ArticleDevelopmental biology2010
Comparing anterior and posterior Hox complex formation reveals guidelines for predicting cis-regulatory elements.
Article in Developmental biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 42 citations in OpenAlex.
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- Cooperative Gsx2-DNA binding requires DNA bending and a novel Gsx2 homeodomain interface.Nucleic acids research · 2024Article
- Prediction of cooperative homeodomain DNA binding sites from high-throughput-SELEX data.Nucleic acids research · 2023Article
- A Drosophila Su(H) model of Adams-Oliver Syndrome reveals cofactor titration as a mechanism underlying developmental defects.PLoS genetics · 2022Article
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- Enhancers with cooperative Notch binding sites are more resistant to regulation by the Hairless co-repressor.PLoS genetics · 2021Article
- Mechanisms of stearoyl CoA desaturase inhibitor sensitivity and acquired resistance in cancer.Science advances · 2021Article
- Conserved Gsx2/Ind homeodomain monomer versus homodimer DNA binding defines regulatory outcomes in flies and mice.Genes & development · 2021Article
- Mechanisms Underlying Hox-Mediated Transcriptional Outcomes.Frontiers in cell and developmental biology · 2021Review
- Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks.eLife · 2020Article
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- Physical interactions between Gsx2 and Ascl1 balance progenitor expansion versus neurogenesis in the mouse lateral ganglionic eminence.Development (Cambridge, England) · 2020Article
- Homotypic cooperativity and collective binding are determinants of bHLH specificity and function.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- A Comprehensive Structure-Function Study of Neurogenin3 Disease-Causing Alleles during Human Pancreas and Intestinal Organoid Development.Developmental cell · 2019Article
- The cis-regulatory logic underlying abdominal Hox-mediated repression versus activation of regulatory elements in Drosophila.Developmental biology · 2019Article
- Degenerate Pax2 and Senseless binding motifs improve detection of low-affinity sites required for enhancer specificity.PLoS genetics · 2018Article
- Using competition assays to quantitatively model cooperative binding by transcription factors and other ligands.Biochimica et biophysica acta. General subjects · 2017Article
- A Hox complex activates and potentiates the Epidermal Growth Factor signaling pathway to specify Drosophila oenocytes.PLoS genetics · 2017Article
- Mechanisms of Specificity for Hox Factor Activity.Journal of developmental biology · 2016Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Hox transcription factors specify numerous cell fates along the anterior-posterior axis by regulating the expression of downstream target genes. While expression analysis has uncovered large numbers of de-regulated genes in cells with altered Hox activity, determining which are direct versus indirect targets has remained a significant challenge. Here, we characterize the DNA binding activity of Hox transcription factor complexes on eight experimentally verified cis-regulatory elements. Hox factors regulate the activity of each element by forming protein complexes with two cofactor proteins, Extradenticle (Exd) and Homothorax (Hth). Using comparative DNA binding assays, we found that a number of flexible arrangements of Hox, Exd, and Hth binding sites mediate cooperative transcription factor complexes. Moreover, analysis of a Distal-less regulatory element (DMXR) that is repressed by abdominal Hox factors revealed that suboptimal binding sites can be combined to form high affinity transcription complexes. Lastly, we determined that the anterior Hox factors are more dependent upon Exd and Hth for complex formation than posterior Hox factors. Based upon these findings, we suggest a general set of guidelines to serve as a basis for designing bioinformatics algorithms aimed at identifying Hox regulatory elements using the wealth of recently sequenced genomes.
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