Optimization of reporter gene architecture for quantitative measurements of gene expression in the drosophila embryo

Fly

Volumn 5, Issue 1, 2011, Pages 1-6

  Sayal, Rupinder ^a   Ryu, Seuk Min ^a   Arnosti, David N ^a  

^a Michigan State University   (United States)

Author keywords

Enhancer; PattB; PhiC31; Promoter; Transcription; UTR

Indexed keywords

EUKARYOTA; SIMIAN VIRUS 40;

EID: 79551568037     PISSN: 19336934     EISSN: 19336942     Source Type: Journal    
DOI: 10.4161/fly.5.1.14459     Document Type: Article

References (18)

1. Bischof J, Maeda RK, Hediger M, Karch F, Basler K. An optimized transgenesis system for Drosophila using germ-line-specific phiC31 integrases. Proc Natl Acad Sci USA 2007; 104:3312-7.
2. Juven-Gershon T, Kadonaga JT. Regulation of gene expression via the core promoter and the basal transcriptional machinery. Dev Biol 2010; 339:225-9.
3. Hsu JY, Juven-Gershon T, Marr MT, 2nd, Wright KJ, Tjian R, Kadonaga JT. TBP, Mot1 and NC2 establish a regulatory circuit that controls DPE-dependent versus TATA-dependent transcription. Genes Dev 2008; 22:2353-8.
4. Butler JE, Kadonaga JT. Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev 2001; 15:2515-9.
5. Merli C, Bergstrom DE, Cygan JA, Blackman RK. Promoter specificity mediates the independent regulation of neighboring genes. Genes Dev 1996; 10:1260-70.
6. Lecuyer E, Yoshida H, Parthasarathy N, Alm C, Babak T, Cerovina T, et al. Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell 2007; 131:174-87.
7. Kulkarni MM, Arnosti DN. cis-regulatory logic of short-range transcriptional repression in Drosophila melanogaster. Mol Cell Biol 2005; 25:3411-20.
8. Wharton KA, Crews ST. CNS midline enhancers of the Drosophila slit and Toll genes. Mech Dev 1993; 40:141-54.
9. Fakhouri WD, Ay A, Sayal R, Dresch J, Dayringer E, Arnosti DN. Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo. Mol Syst Biol 2010; 6:341.
10. Burke TW, Kadonaga JT. The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes Dev 1997; 11:3020-31.
11. Thisse B, Stoetzel C, Gorostiza-Thisse C, Perrin-Schmitt F. Sequence of the twist gene and nuclear localization of its protein in endomesodermal cells of early Drosophila embryos. EMBO J 1988; 7:2175-83.
12. Hendrix DA, Hong JW, Zeitlinger J, Rokhsar DS, Levine MS. Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proc Natl Acad Sci USA 2008; 105:7762-7.
13. Ay A, Fakhouri WD, Chiu C, Arnosti DN. Image processing and analysis for quantifying gene expression from early Drosophila embryos. Tissue Eng Part A 2008; 14:1517-26.
14. Crocker J, Tamori Y, Erives A. Evolution acts on enhancer organization to fine-tune gradient threshold readouts. PLoS Biol 2008; 6:263.
15. Small S, Blair A, Levine M. Regulation of even-skipped stripe 2 in the Drosophila embryo. EMBO J 1992; 11:4047-57.
16. Abramoff MD, Magelhaes PJ, Ram SJ. Image Processing with ImageJ. Biophotonics International 2004; 11:36-42.
17. Ohler U, Liao GC, Niemann H, Rubin GM. Computational analysis of core promoters in the Drosophila genome. Genome Biol 2002; 3:87.
18. Bailey TL, Gribskov M. Combining evidence using p-values: application to sequence homology searches. Bioinformatics 1998; 14:48-54.