Organization of developmental enhancers in the Drosophila embryo Export

@article{citeulike:5348249, abstract = {Most cell-specific enhancers are thought to lack an inherent organization, with critical binding sites distributed in a more or less random fashion. However, there are examples of fixed arrangements of binding sites, such as helical phasing, that promote the formation of higher-order protein complexes on the enhancer DNA template. Here, we investigate the regulatory grammar' of nearly 100 characterized enhancers for developmental control genes active in the early Drosophila embryo. The conservation of grammar is examined in seven divergent Drosophila genomes. Linked binding sites are observed for particular combinations of binding motifs, including Bicoid-Bicoid, Hunchback-Hunchback, Bicoid-Dorsal, Bicoid-Caudal and Dorsal-Twist. Direct evidence is presented for the importance of Bicoid-Dorsal linkage in the integration of the anterior-posterior and dorsal-ventral patterning systems. Hunchback-Hunchback interactions help explain unresolved aspects of segmentation, including the differential regulation of the eve stripe 3 + 7 and stripe 4 + 6 enhancers. We also present evidence that there is an under-representation of nucleosome positioning sequences in many enhancers, raising the possibility for a subtle higher-order structure extending across certain enhancers. We conclude that grammar of gene control regions is pervasively used in the patterning of the Drosophila embryo. 10.1093/nar/gkp619}, author = {Papatsenko, Dmitri and Goltsev, Yury and Levine, Michael}, booktitle = {Nucl. Acids Res.}, citeulike-article-id = {5348249}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/gkp619}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/content/37/17/5665.abstract}, citeulike-linkout-2 = {http://nar.oxfordjournals.org/content/37/17/5665.full.pdf}, citeulike-linkout-3 = {http://nar.oxfordjournals.org/cgi/content/abstract/37/17/5665}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19651877}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19651877}, day = {1}, doi = {10.1093/nar/gkp619}, issn = {1362-4962}, journal = {Nucl. Acids Res.}, keywords = {enhancers, genome-organization}, month = {September}, number = {17}, pages = {5665--5677}, posted-at = {2009-10-20 17:49:49}, priority = {2}, title = {Organization of developmental enhancers in the Drosophila embryo}, url = {http://dx.doi.org/10.1093/nar/gkp619}, volume = {37}, year = {2009} }

TY - JOUR ID - citeulike:5348249 L3 - citeulike-article-id:5348249 N2 - Most cell-specific enhancers are thought to lack an inherent organization, with critical binding sites distributed in a more or less random fashion. However, there are examples of fixed arrangements of binding sites, such as helical phasing, that promote the formation of higher-order protein complexes on the enhancer DNA template. Here, we investigate the regulatory grammar' of nearly 100 characterized enhancers for developmental control genes active in the early Drosophila embryo. The conservation of grammar is examined in seven divergent Drosophila genomes. Linked binding sites are observed for particular combinations of binding motifs, including Bicoid-Bicoid, Hunchback-Hunchback, Bicoid-Dorsal, Bicoid-Caudal and Dorsal-Twist. Direct evidence is presented for the importance of Bicoid-Dorsal linkage in the integration of the anterior-posterior and dorsal-ventral patterning systems. Hunchback-Hunchback interactions help explain unresolved aspects of segmentation, including the differential regulation of the eve stripe 3 + 7 and stripe 4 + 6 enhancers. We also present evidence that there is an under-representation of nucleosome positioning sequences in many enhancers, raising the possibility for a subtle higher-order structure extending across certain enhancers. We conclude that grammar of gene control regions is pervasively used in the patterning of the Drosophila embryo. 10.1093/nar/gkp619 IS - 17 JF - Nucl. Acids Res. SN - 1362-4962 EP - 5677 TI - Organization of developmental enhancers in the Drosophila embryo VL - 37 T2 - Nucl. Acids Res. SP - 5665 KW - enhancers KW - genome-organization AU - Papatsenko, Dmitri AU - Goltsev, Yury AU - Levine, Michael PY - 2009/09/01/ UR - http://dx.doi.org/10.1093/nar/gkp619 ER -