. (2002) RNA interference. Nature, 418, 244-251.
22. Harris, E.H. (1989) The Chlamydomonas Sourcebook - A Comprehensive Guide to Biology and Laboratory Use. San Diego: Academic Press.
23. Hemann, M.T., Fridman, U.S., Zilfou, J.T., Hernando, E., Paddison, P.J., Cordon-Cardo, C., Hannon, G.J. and Lowe, S.W. (2003) An epi-allelic series of p53 hypomorphs created by stable RNAi produces distinct tumor phenotypes in vivo. Nat. Genet. 33, 396-400.
24. Hope, I.A. (2001) Broadcast interference - functional genomics. Trends Genet. 17, 297-299.
25. Iida, S. and Terada, R. (2004) A tale of two integrations, transgene and T-DNA: gene targeting by homologous recombination in rice. Curr. Opin. Biotech. 15, 132-138.
26. Kalidas, S. and Smith, D.P. (2002) Novel genomic cDNA hybrids produce effective RNA interference in adult Drosophila. Neuron, 33, 177-184.
27. Kamath, R.S., Fraser, A.G., Dong, Y. et al. (2003) Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature, 421, 231-237.
28. Kennerdell, J.R. and Carthew, R.W. (2000) Heritable gene silencing in Drosophila using double-stranded RNA. Nat. Biotechnol. 18, 896-898.
29. Kerschen, A., Napoli, C.A., Jorgensen, R.A. and Müller, A.E. (2004) Effectiveness of RNA interference in transgenic plants. FEBS Lett. 566, 223-228.
30. Khrebtukova, I. and Spreitzer, R.J. (1996) Elimination of the Chlamydomonas gene family that encodes the small subunit of ribulose-1,5- bisphosphate carboxylase/oxygenase. Proc. Natl Acad. Sci. USA, 93, 13689-13693.
31. Kindle, K.L. (1990) High frequency nuclear transformation of Chlamydomonas reinhardtii. Proc. Natl Acad. Sci. USA, 87, 1228-1232.
32. Klahre, U., Crete, P., Leuenberger, S.A., Iglesias, V.A. and Meins, F., Jr (2002) High molecular weight RNAs and small interfering RNAs induce systemic posttranscriptional gene silencing in plants. Proc. Natl Acad. Sci. USA, 99, 11981-11986.
33. Kusaba, M. (2004) RNA interference in crop plants. Curr. Opin. Biotechnol. 15, 139-143.
34. Lawrence, R.J. and Pikaard, C.S. (2003) Transgene-induced RNA interference: a strategy for overcoming gene redundancy in polyploids to generate loss-of-function mutations. Plant J. 36, 114-121.
35. Lemaire, S.D., Collin, V., Keryer, E., Quesada, A. and Miginiac-Maslow, M. (2003) Characterization of thioredoxin y, a new type of thioredoxin identified in the genome of Chlamydomonas reinhardtii. FEBS Lett. 543, 87-92.
36. Liu, H., Cottrell, T.R., Pierini, L.M., Goldman, W.E. and Doering, T.L. (2002) RNA interference in the pathogenic fungus Cryptococcus neoformans. Genetics, 160, 463-470.
37. Longman, D., McGarvey, T., McCracken, S., Johnstone, I.L., Blencowe, B.J. and Céceres, J.F. (2001) Multiple interactions between SRm160 and SR family proteins in enhancer-dependent splicing and development in C. elegans. Curr. Biol. 11, 1923-1933.
38. Lumbreras, V., Stevens, D.R. and Purton, S. (1998) Efficient foreign gene expression in Chlamydomonas reinhardtii mediated by an endogenous intron. Plant J. 14, 441-447.
39. Matzke, M., Matzke, A.J. and Kooter, J.M. (2001) RNA: guiding gene silencing. Science, 293, 1080-1083.
40. Matzke, M., Aufsatz, W., Kanno, T., Daxinger, L., Papp, I., Mette, M.F. and Matzke, A.J. (2004) Genetic analysis of RNA-mediated transcriptional gene silencing. Biochim. Biophys. Acta, 15, 129-141.
41. Miki, D. and Shimamoto, K. (2004) Simple RNAi vectors for stable and transient suppression of gene function in rice. Plant Cell Physiol. 45, 490-495.
42. Misquitta, L. and Paterson, B.M. (1999) Targeted disruption of gene function in Drosophila by RNA interference (RNA-i): a role for nautilus in embryonic somatic muscle formation. Proc. Natl Acad. Sci. USA, 96, 1451-1456.
43. Mittal, V. (2004) Improving the efficiency of RNA interference in mammals. Nat. Rev. Genet. 5, 355-365.
44. Murchison, E.P. and Hannon, G.J. (2004) miRNAs on the move: miRNA biogenesis and the RNAi machinery. Curr. Opin. Cell Biol. 16, 223-229.
45. Paddison, P.J. and Hannon, G.J. (2002) RNA interference: the new somatic cell genetics? Cancer Cell, 2, 17-23.
46. Paddison, P.J., Silva, J.M., Conklin, D.S. et al. (2004) A resource for large-scale RNA-interference-based screens in mammals. Nature, 428, 427-431.
47. Palombella, A.L. and Dutcher, S.K. (1998) Identification of the gene encoding the tryptophan synthase β-subunit from Chlamydomonas reinhardtii. Plant Physiol. 117, 455-464.
48. Parrish, S., Fleenor, J., Xu, S., Mello, C. and Fire, A. (2000) Functional anatomy of a dsRNA trigger: differential requirement for the two trigger strands in RNA interference. Mol. Cell, 6, 1077-1087.
49. Paul, C.P., Good, P.D., Winer, I. and Engelke, D.R. (2002) Effective expression of small interfering RNA in human cells. Nat. Biotechnol. 20, 505-508.
50. Peele, C., Jordan, C.V., Muangsan, N., Turnage, M., Egelkrout, E., Eagle, P., Hanley-Bowdoin, L. and Robertson, D. (2001) Silencing of a meristematic gene using geminivirus-derived vectors. Plant J. 27, 357-366.
51. Piccin, A., Salameh, A., Benna, C., Sandrelli, F., Mazzotta, G., Zordan, M., Rosato, E., Kyriacou, C.P. and Costa, R. (2001) Efficient and heritable functional knock-out of an adult phenotype in Drosophila using a GAL-4 driven hairpin RNA incorporating a heterologous spacer. Nucleic Acids Res. 29, e55.
52. Plasterk, R.H.A. (2002) RNA silencing: the genome's immune system. Science, 296, 1263-1265.
53. Ratcliff, F., Martin-Hernandez, A.M. and Baulcombe, D.C. (2001) Tobacco rattle virus as a vector for analysis of virus-induced gene silencing. Plant J. 25, 237-245.
54. Robertson, D. (2004) VIGS vectors for gene silencing: many targets, many tools. Annu. Rev. Plant Biol. 55, 495-519.
55. Sambrook, J. and Russell, D.W. (2001) Molecular Cloning - A Laboratory Manual. Cold Spring Harbor: Cold Spring Harbor Laboratory Press.
56. Schmid, A., Schindelholz, B. and Zinn, K. (2002) Combinatorial RNAi: a method for evaluating the functions of gene families in Drosophila. Trends Neurosci. 25, 71-74.
57. Schweizer, P., Pokorny, J., Schulze-Lefert, P. and Dudler, R. (2000) Double-stranded RNA interferes with gene function at the single-cell level in cereals. Plant J. 24, 895-903.
58. Shi, H., Djikeng, A., Mark, T., Wirtz, E., Tschudi, C. and Ullu, E. (2000) Genetic interference in Trypanosoma brucei by heritable and inducible double-stranded RNA. RNA, 6, 1069-1076.
59. Simmer, F., Moorman, C., van der Linden, A.M., Kuijk, E., van den Berghe, P.V.E., Kamath, R.S., Fraser, A.G., Ahringer, J. and Plasterk, R.H.A. (2003) Genome-wide RNAi of C. elegans using the hypersensitive rrf-3 strain reveals novel gene functions. PLoS Biol. 1, 77-84.
60. Sizova, I., Fuhrmann, M. and Hegemann, P.A. (2001) Streptomyces rimosus aph VIII gene coding for a new type phosphotransferase provides stable antibiotic resistance to Chlamydomonas reinhardtii. Gene, 277, 221-229.
61. Smith, N.A., Singh, S.P., Wang, M.B., Stoutjesdijk, P.A., Green, A.G. and Waterhouse, P.M. (2000) Total silencing by intron-spliced hairpin RNAs. Nature, 407, 319-320.
62. 2. Proc. Natl Acad. Sci. USA, 101, 7787-7792.
63. Stein, M., Jacquot, J.P., Jeannette, E., Decottignies, P., Hodges, M., Lancelin, J.M., Mittard, V., Schmitter, J.M. and Miginiac-Maslow, M. (1995) Chlamydomonas reinhardtii thioredoxins: structure of the genes coding for the chloroplastic m and cytosolic h isoforms; expression in Escherichia coli of the recombinant proteins, purification and biochemical properties. Plant Mol. Biol. 28, 487-503.
64. Tamura, K., Adachi, Y., Chiba, K., Oguchi, K. and Takahashi, H. (2002) Identification of Ku70 and Ku80 homologues in Arabidopsis thaliana: evidence for a role in the repair of DNA double-strand breaks. Plant J. 29, 771-781.
65. Tavernarakis, N., Wang, S.L., Dorovkov, M., Ryazanov, A. and Driscoll, M. (2000) Heritable and inducible genetic interference by double-stranded RNA encoded by transgenes. Nat. Genet. 24, 180-183.
66. Waterhouse, P.M. and Helliwell, C.A. (2003) Exploring plant genomes by RNA-induced gene silencing. Nat. Rev. Genet. 4, 29-38.
67. Wesley, S.V., Helliwell, C.A., Smith, N.A. et al. (2001) Construct design for efficient, effective and high-throughput gene silencing in plants. Plant J. 27, 581-590.
68. Williams, R.W. and Rubin, G.M. (2002) ARGONAUTE1 is required for efficient RNA interference in Drosophila embryos. Proc. Natl Acad. Sci. USA, 99, 6889-6894.
69. Wu-Scharf, D., Jeong, B.-r., Zhang, C. and Cerutti, H. (2000) Transgene and transposon silencing in Chlamydomonas reinhardtii by a DEAH-box RNA helicase. Science, 290, 1159-1162.
70. Yang, D., Lu, H. and Erickson, J.W. (2001) Evidence that processed small dsRNAs may mediate sequence-specific mRNA degradation during RNAi in Drosophila embryos. Curr. Biol. 10, 1191-1200.
71. Yu, J.Y., Taylor, J., DeRuiter, S.L., Vojtek, A.B. and Turner, D.L. (2003) Simultaneous inhibition of GSK3alpha and GSK3beta using hairpin siRNA expression vectors. Mol. Ther. 7, 228-236.
72. Zamore, P.D. (2002) Ancient pathways programmed by small RNAs. Science, 296, 1265-1269.
73. Zhang, C., Wu-Scharf, D., Jeong, B.-r. and Cerutti, H. (2002) A WD40-repeat containing protein, similar to a fungal co-repressor, is required for transcriptional gene silencing in Chlamydomonas. Plant J. 31, 25-36.