Deciphering the genome's regulatory code: The many languages of DNA

BioEssays

Volumn 32, Issue 5, 2010, Pages 381-384

  Rister, Jens ^a   Desplan, Claude ^a  

^a NEW YORK UNIVERSITY   (United States)

Author keywords

Chip on chip; Chromatin immunoprecipitation; Cisregulatory module; Enhancer; Transcription factor

Indexed keywords

DNA; TRANSCRIPTION FACTOR;

CHROMATIN IMMUNOPRECIPITATION; DNA MICROARRAY; DROSOPHILA; GENE EXPRESSION; GENOMICS; MATHEMATICAL COMPUTING; REVIEW;

ANIMALS; CHROMATIN IMMUNOPRECIPITATION; COMPUTATIONAL BIOLOGY; GENOME; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REGULATORY SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS;

EID: 77951731536     PISSN: 02659247     EISSN: 15211878     Source Type: Journal    
DOI: 10.1002/bies.200900197     Document Type: Review

References (31)

1. Johnson LA, Zhao Y, Golden K, et al. 2008. Reverse-engineering a transcriptional enhancer: a case study in Drosophila. Tissue Eng Part A 14: 1549-1559
2. Levine M, Davidson EH. 2005. Gene regulatory networks for development. Proc Natl Acad Sci USA 102: 4936-4942
3. Bonn S, Furlong EE. 2008. Cis-regulatory networks during development: a view of Drosophila. Curr Opin Genet Dev 18: 513-520
4. Mereiles-Filho ACA, Stark A. 2009. Comparative genomics of gene regulation - conservation and divergence of cis-regulatory information. Curr Opin Genet Dev 19: 565-570
5. Zeitlinger J, Zinzen RP, Stark A, et al. 2007. Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes Dev 21: 385-390 (Pubitemid 46310173)
6. Visel A, Blow MJ, Li Z, et al. 2009. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457: 854-858
7. MacArthur S, Li XY, Li J, et al. 2009. Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol 10: R80.
8. Zinzen RP, Girardot C, Gagneur J, et al. 2009. Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature 462: 65-70.
9. Kheradpour P, Stark A, Roy S, et al. 2007. Reliable prediction of regulator targets using 12 Drosophila genomes. Genome Res 17: 1919-1931 (Pubitemid 351360014)
10. Ludwig MZ, Bergman C, Patel NH, et al. 2000. Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403: 564-567 (Pubitemid 30082204)
11. Celniker SE, Dillon LAL, Gernstein MB, et al. 2009. Unlocking the secrets of the genome. Nature 459: 927-930
12. Li XY, MacArthur S, Bourgon R, et al. 2008. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 6: e27.
13. Segal E, Raveh-Sadka T, Schroeder M, et al. 2008. Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 451: 535-540 (Pubitemid 351186263)
14. Chopra VS, LevineM. 2009. Combinatorial patterning mechanisms in the Drosophila embryo. Brief Funct Genomic Proteomic 8: 243-249
15. Clyde DE, Corado MS, Wu X, et al. 2003. A self-organizing system of repressor gradients establishes segmental complexity in Drosophila. Nature 426: 849-853 (Pubitemid 38056871)
16. Ochoa-Espinosa A, Small S. 2006. Developmental mechanisms and cis-regulatory codes. Curr Opin Genet Dev 16: 165-170
17. Brown CD, Johnson DS, Sidow A. 2007. Functional architecture and evolution of transcriptional elements that drive gene coexpression. Science 317: 1557-1560 (Pubitemid 47417436)
18. Arnosti DN, Kulkarni MM. 2005. Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards? J Cell Biochem 94: 890-898
19. Panne D, Maniatis T, Harrison SC. 2007. An atomic model of the interferon-beta enhanceosome. Cell 129: 1111-1123
20. Pichaud F, Desplan C. 2001. A new visualization approach for identifying mutations that affect differentiation and organization of the Drosophila ommatidia. Development 128: 815-826 (Pubitemid 32288193)
21. Sheng G, Thouvenot E, Schmucker D, et al. 1997. Direct Regulation of rhodopsin1 by Pax-6/eyeless in Drosophila: Evidence for the evolutionarily conserved function of Pax-6 in photoreceptors. Genes Dev 11: 1122-1131 (Pubitemid 27225220)
22. Papatsenko D, Nazina A, 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 (Pubitemid 32186318)
23. Tahayato A, Sonneville R, Pichaud F, et al. 2003. Otd/Crx, a dual regulator for the specification of ommatidia subtypes in the Drosophila retina. Dev Cell 5: 391-402. (Pubitemid 37107669)
24. Biggin MD. 2001. To bind or not to bind. Nat Genet 28: 303-304
25. Berger MF, Badis G, Gehrke AR, et al. 2008. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133: 1266-1276 (Pubitemid 351852913)
26. Noyes MB, Christensen RG, Wakabayashi A, et al. 2008. Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell 133: 1277-1289 (Pubitemid 351852912)
27. AffolterM, SlatteryM, Mann RS. 2008. A lexicon for homeodomain-DNA recognition. Cell 133: 1133-1135
28. Parker SC, Hansen L, Abaan HO, et al. 2009. Local DNA topography correlates with functional noncoding regions of the human genome. Science 324: 389-392
29. Rohs R, West SM, Sosinsky A, et al. 2009. The role of DNA shape in protein-DNA recognition. Nature 461: 1248-1253
30. Joshi R, Passner J, Rohs R, et al. 2007. Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell 131: 530-543 (Pubitemid 350007697)
31. Keränen SV, Fowlkes CC, Luengo Hendriks CL, et al. 2006. Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution. II: dynamics. Genome Biol 7: R124.