A systematic approach to identify functional motifs within vertebrate developmental enhancers.
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.
Li
Qiang
Q
Department of Biopharmaceutical Sciences, Programs in Biological Sciences and Human Genetics, University of California, San Francisco, CA 94143-2811, USA. qiang.li@ucsf.edu
Ritter
Deborah
D
Yang
Nan
N
Dong
Zhiqiang
Z
Li
Hao
H
Chuang
Jeffrey H
JH
Guo
Su
S
D000818:Animals; D001483:Base Sequence; D001921:Brain / Q000196:embryology / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D021901:DNA, Intergenic / Q000235:genetics; D030541:Databases, Genetic; D004742:Enhancer Elements, Genetic; D018507:Gene Expression Regulation, Developmental; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D009928:Organ Specificity / Q000235:genetics; D015203:Reproducibility of Results; D013997:Time Factors; D015027:Zebrafish / Q000196:embryology* / Q000235:genetics*
D021901:DNA, Intergenic