Generation of an oligonucleotide array for analysis of gene expression in Chlamydomonas reinhardtii

Current Genetics

Volumn 49, Issue 2, 2006, Pages 106-124

  Eberhard, Stephan ^a,b   Jain, Monica ^a   Im, Chung Soon ^a   Pollock, Steve ^a   Shrager, Jeff ^a   Lin, Yuan ^c   Peek, Andrew S ^c   Grossman, Arthur R ^a  

^a GEOPHYSICAL LABORATORY   (United States)

^b National de la Recherche Scientifique Université Pierre et Marie Curie   (France)

^c INTEGRATED DNA TECHNOLOGIES   (United States)

Author keywords

Chlamydomonas; Gene expression; Genomics; Oligo array

Indexed keywords

COMPLEMENTARY DNA; TRANSCRIPTOME;

ARTICLE; CHLAMYDOMONAS REINHARDTII; CONTROLLED STUDY; DNA CONTENT; DNA LIBRARY; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE SEQUENCE; GENETIC CODE; GENETIC CONSERVATION; NONHUMAN; PRIORITY JOURNAL; QUALITY CONTROL; RNA ISOLATION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE;

ANIMALS; CELL NUCLEUS; CHLAMYDOMONAS REINHARDTII; DATABASES, NUCLEIC ACID; GENE EXPRESSION PROFILING; GENES, PROTOZOAN; GENOME, PROTOZOAN; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SULFUR;

CHLAMYDOMONAS; CHLAMYDOMONAS REINHARDTII;

EID: 31444451295     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00294-005-0041-2     Document Type: Article

References (59)

1. Asamizu E, Nakamura Y, Sato S, Fukuzawa H, Tabata S (1999) A large scale structural analysis of cDNAs in a unicellular green alga, Chlamydomonas reinhardtii I Generation of 3433 non-redundant expressed sequence tags. DNA Res 6:369-373
2. 2 adapted cells of Chlamydomonas reinhardtii. DNA Res 7:305-307
3. Barrett JC, Kawasaki ES (2003) Microarrays: The use of oligonucleotides and cDNA for the analysis of gene expression. Drug Discov Today 8(3):134-141
4. Choudhuri S (2004) Microarrays in biology and medicine. J Biochem Mol Toxicol 18:171-179
5. Davies J, Yildiz F, Grossman AR (1996) Sac1, a putative regulator that is critical for survival of Chlamydomonas reinhardtii during sulfur deprivation. EMBO J 15:2150-2159
6. Dent RM, Han M, Niyogi KK (2001) Functional genomics of plant photosynthesis in the fast lane using Chlamydomonas reinhardtii. Trends Plant Sci 6:364-371
7. Dharmadi Y, Gonzalez R (2004) DNA microarrays: Experimental issues, data analysis, and application to bacterial systems. Biotechnol Prog 20:1309-1324
8. Dutcher SK (2000) Chlamydomonas reinhardtii: Biological rationale for genomics. J Eukaryot Microbiol 47:340-349
9. Dutcher SK (2003) Elucidation of basal body and centriole functions in Chlamydomonas reinhardtii. Traffic 4:443-451
10. Elrad D, Grossman AR (2004) A genome's-eye view of the light-harvesting polypeptides of Chlamydomonas reinhardtii. Curr Genet 45:61-75
11. Grossman AR (2000) Chlamydomonas reinhardtii and photosynthesis: genetics to genomics. Curr Opin Plant Biol 3:132-137
12. Grossman AR, Harris EE, Hauser C, Lefebvre PA, Martinez D, Rokhsar D, Shrager J, Silflow CD, Stern D, Vallon O, Zhang Z (2003) Chlamydomonas reinhardtii at the crossroads of genomics. Eukaryot Cell 2:1137-1150
13. Grossman AR, Lohr M, Im CS (2004) Chlamydomonas reinhardtii in the landscape of pigments. Annu Rev Genet 38:119-173
14. Harris EH (2001) Chlamydomonas as a model organism. Annu Rev Plant Physiol Plant Mol Biol 52:363-406
15. He Z, Wu L, Fields MW, Zhou J (2005) Use of microarrays with different probe sizes for monitoring gene expression. Appl Environ Microbiol 71(9):5154-5162
16. Hollingshead D, Lewis DA, Mirnics K (2005) Platform influence on DNA microarray data in postmortem brain research. Neurobiol Dis 18(3):649-655
17. Huang K, Merkle T, Beck CF (2002) Isolation and characterization of a Chlamydomonas gene that encodes a putative blue-light photoreceptor of the phototropin family. Physiol Plant 115:613-622
18. Im CS, Grossman AR (2002) Identification and regulation of high light-induced genes in Chlamydomonas reinhardtii. Plant J 30:301-313
19. Kamiya R (2002) Functional diversity of axonemal dyneins as studied in Chlamydomonas mutants. Int Rev Cytol 219:115-155
20. Kane MD, jatkoe TA, Stumpf CR, Lu J, Thomas JD, Madore SJ (2000) Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res 28(22):4552-4557
21. Kateriya S, Nagel G, Bamberg E, Hegemann P (2004) "Vision" in single-celled algae. News Physiol Sci 19:133-137
22. Kim HL (2003) Comparison of oligonucleotide-microarray and serial analysis of gene expression (SAGE) in transcript profiling analysis of megakaryocytes derived from CD34+ cells. Exp Mol Med 35:460-466
23. Kothapalli R, Yoder SJ, Mane S, Loughran TP Jr (2002) Microarray results: How accurate are they? BMC Bioinform 3:22
24. Kuo WP, Jenssen T-K, Butte AJ, Ohno-Machado L, Kohane IS (2002) Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 18:405-412
25. LaFontaine S, Quinn JM, Nakamoto SS, Page MD, Gohre V, Moseley JL, Kropat J, Merchant S (2002) Copper-dependent iron assimilation pathway in the model photosynthetic eukaryote Chlamydomonas reinhardtii. Eukaryot Cell 1:736-757
26. Ledford HK, Baroli I, Shin JW, Fischer BB, Eggen RI, Niyogi KK (2004) Comparative profiling of lipid-soluble antioxidants and transcripts reveals two phases of photo-oxidative stress in a xanthophyll-deficient mutant of Chlamydomonas reinhardtii. Mol Genet Genomics 272:470-479
27. Li JB, Gerdes JM, Haycraft CJ, Fan Y, Teslovich TM, May-Simera H, Li H, Blacque OE, Li L, Leitch CC, Lewis RA, Green JS, Parfrey PS, Leroux MR, Davidson WS, Beales PL, Guay-Woodford LM, Yoder BK, Stormo GD, Katsanis N, Dutcher SK (2004) Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene. Cell 117:541-552
28. Lohr M, Im CS, Grossman AR (2005) Genome-based examination of chlorophyll and carotenoid biosynthesis in Chlamydomonas reinhardtii. Plant Physiol 138:490-515
29. Mantripragada KK, Buckley PG, de Stahl TD, Dumanski JP (2004) Genomic microarrays in the spotlight. Trends Genet 20:87-94
30. Mittag M, Wagner V (2003) The circadian clock of the unicellular eukaryotic model organism Chlamydomonas reinhardti i. Biol Chem 384:689-695
31. Mittag M, Kiaulehn S, Johnson CH (2005) The circadian clock in Chlamydomonas reinhardtii. What is it for? What is it similar to? Plant Physiol 137:399-409
32. 2-responsive genes regulated by CCM1 controlling a carbon-concentrating mechanism in Chlamydomonas reinhardtii. Plant Physiol 135:1595-1607
33. Moseley JL, Chang, C-W, Grossman AR (2005) Genome-based approaches to understanding phosphorus deprivation responses and PSR1 Control in Chlamydomonas reinhardtii. Eukaryot Cell (in press)
34. Nagel G, Szellas T, Huhn W, Kateriya S, Adeishvili N, Berthold P, Ollig D, Hegemann P, Bamberg E (2003) Channelrhodopsin-2, a directly light-gated cation-selective membrane channel. Proc Natl Acad Sci USA 100:13940-13945
35. Omran H, Haffner K, Volkel A, Kuehr J, Ketelsen UP, Ross UH, Konietzko N, Wienker T, Brandis M, Hildebrandt F (2000) Homozygosity mapping of a gene locus for primary ciliary dyskinesia on chromosome 5p and identification of the heavy dynein chain DNAH5 as a candidate gene. Am J Respir Cell Mol Biol 23:696-702
36. Park PJ, Cao YA, Lee SY, Kim JW, Chang MS, Hart R, Choi S (2004) Current issues for DNA microarrays: Platform comparison, double linear amplification and universal RNA reference. J Biotech 112:225-245
37. Pazour GJ (2004) Intraflagellar transport and cilia-dependent renal disease: The ciliary hypothesis of polycystic kidney disease. J Am Soc Nephrol 15:2528-2536
38. Pazour GJ, Dickert BL, Vucica Y, Seeley ES, Rosenbaum JL, Witman GB, Cole DG (2000) Chlamydomonas IFT88 and its mouse homologue, polycystic kidney disease gene tg737, are required for assembly of cilia and flagella. J Cell Biol 151:709-718
39. Petersen D, Chandramouli GVR, Geoghegan J, Hilburn J, Paarlberg J, Kim CH, Munroe D, Gangi L, Han J, Puri R, Staudt L, Weinstein J, Barret JC, Green J, Kawasaki ES (2005) Three microarray platforms: An analysis of their concordance in profiling gene expression. BMC Genomics 6(1):63
40. Qin H, Rosenbaum JL, Barr MM (2001) An autosomal recessive polycystic kidney disease gene homolog is involved in intraflagellar transport in C. elegans ciliated sensory neurons. Curr Biol 11:457-461
41. Rochaix JD (2002) Chlamydomonas, a model system for studying the assembly and dynamics of photosynthetic complexes. FEBS Lett 529:34-38
42. Rochaix JD (2004) Genetics of the biogenesis and dynamics of the photosynthetic machinery in eukaryotes. Plant Cell 16:1650-1660
43. Scholey JM (2003) Intraflagellar transport. Annu Rev Cell Dev Biol 19:423-443
44. Shrager J, Hauser C, Chang CW, Harris EH, Davies J, McDermott J, Tamse R, Zhang Z, Grossman AR (2003) Chlamydomonas reinhardtii genome project. A guide to the generation and use of the cDNA information. Plant Physiol 131:401-408
45. Silflow CD, Lefebvre PA (2001) Assembly and motility of eukaryotic cilia and flagella. Lessons from Chlamydomonas reinhardtii. Plant Physiol 127:1500-1507
46. Sineshchekov OA, Jung KH, Spudich JL (2002) The rhodopsins mediate phototaxis to low- and high-intensity light in Chlamydomonas reinhardtii. Proc Natl Acad Sci USA 99:225-230
47. Snell WJ, Pan J, Wang Q (2004) Cilia and flagella revealed: From flagellar assembly in Chlamydomonas to human obesity disorders. Cell 117:693-697
48. Stauber EJ, Fink A, Markert C, Kruse O, Johanningmeier U, Hippler M (2003) Proteomics of Chlamydomonas reinhardtii light-harvesting proteins. Eukaryot Cell 2:978-994
49. Stears RL, Martinsky T, Schena M (2003) Trends in microarray analysis. Nature Med 9(1):140-145
50. Stoughton RB (2005) Applications of DNA microarrays in biology. Annu Rev Biochem 74:53-82
51. Takahashi H, Braby CE, Grossman AR (2001) Sulfur economy and cell wall biosynthesis during sulfur limitation of Chlamydomonas reinhardtii. Plant Physiol 127:665-673
52. Tan PK, Downey TJ, Spitznagel EL Jr, Xu P, Fu D, Dimitrov DS, Lempicki RA, Raaka BM, Cam MC (2003) Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 31:5676-5684
53. Tiquia SM, Wu L, Chong SC, Passovets S, Xu D, Xu Y, Zhou J (2004) Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Bio Tech 36(4):664-675
54. Wagner V, Fiedler M, Markert C, Hippler M, Mittag M (2004) Functional proteomics of circadian expressed proteins from Chlamydomonas reinhardtii. FEBS Lett 559:129-135
55. Wang H, He X, Band M, Wilson C, Liu L (2005) A study of inter-lab and inter-platform agreement of DNA microarray data. BMC Genomics 6(1):71
56. Werner R (2002) Chlamydomonas reinhardtii as a unicellular model for circadian rhythm analysis. Chronobiol Int 19:325-343
57. Wostrikoff K, Girard-Bascou J, Wollman FA, Choquet Y (2004) Biogenesis of PSI involves a cascade of translational autoregulation in the chloroplast of Chlamydomonas. EMBO J 23:2696-2705
58. Wykoff D, Grossman A, Weeks DP, Usuda H, Shimogawara K (1999) Psr1, a nuclear localized protein that regulates phosphorus metabolism in Chlamydomonas. Proc Natl Acad Sci USA 96:15336-15341
59. Zhang Z, Shrager J, Jain M, Chang CW, Vallon O, Grossman AR (2004) Insights into the survival of Chlamydomonas reinhardtii during sulfur starvation based on microarray analysis of gene expression. Eukaryot Cell 3:1331-1348