Nonclassical regulation of transcription: Interchromosomal interactions at the Malic enzyme locus of Drosophila melanogaster

Genetics

Volumn 189, Issue 3, 2011, Pages 837-849

  Lum, Thomas E ^a   Merritt, Thomas J S ^a  

^a LAURENTIAN UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; BIOINFORMATICS; CELL INTERACTION; CHROMOSOME; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; GENE; GENE EXPRESSION; GENE FUNCTION; GENE LOCUS; HETEROZYGOTE; MEN GENE; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; TRANSCRIPTION REGULATION;

ALLELES; ANIMALS; CHROMOSOMES, INSECT; CONSERVED SEQUENCE; DROSOPHILA MELANOGASTER; EVOLUTION, MOLECULAR; FEMALE; GENE EXPRESSION REGULATION; GENE KNOCKOUT TECHNIQUES; GENETIC LOCI; HETEROZYGOTE; MALATE DEHYDROGENASE; MALE; PHYLOGENY; REGULATORY SEQUENCES, NUCLEIC ACID; TRANSCRIPTION, GENETIC;

DROSOPHILA MELANOGASTER;

EID: 81255211376     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.111.133231     Document Type: Article

References (60)

1. Babu, P., K. S. Selvakumar, and S. Bhosekar, 1987 Studies on transvection at the bithorax complex in Drosophila melanogaster. Mol. Gen. Genet. 210: 557-563.
2. Bacher, C. P., M. Guggiari, B. Brors, S. Augui, P. Clerc et al., 2006 Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation. Nat. Cell Biol. 8: 293-299.
3. Benson, M., and V. Pirrotta, 1988 The Drosophila zeste protein binds cooperatively to sites in many gene regulatory regions: implications for transvection and gene regulation. EMBO J. 7: 3907-3915.
4. Bickel, S., and V. Pirrotta, 1990 Self-association of the Drosophila zeste protein is responsible for transvection effects. EMBO J. 9: 2959-2967.
5. Blanchette, M., B. Schwikowski, and M. Tompa, 2002 Algorithms for phylogenetic footprinting. J. Comput. Biol. 9: 211-223.
6. Cartharius, K., K. Frech, K. Grote, B. Klocke, M. Haltmeier et al., 2005 MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics 21: 2933-2942.
7. Chandler, V. L., and M. Stam, 2004 Chromatin conversations: mechanisms and implications of paramutation. Nat. Rev. Genet. 5: 532-544.
8. Cooley, L., R. Kelley, and A. Spradling, 1988 Insertional mutagenesis of the Drosophila genome with single P elements. Science 239: 1121-1128.
9. Coulthard, A. B., N. Nolan, J. B. Bell, and A. J. Hilliker, 2005 Transvection at the vestigial locus of Drosophila melanogaster. Genetics 170: 1711-1721.
10. Davison, D., C. H. Chapman, C. Wedeen, and P. M. Bingham, 1985 Genetic and physical studies of a portion of the white locus participating in transcriptional regulation and in synapsisdependent interactions in Drosophila adult tissues. Genetics 110: 479-494.
11. Duncan, I., 1987 The bithorax complex. Annu. Rev. Genet. 21: 285-319.
12. Duncan, I. W., 2002 Transvection effects in Drosophila. Annu. Rev. Genet. 36: 521-556.
13. Duvernell, D. D., and W. F. Eanes, 2000 Contrasting molecular population genetics of four hexokinases in Drosophila melanogaster, D. simulans and D. yakuba. Genetics 156: 1191-1201.
14. Fung, J. C., W. F. Marshall, A. Dernburg, D. A. Agard, and J. W. Sedat, 1998 Homologous chromosome pairing in Drosophila melanogaster proceeds through multiple independent initiations. J. Cell Biol. 141: 5-20.
15. Gelbart, W. M., and C. T. Wu, 1982 Interactions of zeste mutations with loci exhibiting transvection effects in Drosophila melanogaster. Genetics 102: 179-189.
16. Geyer, P. K., M. M. Green, and V. G. Corces, 1990 Tissue-specific transcriptional enhancers may act in trans on the gene located in the homologous chromosome: the molecular basis of transvection in Drosophila. EMBO J. 9: 2247-2256.
17. Gindhart, J. G. Jr. and T. C. Kaufman, 1995 Identification of Polycomb and trithorax group responsive elements in the regulatory region of the Drosophila homeotic gene Sex combs reduced. Genetics 139: 797-814.
18. Gohl, D., M. Muller, V. Pirrotta, M. Affolter, and P. Schedl, 2008 Enhancer blocking and transvection at the Drosophila apterous locus. Genetics 178: 127-143.
19. Grant-Downton, R. T., and H. G. Dickinson, 2004 Plants, pairing and phenotypes: Two's company? Trends Genet. 20: 188-195.
20. Henikoff, S., 1997 Nuclear organization and gene expression: homologous pairing and long-range interactions. Curr. Opin. Cell Biol. 9: 388-395.
21. Henikoff, S., and L. Comai, 1998 Trans-sensing effects: the ups and downs of being together. Cell 93: 329-332.
22. Hopmann, R., D. Duncan, and I. Duncan, 1995 Transvection in the iab-5,6,7 region of the bithorax complex of Drosophila: homology independent interactions in trans. Genetics 139: 815-833.
23. Irish, V. F., A. Martinez-Arias, and M. Akam, 1989 Spatial regulation of the Antennapedia and Ultrabithorax homeotic genes during Drosophila early development. EMBO J. 8: 1527-1537.
24. Koeman, J. M., R. C. Russell, M. H. Tan, D. Petillo, M. Westphal et al., 2008 Somatic pairing of chromosome 19 in renal oncocytoma is associated with deregulated EGLN2-mediated [corrected] oxygen-sensing response. PLoS Genet. 4: e1000176.
25. Lanctot, C., T. Cheutin, M. Cremer, G. Cavalli, and T. Cremer, 2007 Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat. Rev. Genet. 8: 104-115.
26. Lee, A. M., and C. T. Wu, 2006 Enhancer-promoter communication at the yellow gene of Drosophila melanogaster: diverse promoters participate in and regulate trans interactions. Genetics 174: 1867-1880.
27. Leiserson, W. M., N.M. Bonini, and S. Benzer, 1994 Transvection at the eyes absent gene of Drosophila. Genetics 138: 1171-1179.
28. Lewis, E. B., 1954 The theory and application of a new method of detecting chromosomal rearrangements in Drosophila melanogaster. Am. Nat. 89: 73-89.
29. Lim, C. Y., B. Santoso, T. Boulay, E. Dong, U. Ohler et al., 2004 The MTE, a new core promoter element for transcription by RNA polymerase II. Genes Dev. 18: 1606-1617.
30. Livak, K. J., and T. D. Schmittgen, 2001 Analysis of relative gene expression data using real-time quantitative PCR and the 2 (-Delta Delta C(T)). Methods 25: 402-408.
31. Lunde, K., B. Biehs, U. Nauber, and E. Bier, 1998 The knirps and knirps-related genes organize development of the second wing vein in Drosophila. Development 125: 4145-4154.
32. McKee, B. D., 2004 Homologous pairing and chromosome dynamics in meiosis and mitosis. Biochim. Biophys. Acta 1677: 165-180.
33. Merritt, T. J., D. Duvernell, and W. F. Eanes, 2005 Natural and synthetic alleles provide complementary insights into the nature of selection acting on the Men polymorphism of Drosophila melanogaster. Genetics 171: 1707-1718.
34. Merritt, T. J., C. Kuczynski, E. Sezgin, C. T. Zhu, S. Kumagai et al., 2009 Quantifying interactions within the NADP(H) enzyme network in Drosophila melanogaster. Genetics 182: 565-574.
35. Metz, C. W., 1916 Chromosome studies on the Diptera. II. The paired association of chromosomes in the Diptera, and its significance. J. Exp. Zool. 21: 213-279.
36. Morris, J. R., J. L. Chen, P. K. Geyer, and C. T. Wu, 1998 Two modes of transvection: enhancer action in trans and bypass of a chromatin insulator in cis. Proc. Natl. Acad. Sci. USA 95: 10740-10745.
37. Morris, J. R., J. Chen, S. T. Filandrinos, R. C. Dunn, R. Fisk et al., 1999 An analysis of transvection at the yellow locus of Drosophila melanogaster. Genetics 151: 633-651.
38. Morris, J. R., D. A. Petrov, A. M. Lee, and C. T. Wu, 2004 Enhancer choice in cis and in trans in Drosophila melanogaster: role of the promoter. Genetics 167: 1739-1747.
39. Ni, T., D. L. Corcoran, E. A. Rach, S. Song, E. P. Spana et al., 2010 A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nat. Methods 7: 521-527.
40. Ou, S. A., E. Chang, S. Lee, K. So, C. T. Wu et al., 2009 Effects of chromosomal rearrangements on transvection at the yellow gene of Drosophila melanogaster. Genetics 183: 483-496.
41. Pirrotta, V., 1999 Transvection and chromosomal trans-interaction effects. Biochim. Biophys. Acta 1424: M1-M8.
42. Qian, S., M. Capovilla, and V. Pirrotta, 1991 The bx region enhancer, a distant cis-control element of the Drosophila Ubx gene and its regulation by hunchback and other segmentation genes. EMBO J. 10: 1415-1425.
43. Rorth, P., 1996 A modular misexpression screen in Drosophila detecting tissue-specific phenotypes. Proc. Natl. Acad. Sci. USA 93: 12418-12422.
44. Salz, H. K., T. W. Cline, and P. Schedl, 1987 Functional changes associated with structural alterations induced by mobilization of a P element inserted in the Sex-lethal gene of Drosophila. Genetics 117: 221-231.
45. Satija, R., A. Novak, I. Miklos, R. Lyngso, and J. Hein, 2009 BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC. BMC Evol. Biol. 9: 217.
46. Sezgin, E., D. D. Duvernell, L. M. Matzkin, Y. Duan, C. T. Zhu et al., 2004 Single-locus latitudinal clines and their relationship to temperate adaptation in metabolic genes and derived alleles in Drosophila melanogaster. Genetics 168: 923-931.
47. Shiu, P. K., D. Zickler, N. B. Raju, G. Ruprich-Robert, and R. L. Metzenberg, 2006 SAD-2 is required for meiotic silencing by unpaired DNA and perinuclear localization of SAD-1 RNAdirected RNA polymerase. Proc. Natl. Acad. Sci. USA 103: 2243-2248.
48. Southworth, J. W., and J. A. Kennison, 2002 Transvection and silencing of the Scr homeotic gene of Drosophila melanogaster. Genetics 161: 733-746.
49. Spradling, A. C., D. M. Stern, I. Kiss, J. Roote, T. Laverty et al., 1995 Gene disruptions using P transposable elements: an integral component of the Drosophila genome project. Proc. Natl. Acad. Sci. USA 92: 10824-10830.
50. Stam, M., 2009 Paramutation: a heritable change in gene expression by allelic interactions in trans. Mol. Plant 2: 578-588.
51. Stevens, N. M., 1908 A study of the germ cells of certain diptera, with reference to the heterochromosomes and the phenomena of synapsis. J. Exp. Zool. 5: 359-374.
52. Tagle, D. A., B. F. Koop, M. Goodman, J. L. Slightom, D. L. Hess et al., 1988 Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus): nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J. Mol. Biol. 203: 439-455.
53. Thatcher, K. N., S. Peddada, D. H. Yasui, and J. M. Lasalle, 2005 Homologous pairing of 15q11-13 imprinted domains in brain is developmentally regulated but deficient in Rett and autism samples. Hum. Mol. Genet. 14: 785-797.
54. Tsubota, S., and P. Schedl, 1986 Hybrid dysgenesis-induced revertants of insertions at the 5' end of the rudimentary gene in Drosophila melanogaster: transposon-induced control mutations. Genetics 114: 165-182.
55. Vyas, M., C. Ravindran, and D. P. Kasbekar, 2006 Chromosome segment duplications in Neurospora crassa and their effects on repeat-induced point mutation and meiotic silencing by unpaired DNA. Genetics 172: 1511-1519.
56. White, R. A., and R. Lehmann, 1986 A gap gene, hunchback, regulates the spatial expression of Ultrabithorax. Cell 47: 311-321.
57. Wise, E. M. Jr. and E. G. Ball, 1964 Malic enzyme and lipogenesis. Proc. Natl. Acad. Sci. USA 52: 1255-1263.
58. Wu, C. T., and J. R. Morris, 1999 Transvection and other homology effects. Curr. Opin. Genet. Dev. 9: 237-246.
59. Xu, M., and P. R. Cook, 2008 The role of specialized transcription factories in chromosome pairing. Biochim. Biophys. Acta 1783: 2155-2160.
60. Xu, N., C. L. Tsai, and J. T. Lee, 2006 Transient homologous chromosome pairing marks the onset of X inactivation. Science 311: 1149-1152.