ArticleDevelopmental biology2009
Design flexibility in cis-regulatory control of gene expression: synthetic and comparative evidence.
Article in Developmental biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 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.
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Who cites it
51 citing papers in PubMed, 78 citations in OpenAlex.
- ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants.bioRxiv : the preprint server for biology · 2025Article
- Two sequential gene expression programs bridged by cell division support long-distance collective cell migration.Development (Cambridge, England) · 2024Article
- Shadow enhancers modulate distinct transcriptional parameters that differentially effect downstream patterning events.Development (Cambridge, England) · 2022Article
- Base-resolution models of transcription-factor binding reveal soft motif syntax.Nature genetics · 2021Article
- Setting up for gastrulation: D. melanogaster.Current topics in developmental biology · 2020Review
- Coacting enhancers can have complementary functions within gene regulatory networks and promote canalization.PLoS genetics · 2019Article
- Distinct Roles of Broadly Expressed Repressors Support Dynamic Enhancer Action and Change in Time.Cell reports · 2019Article
- Shaping ofGenetics · 2019Article
- The dorsoventral patterning ofEvoDevo · 2018Article
- Regulatory states in the developmental control of gene expression.Briefings in functional genomics · 2017Review
- Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity.eLife · 2017Article
- Broadly expressed repressors integrate patterning across orthogonal axes in embryos.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- The Zic family homologue Odd-paired regulates Alk expression in Drosophila.PLoS genetics · 2017Article
- Stepwise Progression of Embryonic Patterning.Trends in genetics : TIG · 2016Review
- Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks.Current biology : CB · 2016Article
- A Systematic Ensemble Approach to Thermodynamic Modeling of Gene Expression from Sequence Data.Cell systems · 2015Article
- Gene Regulatory Mechanisms Underlying the Spatial and Temporal Regulation of Target-Dependent Gene Expression in Drosophila Neurons.PLoS genetics · 2015Article
- Midline enhancer activity of the short gastrulation shadow enhancer is characterized by three unusual features for cis-regulatory DNA.BMB reports · 2015Article
- BAC transgenic mice provide evidence that p53 expression is highly regulated in vivo.Cell death & disease · 2015Article
- Dynamic BMP signaling polarized by Toll patterns the dorsoventral axis in a hemimetabolous insect.eLife · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
In early Drosophila embryos, the transcription factor Dorsal regulates patterns of gene expression and cell fate specification along the dorsal-ventral axis. How gene expression is produced within the broad lateral domain of the presumptive neurogenic ectoderm is not understood. To investigate transcriptional control during neurogenic ectoderm specification, we examined divergence and function of an embryonic cis-regulatory element controlling the gene short gastrulation (sog). While transcription factor binding sites are not completely conserved, we demonstrate that these sequences are bona fide regulatory elements, despite variable regulatory architecture. Mutation of conserved sequences revealed that putative transcription factor binding sites for Dorsal and Zelda, a ubiquitous maternal transcription factor, are required for proper sog expression. When Zelda and Dorsal sites are paired in a synthetic regulatory element, broad lateral expression results. However, synthetic regulatory elements that contain Dorsal and an additional activator also drive expression throughout the neurogenic ectoderm. Our results suggest that interaction between Dorsal and Zelda drives expression within the presumptive neurogenic ectoderm, but they also demonstrate that regulatory architecture directing expression in this domain is flexible. We propose a model for neurogenic ectoderm specification in which gene regulation occurs at the intersection of temporal and spatial transcription factor inputs.
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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.