ArticleDevelopmental biology2010
A systematic approach to identify functional motifs within vertebrate developmental enhancers.
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 49 papers.
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Who cites it
49 citing papers in PubMed.
- Article
- Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci.Nature communications · 2024Article
- Regulatory elements inGenetics in medicine open · 2024Article
- Next-generation plasmids for transgenesis in zebrafish and beyond.Development (Cambridge, England) · 2023Article
- Regeneration and developmental enhancers are differentially compatible with minimal promoters.Developmental biology · 2022Article
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- Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos.Cell genomics · 2022Article
- Coordination of two enhancers drives expression of olfactory trace amine-associated receptors.Nature communications · 2021Article
- Article
- Combinatorial action of NF-Y and TALE at embryonic enhancers defines distinct gene expression programs during zygotic genome activation in zebrafish.Developmental biology · 2020Article
- Article
- Chromatin Conformation Links Putative Enhancers in Intracranial Aneurysm-Associated Regions to Potential Candidate Genes.Journal of the American Heart Association · 2019Article
- Functional characterization of the ZEB2 regulatory landscape.Human molecular genetics · 2019Article
- A neuronal enhancer network upstream of MEF2C is compromised in patients with Rett-like characteristics.Human molecular genetics · 2019Article
- Unraveling the transcriptional regulation of TWIST1 in limb development.PLoS genetics · 2018Article
- Functionally conserved enhancers with divergent sequences in distant vertebrates.BMC genomics · 2015Article
- Uncovering the Role of Hypermethylation by CTG Expansion in Myotonic Dystrophy Type 1 Using Mutant Human Embryonic Stem Cells.Stem cell reports · 2015Article
- A PAX1 enhancer locus is associated with susceptibility to idiopathic scoliosis in females.Nature communications · 2015Article
- Article
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7 authors.
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Abstract
Uncovering the cis-regulatory logic of developmental enhancers is critical to understanding the role of non-coding DNA in development. However, it is cumbersome to identify functional motifs within enhancers, and thus few vertebrate enhancers have their core functional motifs revealed. Here we report a combined experimental and computational approach for discovering regulatory motifs in developmental enhancers. Making use of the zebrafish gene expression database, we computationally identified conserved non-coding elements (CNEs) likely to have a desired tissue-specificity based on the expression of nearby genes. Through a high throughput and robust enhancer assay, we tested the activity of approximately 100 such CNEs and efficiently uncovered developmental enhancers with desired spatial and temporal expression patterns in the zebrafish brain. Application of de novo motif prediction algorithms on a group of forebrain enhancers identified five top-ranked motifs, all of which were experimentally validated as critical for forebrain enhancer activity. These results demonstrate a systematic approach to discover important regulatory motifs in vertebrate developmental enhancers. Moreover, this dataset provides a useful resource for further dissection of vertebrate brain development and function.
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