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A systematic approach to identify functional motifs within vertebrate developmental enhancers
- Source :
-
Developmental Biology . Jan2010, Vol. 337 Issue 2, p484-495. 12p. - Publication Year :
- 2010
-
Abstract
- 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 ∼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. [Copyright &y& Elsevier]
Details
- Language :
- English
- ISSN :
- 00121606
- Volume :
- 337
- Issue :
- 2
- Database :
- Academic Search Index
- Journal :
- Developmental Biology
- Publication Type :
- Academic Journal
- Accession number :
- 47359817
- Full Text :
- https://doi.org/10.1016/j.ydbio.2009.10.019