Automated protein-DNA interaction screening of Drosophila regulatory elements

Nature Methods

Volumn 8, Issue 12, 2011, Pages 1065-1073

  Hens, Korneel ^a   Feuz, Jean Daniel ^a   Isakova, Alina ^a   Iagovitina, Antonina ^a   Massouras, Andreas ^a   Bryois, Julien ^a   Callaerts, Patrick ^b,c   Celniker, Susan E ^d   Deplancke, Bart ^a  

^a Chemical Engineering and Biochemistry Section   (Switzerland)

^b DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^c UNIVERSITY OF LEUVEN   (Belgium)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE I; TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; DNA SEQUENCE; DROSOPHILA; GENE EXPRESSION; INSECT GENETICS; MICROFLUIDICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; REGULATORY SEQUENCE;

ANIMALS; AUTOMATION; BINDING SITES; DNA; DNA-BINDING PROTEINS; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; HIGH-THROUGHPUT SCREENING ASSAYS; MICROFLUIDICS; OPEN READING FRAMES; REGULATORY ELEMENTS, TRANSCRIPTIONAL; REPRODUCIBILITY OF RESULTS; TRANSCRIPTION FACTORS; TWO-HYBRID SYSTEM TECHNIQUES;

DROSOPHILA MELANOGASTER; METAZOA;

EID: 82355191645     PISSN: 15487091     EISSN: 15491676     Source Type: Journal    
DOI: 10.1038/nmeth.1763     Document Type: Article

References (36)

1. Adams, M.D. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185-2195 (2000). (Pubitemid 30177013)
2. O'Kane, C.J. & Gehring, W.J. Detection in situ of genomic regulatory elements in Drosophila. Proc. Natl. Acad. Sci. USA 84, 9123-9127 (1987).
3. Zinzen, R.P., Girardot, C., Gagneur, J., Braun, M. & Furlong, E.E.M. Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature 462, 65-70 (2009).
4. Filion, G.J. et al. Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 143, 212-224 (2010).
5. Bischof, J., Maeda, R.K., Hediger, M., Karch, F. & Basler, K. An optimized transgenesis system for Drosophila using germ-line-specific phic31 integrases. Proc. Natl. Acad. Sci. USA 104, 3312-3317 (2007). (Pubitemid 46364156)
6. Stark, A. et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450, 219-232 (2007). (Pubitemid 350100553)
7. Simicevic, J. & Deplancke, B. DNA-centered approaches to characterize regulatory protein-DNA interaction complexes. Mol. Biosyst. 6, 462-468 (2010).
8. Deplancke, B. et al. A gene-centered C. elegans protein-DNA interaction network. Cell 125, 1193-1205 (2006). (Pubitemid 43866204)
9. Adryan, B. & Teichmann, S.A. Flytf: A systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster. Bioinformatics 22, 1532-1533 (2006). (Pubitemid 43985326)
10. Gallo, S.M. et al. Redfly v3.0: Toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res. 39, D118-D123 (2011).
11. Massouras, A., Decouttere, F., Hens, K. & Deplancke, B. Webprinses: Automated full-length clone sequence identification and verification using high-throughput sequencing data. Nucleic Acids Res. 38 (suppl.), W378-W384 (2010).
12. Vermeirssen, V. et al. Matrix and steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping. Nat. Methods 4, 659-664 (2007). (Pubitemid 47202478)
13. Reece-Hoyes, J.S. et al. Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. Nat. Methods doi.10.1038/nmeth.1764 (30 October 2011).
14. Reece-Hoyes, J.S. et al. Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping. Nat. Methods doi:10.1038/nmeth.1748 (30 October 2011).
15. Koegl, M. & Uetz, P. Improving yeast two-hybrid screening systems. Brief. Funct. Genomics Proteomics 6, 302-312 (2007). (Pubitemid 351890477)
16. Vermeirssen, V. et al. Matrix and steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping. Nat. Methods 4, 659-664 (2007). (Pubitemid 47202478)
17. Braun, P. et al. An experimentally derived confidence score for binary protein-protein interactions. Nat. Methods 6, 91-97 (2009).
18. Deplancke, B., Dupuy, D., Vidal, M. & Walhout, A.J. A gateway-compatible yeast one-hybrid system. Genome Res. 1410B, 2093-2101 (2004). (Pubitemid 39440191)
19. Maerkl, S.J. & Quake, S.R. A systems approach to measuring the binding energy landscapes of transcription factors. Science 315, 233-237 (2007). (Pubitemid 46166367)
20. Punzo, C., Seimiya, M., Flister, S., Gehring, W.J. & Plaza, S. Differential interactions of eyeless and twin of eyeless with the sine oculis enhancer. Development 129, 625-634 (2002). (Pubitemid 34863826)
21. Czerny, T. et al. Twin of eyeless, a second pax-6 gene of Drosophila, acts upstream of eyeless in the control of eye development. Mol. Cell 3, 297-307 (1999). (Pubitemid 29290670)
22. Burtis, K.C., Coschigano, K.T., Baker, B.S. & Wensink, P.C. The doublesex proteins of Drosophila melanogaster bind directly to a sex-specific yolk protein gene enhancer. EMBO J. 10, 2577-2582 (1991). (Pubitemid 21905732)
23. Serikaku, M.A. & Otousa, J.E. Sine oculis is a homeobox gene required for Drosophila visual-system development. Genetics 138, 1137-1150 (1994). (Pubitemid 24375260)
24. Cheyette, B.N.R. et al. The Drosophila sine oculis locus encodes a homeodomain-containing protein required for the development of the entire visual-system. Neuron 12, 977-996 (1994). (Pubitemid 24178192)
25. Callaerts, P. et al. Drosophila pax-6/eyeless is essential for normal adult brain structure and function. J. Neurobiol. 46, 73-88 (2001). (Pubitemid 32064384)
26. Lai, Z.C. & Li, Y. Tramtrack69 is positively and autonomously required for Drosophila photoreceptor development. Genetics 152, 299-305 (1999). (Pubitemid 29222535)
27. Chen, Y.C., Rajagopala, S.V., Stellberger, T. & Uetz, P. Exhaustive benchmarking of the yeast two-hybrid system. Nat. Methods 7, 667-668 (2010).
28. Mito, T. et al. Divergent and conserved roles of extradenticle in body segmentation and appendage formation, respectively, in the cricket Gryllus bimaculatus. Dev. Biol. 313, 67-79 (2008). (Pubitemid 350298305)
29. Hutson, S.F. & Bownes, M. The regulation of yp3 expression in the Drosophila melanogaster fat body. Dev. Genes Evol. 213, 1-8 (2003). (Pubitemid 36305547)
30. Li, M.A., Alls, J.D., Avancini, R.M., Koo, K. & Godt, D. The large maf factor traffic jam controls gonad morphogenesis in Drosophila. Nat. Cell Biol. 5, 994-1000 (2003). (Pubitemid 37406913)
31. Turatsinze, J.V., Thomas-Chollier, M., Defrance, M. & van Helden, J. Using rsat to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat. Protoc. 3, 1578-1588 (2008).
32. Bryne, J.C. et al. Jaspar, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res. 36, D102-D106 (2008). (Pubitemid 351149704)
33. Matys, V. et al. Transfac and its module transcompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34, D108-D110 (2006).
34. Dietzl, G. et al. A genome-wide transgenic rnai library for conditional gene inactivation in Drosophila. Nature 448, 151-156 (2007). (Pubitemid 47067374)
35. Ni, J.Q. et al. A Drosophila resource of transgenic rnai lines for neurogenetics. Genetics 182, 1089-1100 (2009).
36. Gubelmann, C. et al. Getprime: A gene-or transcript-specific primer database for quantitative real-time PCR. Database doi:10.1093/database/bar040 (2011).