ArticleThe EMBO journal2012
The cis-regulatory code of Hox function in Drosophila.
Article in The EMBO journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 26 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
26 citing papers in PubMed.
- Identification of a novel enhancer essential forLife science alliance · 2023Article
- Dachshund acts with Abdominal-B to trigger programmed cell death in the Drosophila central nervous system at the frontiers of Abd-B expression.Developmental neurobiology · 2022Article
- Specificity of the Hox member Deformed is determined by transcription factor levels and binding site affinities.Nature communications · 2022Article
- Article
- Single-cell RNA sequencing of motoneurons identifies regulators of synaptic wiring in Drosophila embryos.Molecular systems biology · 2022Article
- Diversification and Functional Evolution of HOX Proteins.Frontiers in cell and developmental biology · 2022Review
- Enhancer grammar in development, evolution, and disease: dependencies and interplay.Developmental cell · 2021Review
- Roles ofFrontiers in cell and developmental biology · 2021Review
- Learning and interpreting the gene regulatory grammar in a deep learning framework.PLoS computational biology · 2020Article
- Multi-level and lineage-specific interactomes of the Hox transcription factor Ubx contribute to its functional specificity.Nature communications · 2020Article
- The Hox geneDevelopment (Cambridge, England) · 2019Article
- True equilibrium measurement of transcription factor-DNA binding affinities using automated polarization microscopy.Nature communications · 2018Article
- Combinatorial action of Grainyhead, Extradenticle and Notch in regulating Hox mediated apoptosis in Drosophila larval CNS.PLoS genetics · 2017Article
- HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets.Genome research · 2017Article
- Downregulation of Homeobox B7 Inhibits the Tumorigenesis and Progression of Osteosarcoma.Oncology research · 2017Article
- The function of homeobox genes and lncRNAs in cancer.Oncology letters · 2016Article
- Deregulation of the HOXA9/MEIS1 axis in acute leukemia.Current opinion in hematology · 2016Review
- Review
- Article
- Roles of cofactors and chromatin accessibility in Hox protein target specificity.Epigenetics & chromatin · 2016Article
Corrections and comments
- Erratum issued
Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Precise gene expression is a fundamental aspect of organismal function and depends on the combinatorial interplay of transcription factors (TFs) with cis-regulatory DNA elements. While much is known about TF function in general, our understanding of their cell type-specific activities is still poor. To address how widely expressed transcriptional regulators modulate downstream gene activity with high cellular specificity, we have identified binding regions for the Hox TF Deformed (Dfd) in the Drosophila genome. Our analysis of architectural features within Hox cis-regulatory response elements (HREs) shows that HRE structure is essential for cell type-specific gene expression. We also find that Dfd and Ultrabithorax (Ubx), another Hox TF specifying different morphological traits, interact with non-overlapping regions in vivo, despite their similar DNA binding preferences. While Dfd and Ubx HREs exhibit comparable design principles, their motif compositions and motif-pair associations are distinct, explaining the highly selective interaction of these Hox proteins with the regulatory environment. Thus, our results uncover the regulatory code imprinted in Hox enhancers and elucidate the mechanisms underlying functional specificity of TFs in vivo.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.