ArticleGenome research2011
High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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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.
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Who cites it
43 citing papers in PubMed, 58 citations in OpenAlex.
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- Early life-stage thermal resilience is determined by climate-linked regulatory variation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Exploring the role and mechanisms of MAGEA4 in tumorigenesis, regulation, and immunotherapy.Molecular medicine (Cambridge, Mass.) · 2025Review
- Recruitment of homodimeric proneural factors by conserved CAT-CAT E-boxes drives major epigenetic reconfiguration in cortical neurogenesis.Nucleic acids research · 2024Article
- Article
- Protein-intrinsic properties and context-dependent effects regulate pioneer factor binding and function.Nature structural & molecular biology · 2024Article
- Transcriptional Targets of TWIST1 in Human Mesenchymal Stem/Stromal Cells Mechanistically Link Stem/Progenitor and Paracrine Functions.Stem cells (Dayton, Ohio) · 2023Article
- Sequence reliance of abioRxiv : the preprint server for biology · 2023Article
- Protein-intrinsic properties and context-dependent effects regulate pioneer-factor binding and function.bioRxiv : the preprint server for biology · 2023Article
- Contribution of TWIST1-EVX1 Axis in Invasiveness of Esophageal Squamous Cell Carcinoma; a Functional Study.Iranian journal of biotechnology · 2022Article
- Fitting thermodynamic-based models: Incorporating parameter sensitivity improves the performance of an evolutionary algorithm.Mathematical biosciences · 2021Article
- Mechanisms of Binding Specificity among bHLH Transcription Factors.International journal of molecular sciences · 2021Review
- Dynamic patterning by morphogens illuminated by cis-regulatory studies.Development (Cambridge, England) · 2021Review
- Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling.Cancers · 2020Article
- Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos.eLife · 2020Article
- Twist-dependent ratchet functioning downstream from Dorsal revealed using a light-inducible degron.Genes & development · 2020Article
- Spatiotemporal control of gene expression boundaries using a feedforward loop.Developmental dynamics : an official publication of the American Association of Anatomists · 2020Article
- Coacting enhancers can have complementary functions within gene regulatory networks and promote canalization.PLoS genetics · 2019Article
- Migrating cells control morphogenesis of substratum serving as track to promote directional movement of the collective.Development (Cambridge, England) · 2019Article
- Broadly expressed repressors integrate patterning across orthogonal axes in embryos.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
Cis-regulatory modules (CRMs) function by binding sequence specific transcription factors, but the relationship between in vivo physical binding and the regulatory capacity of factor-bound DNA elements remains uncertain. We investigate this relationship for the well-studied Twist factor in Drosophila melanogaster embryos by analyzing genome-wide factor occupancy and testing the functional significance of Twist occupied regions and motifs within regions. Twist ChIP-seq data efficiently identified previously studied Twist-dependent CRMs and robustly predicted new CRM activity in transgenesis, with newly identified Twist-occupied regions supporting diverse spatiotemporal patterns (>74% positive, n = 31). Some, but not all, candidate CRMs require Twist for proper expression in the embryo. The Twist motifs most favored in genome ChIP data (in vivo) differed from those most favored by Systematic Evolution of Ligands by EXponential enrichment (SELEX) (in vitro). Furthermore, the majority of ChIP-seq signals could be parsimoniously explained by a CABVTG motif located within 50 bp of the ChIP summit and, of these, CACATG was most prevalent. Mutagenesis experiments demonstrated that different Twist E-box motif types are not fully interchangeable, suggesting that the ChIP-derived consensus (CABVTG) includes sites having distinct regulatory outputs. Further analysis of position, frequency of occurrence, and sequence conservation revealed significant enrichment and conservation of CABVTG E-box motifs near Twist ChIP-seq signal summits, preferential conservation of ±150 bp surrounding Twist occupied summits, and enrichment of GA- and CA-repeat sequences near Twist occupied summits. Our results show that high resolution in vivo occupancy data can be used to drive efficient discovery and dissection of global and local cis-regulatory logic.
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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.