Identification and Validation of Novel Hedgehog-Responsive Enhancers Predicted by Computational Analysis of Ci/Gli Binding Site Density
Year: 2015
Type: article
Abstract: The Hedgehog (Hh) signaling pathway directs a multitude of cellular responses during embryogenesis and adult tissue homeostasis. Stimulation of the pathway results in activation of Hh target genes by the transcription factor Ci/Gli, which binds to specific motifs in genomic enhancers. In Drosophila, only a few enhancers (patched, decapentaplegic, wingless, stripe, knot, hairy, orthodenticle) have been shown by in vivo functional assays to depend on direct Ci/Gli regulation. All but one (orthodenticle) contain more than one Ci/Gli site, prompting us to directly test whether homotypic clustering of Ci/Gli binding sites is sufficient to define a Hh-regulated enhancer. We therefore developed a computational algorithm to identify Ci/Gli clusters that are enriched over random expectation, within a given region of the genome. Candidate genomic regions containing Ci/Gli clusters were functionally tested in chicken neural tube electroporation assays and in transgenic flies. Of the 22 Ci/Gli clusters tested, seven novel enhancers (and the previously known patched enhancer) were identified as Hh-responsive and Ci/Gli-dependent in one or both of these assays, including: Cuticular protein 100A (Cpr100A); invected (inv), which encodes an engrailed-related transcription factor expressed at the anterior/posterior wing disc boundary; roadkill (rdx), the fly homolog of vertebrate Spop; the segment polarity gene gooseberry (gsb); and two previously untested regions of the Hh receptor-encoding patched (ptc) gene. We conclude that homotypic Ci/Gli clustering is not sufficient information to ensure Hh-responsiveness; however, it can provide a clue for enhancer recognition within putative Hedgehog target gene loci.
Source: PLoS ONE
Institution: University of Michigan
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,382
Funders: National Science Foundation, American Heart Association, University of Michigan, National Institutes of Health, Directorate for Biological Sciences, National Cancer Institute, National Institute on Deafness and Other Communication Disorders, National Institute of General Medical Sciences, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Dental and Craniofacial Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development
Awards: G1078564700, G1130036750, Cellular Decisions of Differentiation in the GI Tract, G1287925916, University of Michigan Center for Gastrointestinal Research, G141600148, G1619971191, Transcriptional control of epithelial identity during pyloric border formation, G2509478207, G3137763225, G3245121444, G3425668595, G3549828030, Interpreting Hedgehog Signaling Gradients With Cis-Regulatory DNA: A Quantitative In Vivo/Computational Approach, G4376152923, G5520316217, Structure and Function of a Signal-Regulated Developmental Enhancer, G67213621, G7191820945, G8360937462, Hedgehog signaling in maintaining taste organ structure and function: basic and clinical studies, G9000006758, G9000030401, G9000031400, G9000046116, G9000130709, G9000198288, G9000308391, G9000334620, Tissue Engineering and Regeneration
OpenAlex ID: W2200487348