Project description:We performed ChIP-chip analysis using sheared chromatin isolated from Drosophila embryos of 1-3 hours in age. Keywords: high-resolution tiling array, drosophila, twist, dorsal, snail, weckle ChIP-chip of twist, dorsal, snail, and weckle
Project description:Identifying putative transcription factor target genes by combining CRISPR/Cas9-based transcriptional activation with RNAseq in Drosophila S2R+ cells. This study focuses on the transcription factors Twist and Snail, singly and together. RNA from Drosophila cells following CRISPR/Cas9-based activation of Twist, Snail, or Twist and Snail together, compared with non-targeting sgRNA. Two biological replicates for each experiment
Project description:Genetic studies have identified numerous sequence-specific transcription factors that control development, yet little is known about their in vivo distribution across animal genomes. We determine the genome-wide occupancy of the dorsoventral determinants Dorsal, Twist and Snail in the Drosophila embryo using ChIP-chip analysis. There is a tight correlation between the limits of known enhancers and the in vivo binding of these proteins. The analysis predicts substantially more target genes than previously estimated, including Dpp signaling components and genes encoding anteroposterior segmentation determinants. Thus, the ChIP-chip data uncovers a much larger network, which integrates diverse patterning processes during development.
Project description:Genetic studies have identified numerous sequence-specific transcription factors that control development, yet little is known about their in vivo distribution across animal genomes. We determine the genome-wide occupancy of the dorsoventral determinants Dorsal, Twist and Snail in the Drosophila embryo using ChIP-chip analysis. There is a tight correlation between the limits of known enhancers and the in vivo binding of these proteins. The analysis predicts substantially more target genes than previously estimated, including Dpp signaling components and genes encoding anteroposterior segmentation determinants. Thus, the ChIP-chip data uncovers a much larger network, which integrates diverse patterning processes during development.
Project description:Identifying putative transcription factor target genes by combining CRISPR/Cas9-based transcriptional activation with RNAseq in Drosophila S2R+ cells. This study focuses on the transcription factors Twist and Snail, singly and together.
Project description:Chromosome conformation capture (4C-Seq) in Drosophila Twist-H2B embryos (carrying nuclear tag specifically in the mesoderm) during embryogenesis was performed, anchoring on 107 different viewpoints. Two timepoints (3-4hrs and 6-8hrs after egg laying) and two tissue context (whole embryo and mesoderm) were assayed. Two independent collections were performed at each timepoint.
Project description:Chromosome conformation capture (4C-Seq) in Drosophila embryos from a wild-type line and from transgenic fly lines carrying the E3 enhancer of twist at ectopic locations. Two time points (2-5 hrs and 5-8 hrs after egg lay) and two viewpoints located near the twist promoter were assayed. Two independent collections were performed at each timepoint and each viewpoint.
Project description:The initially homogeneous epithelium of the early Drosophila embryo differentiates into regional subpopulations with different behaviours and physical properties that are needed for morphogenesis. The factors at top of the genetic hierarchy that control these behaviours are known, but many of their targets are not. To understand how proteins work together to mediate differential cellular activities, we studied in an unbiased manner the proteomes and phosphoproteomes of the three main cell populations along the dorso-ventral axis during gastrulation using mutant embryos that represent the different populations. We detected 6111 protein groups and 6259 phosphosites of which 3399 and 3433 respectively, were differentially regulated. The changes in phosphosite abundance did not correlate with changes in host protein abundance, showing phosphorylation to be a regulatory step during gastrulation. Hierarchical clustering of protein groups and phosphosites identified clusters that contain known fate determinants such as Doc1, Sog, Snail and Twist. The recovery of the appropriate known marker proteins in each of the different mutants we used validated the approach, but also revealed that two mutations that both interfere with the dorsal fate pathway, Toll10B and serpin27aex do this in very different manners. Diffused network analyses within each cluster point to microtubule components as one of the main groups of regulated proteins. Functional studies on the role of microtubules provide the proof of principle that microtubules have different functions in different domains along the DV axis of the embryo.
