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Enhancer activity-based identification of functional enhancers using zebrafish embryos
Tomohito Taminato1, Daisuke Yokota1, Soh Araki1
1Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan.
Genomics
|June 4, 2016
Summary
We developed ChIP-Injection to identify functional enhancers in zebrafish embryos. This method efficiently reveals active enhancers for diverse developmental applications.
Area of Science:
- Developmental Biology
- Genomics
- Molecular Biology
Background:
- Chromatin immunoprecipitation followed by massive sequencing (ChIP-seq) identifies potential enhancers genome-wide.
- Functional validation of these predicted enhancers in vivo is crucial but challenging.
Purpose of the Study:
- To establish an efficient method for identifying functional enhancers in vivo.
- To validate the activity of putative enhancers identified through ChIP-seq.
Main Methods:
- Developed the ChIP-Injection method using zebrafish embryos.
- Injected reporter genes linked to ChIP-enriched genomic regions into zebrafish embryos.
- Analyzed enhancer activity by observing reporter gene expression patterns.
Main Results:
- Identified 32 distinct putative enhancers driving specific expression patterns in zebrafish embryos.
- Generated transgenic zebrafish lines reflecting the observed enhancer activities.
- Characterized a somite-specific enhancer whose expression pattern matched the acta2 gene.
Conclusions:
- ChIP-Injection is an efficient technique for identifying active enhancers.
- This method is applicable across various developmental tissues and stages.
- Facilitates functional analysis of predicted enhancers in vivo.
