Toward the gene catalogue of sea urchin development: The construction and analysis of an unfertilized egg cDNA library highly normalized by oligonucleotide fingerprinting

Genomics

Volumn 59, Issue 2, 1999, Pages 122-133

  Poustka, Albert J ^a   Herwig, Ralf ^a   Krause, Antje ^b   Hennig, Steffen ^a   Meier Ewert, Sebastian ^a   Lehrach, Hans ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^b GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; OLIGONUCLEOTIDE;

ANIMAL CELL; ARTICLE; CHROMOSOME IDENTIFICATION; DNA FINGERPRINTING; DNA LIBRARY; EGG; GENE SEQUENCE; HYBRIDIZATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEA URCHIN; SEQUENCE ANALYSIS;

ANIMALIA; ECHINOIDEA; INVERTEBRATA;

EID: 0033566228     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1006/geno.1999.5852     Document Type: Article

References (57)

1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
2. Altschul S. F., Madden T. L., Schaffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
3. Arnone M. I., Bogarad L. D., Collazo A., Kirchhamer C. V., Cameron R. A., Rast J. P., Gregorians A., Davidson E. H. Green fluorescent protein in the sea urchin: New experimental approaches to transcriptional regulatory analysis in embryos and larvae. Development. 124:1997;4649-4659.
4. Arnone M. I., Davidson E. H. The hardwiring of development: Organization and function of genomic regulatory systems. Development. 124:1997;1851-1864.
5. Bachvarova R., Davidson E. H., Allfrey V. G., Mirsky A. E. Activation of RNA synthesis associated with gastrulation. Proc. Natl. Acad. Sci. USA. 55:1966;358-365.
6. Beck S., Kelly A., Radley E., Khurshid F., Alderton R. P., Trowsdale J. DNA sequence analysis of 66 kb of the human MHC class II region encoding a cluster of genes for antigen processing. J. Mol. Biol. 228:1992;433-441.
7. Bisgrove B. W., Raff R. A. The SpEGF III gene encodes a member of the fibropellins: EGF repeat-containing proteins that form the apical lamina of the sea urchin embryo. Dev. Biol. 157:1993;526-538.
8. Bogarad L. D., Arnone M. I., Chang C., Davidson E. H. Interference with gene regulation in living sea urchin embryos: Transcription factor knock out (TKO), a genetically controlled vector for blockade of specific transcription factors. Proc. Natl. Acad. Sci. USA. 95:1998;14827-14832.
9. Bonaldo M. F., Lennon G., Soares M. B. Normalization and subtraction: Two approaches to facilitate gene discovery. Genome Res. 6:1996;791-806.
10. Bowerman B., Ingram M. K., Hunter C. P. The maternal par genes and the segregation of cell fate specification activities in early Caenorhabditis elegans embryos. Development. 124:1997;3815-3826.
11. Burge C., Karlin S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268:1997;78-94.
12. Calzone F. J., Lee J. J., Le N., Britten R. J., Davidson E. H. A long, nontranslatable poly(A) RNA stored in the egg of the sea urchin Strongylocentrotus purpuratus. Genes Dev. 2:1988;305-318.
13. Chen C. Y., Shyu A. B. AU-rich elements: Characterization and importance in mRNA degradation. Trends Biochem. Sci. 20:1995;465-470.
14. + RNAs. Nature. 287:1980;111-117.
15. Costantini F. D., Scheller R. H., Britten R. J., Davidson E. H. Repetitive sequence transcripts in the mature sea urchin oocyte. Cell. 15:1978;173-187.
16. Davidson E. H. Gene Activity in Early Development. 1986;Acadamic Press, Orlando.
17. Davidson E. H., Britten R. J. Regulation of gene expression: Possible role of repetitive sequences. Science. 204:1979;1052-1059.
18. Davidson E. H., Hough B. R. Genetic information in oocyte RNA. J. Mol. Biol. 56:1971;491-506.
19. Deshler J. O., Highett M. I., Schnapp B. J. Localization of Xenopus Vg1 mRNA by Vera protein and the endoplasmic reticulum. Science. 276:1997;1128-1131.
20. Draper B. W., Mello C. C., Bowerman B., Hardin J., Priess J. R. MEX-3 is a KH domain protein that regulates blastomere identity in early C. elegans embryos. Cell. 87:1996;205-216.
21. Drmanac R., Strezoska Z., Labat I., Drmanac S., Crkvenjakov R. Reliable hybridization of oligonucleotides as short as six nucleotides. DNA Cell Biol. 9:1990;527-534.
22. Drmanac S., Stavropoulos N. A., Labat I., Vonau J., Hauser B., Soares M. B., Drmanac R. Gene-representing cDNA clusters defined by hybridization of 57,419 clones from infant brain libraries with short oligonucleotide probes. Genomics. 37:1996;29-40.
23. Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 132:1983;6-13.
24. Galau G. A., Klein W. H., Davis M. M., Wold B. J., Britten R. J., Davidson E. H. Structural gene sets active in embryos and adult tissues of the sea urchin. Cell. 7:1976;487-505.
25. Gish W., States D. J. Identification of protein coding regions by database similarity search. Nat. Genet. 3:1993;266-272.
26. Gress T. M., Hoheisel J. D., Lennon G. G., Zehetner G., Lehrach H. Hybridization fingerprinting of high-density cDNA-library arrays with cDNA pools derived from whole tissues. Mamm. Genome. 3:1992;609-619.
27. Gross P. R., Cousineau G. H. Macromolecular synthesis and the influence of actinomycin D on early development. Exp. Cell Res. 33:1964;368-395.
28. Grunert S., St. Johnston D. RNA localization and the development of asymmetry during Drosophila oogenesis. Curr. Opin. Genet. Dev. 6:1996;395-402.
29. Harada Y., Yasuo H., Satoh N. A sea urchin homologue of the chordate Brachyury (T) gene is expressed in the secondary mesenchyme founder cells. Dev. 121:1995;2747-2754.
30. Holland P. W., G.-F. J., Williams N. A., Sidow A. Gene duplications and the origins of vertebrate development. Dev. Suppl. 36:1994;125-133.
31. Hough-Evans B. R., Ernst S. G., Britten R. J., Davidson E. H. RNA complexity in developing sea urchin oocytes. Dev. Biol. 69:1979;258-269.
32. Hough-Evans B. R., Wold B. J., Ernst S. G., Britten R. J., Davidson E. H. Appearance and persistence of maternal RNA sequences in sea urchin development. Dev. Biol. 60:1977;258-277.
33. Kirchhamer C. V., Yuh C. H., Davidson E. H. Modular cis-regulatory organization of developmentally expressed genes: Two genes transcribed territorially in the sea urchin embryo, and additional examples. Proc. Natl. Acad. Sci. USA. 93:1996;9322-9328.
34. Lai E. C., Burks C., Posakony J. W. The K box, a conserved 3′ UTR sequence motif, negatively regulates accumulation of enhancer of split complex transcripts. Development. 125:1998;4077-4088.
35. Lee R. C., Feinbaum R. L., Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 75:1993;843-854.
36. Lennon G., Auffray C., Polymeropoulos M., Soares M. B. The I.M.A.G.E. Consortium: An integrated molecular analysis of genomes and their expression. Genomics. 33:1996;151-152.
37. Maier E., Meier-Ewert S., Ahmadi A. R., Curtis J., Lehrach H. Application of robotic technology to automated sequence fingerprint analysis by oligonucleotide hybridisation. J. Biotechnol. 35:1994;191-203.
38. Mandl B., Brandt W. F., Superti-Furga G., Graninger P. G., Birnstiel M. L., Busslinger M. The five cleavage-stage (CS) histones of the sea urchin are encoded by a maternally expressed family of replacement histone genes: Functional equivalence of the CS H1 and frog H1M (B4) proteins. Mol. Cell. Biol. 17:1997;1189-1200.
39. Mehlhorn K., Naher S. LEDA: A platform for combinatorial and geometric computing. Commun. ACM. 83:1995;96-102.
40. Meier-Ewert S., Lange J., Gerst H., Herwig R., Schmitt A., Freund J., Elge T., Mott R., Herrmann B., Lehrach H. Comparative gene expression profiling by oligonucleotide fingerprinting. Nucleic Acids Res. 26:1998;2216-2223.
41. Meier-Ewert S., Maier E., Ahmadi A., Curtis J., Lehrach H. An automated approach to generating expressed sequence catalogues. Nature. 361:1993;375-376.
42. Milosavljevic A., Zeremski M., Strezoska Z., Grujic D., Dyanov H., Batus S., Salbego D., Paunesku T., Soares M. B., Crkvenjakov R. Discovering distinct genes represented in 29,570 clones from infant brain cDNA libraries by applying sequencing by hybridization methodology. Genome Res. 6:1996;132-141.
43. Popodi E., Kissinger J. C., Andrews M. E., Raff R. A. Sea urchin Hox genes: Insights into the ancestral Hox cluster. Mol. Biol. Evol. 13:1996;1078-1086.
44. Posakony J. W., Scheller R. H., Anderson D. M., Britten R. J., Davidson E. H. Repetitive sequences of the sea urchin genome. Nucleotide sequences of cloned repeat elements. J. Mol. Biol. 149:1981;41-67.
45. Poustka A., Pohl T., Barlow D. P., Zehetner G., Craig A., Michiels F., Ehrich E., Frischauf A. M., Lehrach H. Molecular approaches to mammalian genetics. Cold Spring Harbor Symp. Quant. Biol. 51:1986;131-139.
46. Radelof U., Hennig S., Seranski P., Steinfath M., Ramser J., Reinhardt R., Poustka A., Francis F., Lehrach H. Preselection of shotgun clones by oligonucleotide fingerprinting: An efficient and high throughput strategy to reduce redundancy in large-scale sequencing projects. Nucleic Acids Res. 26:1998;5358-5364.
47. Ross J. mRNA stability in mammalian cells. Microbiol. Rev. 59:1995;423-450.
48. Schena M., Shalon D., Davis R. W., Brown P. O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 270:1995;467-470.
49. Sidow A. Gen(om)e duplications in the evolution of early vertebrates. Curr. Opin. Genet. Dev. 6:1996;715-722.
50. Sokal R. R., Sneath P. H. A. Principles of Numerical Taxonomy. 1963;Freeman, London.
51. Wang J., Dong Z., Bell L. R. Sex-lethal interactions with protein and RNA. Roles of glycine-rich and RNA binding domains. J. Biol. Chem. 272:1997;22227-22235.
52. Wickens M., Anderson P., Jackson R. J. Life and death in the cytoplasm: Messages from the 3′ end. Curr. Opin. Genet. Dev. 7:1997;220-232.
53. Wylie C., Kofron M., Payne C., Anderson R., Hosobuchi M., Joseph E., Heasman J. Maternal beta-catenin establishes a 'dorsal signal' in early Xenopus embryos. Development. 122:1996;2987-2996.
54. Yamaha E., Mizuno T., Hasebe Y., Takeda H., Yamazaki F. Dorsal specification in blastoderm at the blastula stage in the goldfish, Carassius auratus. Dev. Growth Differ. 40:1998;267-275.
55. Yuh C. H., Bolouri H., Davidson E. H. Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene. Science. 279:1998;1896-1902.
56. Yulug I. G., Yulug A., Fisher E. M. The frequency and position of Alu repeats in cDNAs, as determined by database searching. Genomics. 27:1995;544-548.
57. Zhang M. Q. Identification of protein coding regions in the human genome by quadratic discriminant analysis. Proc. Natl. Acad. Sci. USA. 94:1997;565-568.