Exploration of Drosophila Regulatory Networks and Embryonic Development
Exploration of Drosophila Regulatory Networks and Embryonic Development
A review of Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo
Note: This is a review of the published article listed below. All information, quotes, figures, methods, and findings mentioned in this review are from that article, and are the property of its authors and/or the publication in which the article originally appeared.
Sequence-specific transcription factors have been correlated to developmental control, yet little research has been performed to identify in vivo characteristics across genomes. Past analysis of Drosophila embryo development has revealed an essential role for sequence-specific transcription factors in axis formation and cell differentiation, but the details regarding the actual regulatory mechanisms remain elusive. Zeitlinger and colleagues (2007) examined the genome-wide occupancy of the dorsoventral (DV) determinants Dorsal, Twist, and Snail in the Drosophila embryo using Agilent ChIP-on-chip microarrays, uncovering a “much larger than expected regulatory network that integrates diverse patterning processes during development.” This research suggests broad implications in the use of ChIP-on-chip for investigating the role of gene regulation across several different systems, including the patterning processes associated with mammalian development and stem cell differentiation.
Figure 1. Drosophila ChIP-chip identifies known enhancers of Dorsal, Twist, and Snail.
Drosophila embryos, aged 2-4 h, from Toll10b mothers were used to perform ChIP using antibodies against Dorsal, Twist, and Snail. Most enhancers known to be regulated by these factors were successfully identified, including type 1 target genes sna (A), mir-1 (B), and type 2 target genes rho (C) and brk (D). The graphs show unprocessed ChIP enrichment ratios (Y-axis) for Dorsal (red), Twist (blue), and Snail (green), across chromosomal regions (X-axis).
Figure 2. Enrichment of Dorsal-, Twist-, and Snail-binding motifs in bound regions.
Sequences from DTS and TS regions with greater than fivefold ChIP enrichment were searched for the presence of the known Dorsal (red), Twist (blue), or Snail (red) motifs, and the evolutionary conservation of these motifs across the 12 sequenced Drosophila genomes was determined (as percent of branch length within the phylogenetic tree). The graph shows the fraction of regions at each conservation cutoff (0%, 20%, 40%, 60%, 80%, and 100%). As a control, the same analysis was performed with regions of identical length that were randomly distributed among intronic and intergenic regions. Using a 2 test, the motif enrichment and evolutionary conservation was highly significant for
Dorsal (p < 10-148), Twist (p < 10-228), and Snail (p < 10-306).
Figure 3. Integration of new putative target genes into the Dorsal network.
Many newly identified putative target genes of Dorsal, Twist, and Snail are genes that were previously thought to be induced further downstream in the DV patterning network. Thus, Dorsal appears to regulate many target genes both directly and indirectly (a configuration also known as a feed-forward motif) in the suppression of dorsal ectodermal fate (A–C) and neurectodermal fate (D–F). Newly identified connections are marked by a star. Examples of such configurations are shown for target genes of Dpp signaling (A), which are also directly regulated by Dorsal; target genes of the transcription factor Zen (B), which are also directly regulated by Dorsal; target gene suppression by Dorsal (C), which can also be mediated by Snail; targets of EGF signaling (D), which are regulated by Snail at multiple levels; targets of Notch signaling (E), which are also regulated by Snail at multiple levels; and suppression of target genes by Snail or through induction of microRNAs (F). The regulatory relationship (activation, arrow; repression, orthogonal bar) of new connections was inferred based on the tissue-specific expression patterns of the target genes.
Title: Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo.
Authors: Zeitlinger J, Zinzen RP, Stark A, Kellis M, Zhang H, Young RA, Levine M.
Journal: Genes Dev. 2007 Feb 15;21(4):385-90.
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