ArticleNature methods2009
Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos.
Article in Nature methods, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
54 citing papers in PubMed.
- Cis-Regulatory Elements in Mammals.International journal of molecular sciences · 2023Review
- The miR-430 locus with extreme promoter density forms a transcription body during the minor wave of zygotic genome activation.Developmental cell · 2023Article
- Regeneration and developmental enhancers are differentially compatible with minimal promoters.Developmental biology · 2022Article
- Article
- Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome.Molecular cell · 2022Article
- Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.Nature genetics · 2022Article
- Shear stress switches the association of endothelial enhancers from ETV/ETS to KLF transcription factor binding sites.Scientific reports · 2022Article
- Review
- Genomic environments scale the activities of diverse core promoters.Genome research · 2022Article
- Two promoters integrate multiple enhancer inputs to drive wild-type knirps expression in the Drosophila melanogaster embryo.Genetics · 2021Article
- Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters.Nature plants · 2021Article
- Acoustofluidic rotational tweezing enables high-speed contactless morphological phenotyping of zebrafish larvae.Nature communications · 2021Article
- Tools to Image Germplasm Dynamics During Early Zebrafish Development.Frontiers in cell and developmental biology · 2021Article
- Multi-template matching: a versatile tool for object-localization in microscopy images.BMC bioinformatics · 2020Article
- Article
- A Smart Imaging Workflow for Organ-Specific Screening in a Cystic Kidney Zebrafish Disease Model.International journal of molecular sciences · 2019Article
- Asymmetric pitx2 expression in medaka epithalamus is regulated by nodal signaling through an intronic enhancer.Development genes and evolution · 2018Article
- Zebrafish as a Model for Drug Screening in Genetic Kidney Diseases.Frontiers in pediatrics · 2018Review
- Article
- Robust Identification of Developmentally Active Endothelial Enhancers in Zebrafish Using FANS-Assisted ATAC-Seq.Cell reports · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Zebrafish embryos offer a unique combination of high-throughput capabilities and the complexity of the vertebrate animal for a variety of phenotypic screening applications. However, there is a need for automation of imaging technologies to exploit the potential of the transparent embryo. Here we report a high-throughput pipeline for registering domain-specific reporter expression in zebrafish embryos with the aim of mapping the interactions between cis-regulatory modules and core promoters. Automated microscopy coupled with custom-built embryo detection and segmentation software allowed the spatial registration of reporter activity for 202 enhancer-promoter combinations, based on images of thousands of embryos. The diversity of promoter-enhancer interaction specificities underscores the importance of the core promoter sequence in cis-regulatory interactions and provides a promoter resource for transgenic reporter studies. The technology described here is also suitable for the spatial analysis of fluorescence readouts in genetic, pharmaceutical or toxicological screens.
Indexed as
Identifiers
19898487What OpenQuestion holds
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.