Homotypic regulatory cluster in Drosophila

Genome Research

Volumn 13, Issue 4, 2003, Pages 579-588

  Lifanov, Alexander P ^a   Makeev, Vsevolod J ^b   Nazina, Anna G ^c   Papatsenko, Dmitri A ^c  

^a SEMENOV INSTITUTE OF CHEMICAL PHYSICS   (Russian Federation)

^b Scientific Center Genetika   (Russian Federation)

^c NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; REGULATOR PROTEIN; TRANSCRIPTION FACTOR;

ANALYTIC METHOD; ARTICLE; CLUSTER ANALYSIS; CONTROLLED STUDY; DEVELOPMENTAL GENETICS; DROSOPHILA; GENE CLUSTER; GENE EXPRESSION REGULATION; GENOME ANALYSIS; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN MOTIF; REGULATOR GENE; TRANSCRIPTION REGULATION; ANIMAL; BIOLOGY; DNA BASE COMPOSITION; DROSOPHILA MELANOGASTER; GENE; GENETICS; HOMEOBOX; METHODOLOGY; MULTIGENE FAMILY; PHYSIOLOGY; REGULATORY SEQUENCE; STATISTICS;

ARACHNIDA; EUKARYOTA; HEXAPODA;

ANIMALS; BASE COMPOSITION; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DROSOPHILA MELANOGASTER; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENES, HOMEOBOX; GENES, INSECT; GENES, REGULATOR; MULTIGENE FAMILY; REGULATORY SEQUENCES, NUCLEIC ACID; TRANSCRIPTION FACTORS;

EID: 0037398319     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.668403     Document Type: Article

References (44)

1. Arnone, M.I. and Davidson, E.H. 1997. The hardwiring of development: Organization and function of genomic regulatory systems. Development 124: 1851-1864.
2. Berg, O.G. and von Hippel, P.H. 1987. Selection of DNA binding sites by regulatory proteins: Statistical mechanical theory and application to operators and promoters. J. Mol. Biol. 193: 723-750.
3. Berg, O.G. and von Hippel, P.H. 1988. Selection of DNA binding sites by regulatory proteins [published erratum appears in Trends Biochem. Sci. 1988 Aug;13(8):301]. Trends Biochem. Sci. 13: 207-211.
4. Berman, B.P., Nibu, Y., Pfeiffer, B.D., Tomancak, P., Celniker, S.E., Levine, M., Rubin, G.M., and Eisen, M.B. 2002. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl. Acad. Sci. 99: 757-762.
5. Coleman, R.A. and Pugh, B.F. 1995. Evidence for functional binding and stable sliding of the TATA binding protein on nonspecific DNA. J. Biol. Chem. 270: 13850-13859.
6. Crowley, E.M., Roeder, K., and Bina, M. 1997. A statistical model for locating regulatory regions in genomic DNA. J. Mol. Biol. 268: 8-14.
7. Driever, W. and Nusslein-Volhard, C. 1988a. The bicoid protein determines position in the Drosophila embryo in a concentration-dependent manner. Cell 54: 95-104.
8. Driever, W. and Nusslein-Volhard, C. 1988b. A gradient of bicoid protein in Drosophila embryos. Cell 54: 83-93.
9. Driever, W., Thoma, G., and Nusslein-Volhard, C. 1989. Determination of spatial domains of zygotic gene expression in the Drosophila embryo by the affinity of binding sites for the bicoid morphogen. Nature 340: 363-367.
10. Eldon, E.D. and Pirrotta, V. 1991. Interactions of the Drosophila gap gene giant with maternal and zygotic pattern-forming genes. Development 111: 367-378.
11. Fortini, M.E. and Rubin, G.M. 1990. Analysis of cis-acting requirements of the Rh3 and Rh4 genes reveals a bipartite organization to rhodopsin promoters in Drosophila melanogaster. Genes & Dev. 4: 444-463.
12. Frith, M.C., Hansen, U., and Weng, Z. 2001. Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics 17: 878-889.
13. Fujioka, M., Emi-Sarker, Y., Yusibova, G.L., Goto, T., and Jaynes, J.B. 1999. Analysis of an even-skipped rescue transgene reveals both composite and discrete neuronal and early blastoderm enhancers, and multistripe positioning by gap gene repressor gradients. Development 126: 2527-2538.
14. Gao, Q. and Finkelstein, R. 1998. Targeting gene expression to the head: The Drosophila orthodenticle gene is a direct target of the Bicoid morphogen. Development 125: 4185-4193.
15. Gao, Q., Wang, Y., and Finkelstein, R. 1996. Orthodenticle regulation during embryonic head development in Drosophila. Mech. Dev. 56: 3-15.
16. Guigó, R., Agarwal, P., Abril, J.F., Burset, M., and Fickett, J.W. 2000. An assessment of gene prediction accuracy in large DNA sequences. Genome Res. 10: 1631-1642.
17. Halfon, M.S., Grad, Y., Church, G.M., and Michelson, A.M. 2002. Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res. 12: 1019-1028.
18. Hertel, K.J., Lynch, K.W., and Maniatis, T. 1997. Common themes in the function of transcription and splicing enhancers. Current Opinions in Cell Biology 9: 350-357.
19. Kassis, J.A. 1990. Spatial and temporal control elements of the Drosophila engrailed gene. Genes & Dev. 4: 433-443.
20. Khory, A.M., Lee, H.J., Lillis, M., and Lu, P. 1990. Lac repressor-operator interaction: DNA length dependence. Biochim. Biophys. Acta 1087: 55-60.
21. Kim, J.G., Takeda, Y., Matthews, B.W., and Anderson, W.F. 1987. Kinetic studies on Cro repressor-operator DNA interaction. J. Mol. Biol. 196: 149-158.
22. Kolpakov, F.A., Ananko, E.A., Kolesov, G.B., and Kolchanov, N.A. 1998. GeneNet: A gene network database and its automated visualization. Bioinformatics 14: 529-537.
23. Kondrakhin, Y.V., Kel, A.E., Kolchanov, N.A., Romashchenko, A.G., and Milanesi, L. 1995. Eukaryotic promoter recognition by binding sites for transcription factors. Comput. Appl. Biosci. 11: 477-488.
24. Kosman D. and Small, S. 1997. Concentration-dependent patterning by an ectopic expression domain of the Drosophila gap gene knirps. Development 124: 1343-1354.
25. Kraut, R. and Levine, M. 1991. Spatial regulation of the gap gene giant during Drosophila development. Development 111: 601-609.
26. Ludwig, M.Z., Patel, N.H., and Kreitman, M. 1998. Functional analysis of eve stripe 2 enhancer evolution in Drosophila: Rules governing conservation and change. Development 125: 949-958.
27. Ludwig, M.Z., Bergman, C., Patel, N.H., and Kreitman, M. 2000. Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403: 564-567.
28. Markstein, M., Markstein, P., Markstein, V., and Levine, M.S. 2002 Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc. Natl. Acad. Sci. 99: 763-768.
29. Mismer, D. and Rubin, G.M. 1989. Definition of cis-acting elements regulating expression of the Drosophila melanogaster ninaE opsin gene by oligonucleotide-directed mutagenesis. Genetics 121: 77-87.
30. Nasiadka, A. and Krause, H.M. 1999. Kinetic analysis of segmentation gene interactions in Drosophila embryos. Development 126: 1515-1526.
31. Papatsenko, D., Nazina, A., and Desplan, C. 2001. A conserved regulatory element present in all Drosophila rhodopsin genes mediates Pax6 functions and participates in the fine-tuning of cell-specific expression. Mech. Dev. 101: 143-153.
32. Papatsenko, D.A., Makeev, V.J., Lifanov, A.P., Regnier, M., Nazina, A.G., and Desplan, C. 2002. Extraction of functional binding sites from unique regulatory regions: The Drosophila early developmental enhancers. Genome Res. 12: 470-481.
33. Pickert, L., Reuter, I., Klawonn, F., and Wingender, E. 1998. Transcription regulatory region analysis using signal detection and fuzzy clustering [In Process Citation]. Bioinformatics 14: 244-2S1.
34. Rubin, G.M. and Lewis, E.B. 2000. A brief history of Drosophila's contributions to genome research. Science 287: 2216-2218.
35. Sackerson, C., Fujioka, M., and Goto, T. 1999. The even-skipped locus is contained in a 16-kb chromatin domain. Dev. Biol. 211: 39-52.
36. Serov, V.N., Spirov, A.V., and Samsonova, M.G. 1998. Graphical interface to the genetic network database GeNet. Bioinformatics 14: 546-547.
37. Small, S., Blair, A., and Levine, M. 1992. Regulation of even-skipped stripe 2 in the Drosophila embryo. EMBO J. 11: 4047-4057.
38. Small, S., Blair, A., and Levine, M. 1996. Regulation of two pair-rule stripes by a single enhancer in the Drosophila embryo. Dev. Biol. 175: 314-324.
39. Stanojevic, D., Small, S., and Levine, M. 1991. Regulation of a segmentation stripe by overlapping activators and repressors in the Drosophila embryo. Science 254: 1385-1387.
40. Su, X., Wallenstein, S., and Bishop, D. 2001. Nonoverlapping clusters: Approximate distribution and application to molecular biology. Biometrics 57: 420-426.
41. Wagner, A. 1997. A computational genomics approach to the identification of gene networks. Nucleic Acids Res. 25: 3594-3604.
42. Wagner, A. 1999. Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes. Bioinformatics 15: 776-784.
43. Wasserman, W.W. and Fickett, J.W. 1998. Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol. 278: 167-181.
44. Waterman, M.S. 1995. Introduction to computational biology. Chapmen & Hall, CRC Press LLC, Boca Raton, FL.