TY - JOUR
T1 - Interpreting the regulatory genome
T2 - The genomics of transcription factor function in Drosophila melanogaster
AU - Slattery, Matthew
AU - Nègre, Nicolas
AU - White, Kevin P.
PY - 2012/9
Y1 - 2012/9
N2 - Researchers have now had access to the fully sequenced Drosophila melanogaster genome for over a decade, and the sequenced genomes of 11 additional Drosophila species have been available for almost 5 years, with more species' genomes becoming available every year [Adams MD, Celniker SE, Holt RA, et al. The genome sequence of Drosophila melanogaster. Science 2000;287:2185-95; Clark AG, Eisen MB, Smith DR, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature 2007;450:203-18]. Although the best studied of the D. melanogaster transcription factors (TFs) were cloned before sequencing of the genome, the availability of sequence data promised to transform our understanding of TFs and gene regulatory networks. Sequenced genomes have allowed researchers to generate tools for high-throughput characterization of gene expression levels, genome-wide TF localization and analyses of evolutionary constraints on DNA elements across multiple species. With an estimated 700 DNA-binding proteins in the Drosophila genome, it will be many years before each potential sequence-specific TF is studied in detail, yet the last decade of functional genomics research has already impacted our view of gene regulatory networks and TF DNA recognition.
AB - Researchers have now had access to the fully sequenced Drosophila melanogaster genome for over a decade, and the sequenced genomes of 11 additional Drosophila species have been available for almost 5 years, with more species' genomes becoming available every year [Adams MD, Celniker SE, Holt RA, et al. The genome sequence of Drosophila melanogaster. Science 2000;287:2185-95; Clark AG, Eisen MB, Smith DR, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature 2007;450:203-18]. Although the best studied of the D. melanogaster transcription factors (TFs) were cloned before sequencing of the genome, the availability of sequence data promised to transform our understanding of TFs and gene regulatory networks. Sequenced genomes have allowed researchers to generate tools for high-throughput characterization of gene expression levels, genome-wide TF localization and analyses of evolutionary constraints on DNA elements across multiple species. With an estimated 700 DNA-binding proteins in the Drosophila genome, it will be many years before each potential sequence-specific TF is studied in detail, yet the last decade of functional genomics research has already impacted our view of gene regulatory networks and TF DNA recognition.
KW - Drosophila
KW - Enhancer
KW - Genomics
KW - Transcription factor
KW - Zelda
UR - http://www.scopus.com/inward/record.url?scp=84867120185&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84867120185&partnerID=8YFLogxK
U2 - 10.1093/bfgp/els034
DO - 10.1093/bfgp/els034
M3 - Article
C2 - 23023663
AN - SCOPUS:84867120185
SN - 2041-2649
VL - 11
SP - 336
EP - 346
JO - Briefings in Functional Genomics
JF - Briefings in Functional Genomics
IS - 5
M1 - els034
ER -