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The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins
A draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis, is generated, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. Expand
Characterization of a notochord-specific enhancer from the Brachyury promoter region of the ascidian, Ciona intestinalis.
Evidence is presented that the embryo of the ascidian, Ciona intestinalis, is an easily manipulated system for investigating the establishment of basic chordate tissues and organs, thereby raising the possibility that the Notch signaling pathway plays a role in notochord differentiation. Expand
Regulation of even‐skipped stripe 2 in the Drosophila embryo.
It is proposed that the clustering of activator and repressor binding sites in the stripe 2 element is required to bring these weakly interacting regulatory factors into close apposition so that they can function both cooperatively and synergistically to control transcription. Expand
RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo
It is proposed that Pol II stalling facilitates rapid temporal and spatial changes in gene activity during development and is highly enriched for developmental control genes, which are either repressed or poised for activation during later stages of embryogenesis. Expand
The dorsal gradient morphogen regulates stripes of rhomboid expression in the presumptive neuroectoderm of the Drosophila embryo.
Evidence is presented that the maternal morphogen dorsal (dl) acts in concert with basic helix-loop-helix (b-HLH) proteins, possibly including twist (twi), to activate rho in both lateral and ventral regions, suggesting that the dl and bcd morphogens use a similar mechanism to make stripes in the Drosophila embryo. Expand
Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
  • B. Berman, Y. Nibu, +5 authors M. Eisen
  • Biology, Medicine
  • Proceedings of the National Academy of Sciences…
  • 22 January 2002
Evaluated the extent to which the tendency for transcription factor binding sites to be clustered can be used as the basis for the computational identification of cis-regulatory modules and identified genomic regions containing unusually high concentrations of predicted binding sites for these factors. Expand
Characterization and localization of the even‐skipped protein of Drosophila.
The pair‐rule gene even‐skipped of Drosophila is isolated and it is shown that the eve protein is distributed in a series of seven transverse stripes at the cellular blastoderm stage, and is localized primarily within the nuclear regions of those embryonic cells that express the gene. Expand
Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo.
The ChIP-chip data uncover a much larger than expected regulatory network, which integrates diverse patterning processes during development, and includes Dpp signaling components and anteroposterior (AP) segmentation determinants. Expand
Dif, a dorsal-related gene that mediates an immune response in Drosophila
Evidence is presented that once in the nucleus, Dif binds to kappa B-like sequence motifs present in promoter regions of immunity genes, suggesting that mammalian and insect immunity share a common evolutionary origin. Expand
Regulatory Blueprint for a Chordate Embryo
Deduced gene circuit diagrams describing the formation of larval tissues were computationally visualized and constitute a blueprint for the Ciona embryo and provide a foundation for understanding the evolutionary origins of the chordate body plan. Expand