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Genomics. 2016 Aug;108(2):102-7. doi: 10.1016/j.ygeno.2016.05.005. Epub 2016 May 30.

Enhancer activity-based identification of functional enhancers using zebrafish embryos.

Author information

1
Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan.
2
Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan. Electronic address: akawamur@mail.saitama-u.ac.jp.

Abstract

Chromatin immunoprecipitation (ChIP) against enhancer-associated marks with massive sequencing is a powerful approach to identify genome-wide distributions of putative enhancers. However, functional in vivo analysis is required to elucidate the activities of predicted enhancers. Using zebrafish embryos, we established a ChIP-Injection method that enables identification of functional enhancers based on their enhancer activities in embryos. Each reporter gene possessing the enhancer-associated genomic region enriched by ChIP was injected into zebrafish embryos to analyze the activity of putative enhancers. By using the ChIP-Injection, we identified 32 distinct putative enhancers that drove specific expression. Additionally, we generated transgenic lines that exhibit distributions of the EGFP signal as was observed in the screening. Furthermore, the expression pattern driven by the identified somite-specific enhancer resembled that of the gene acta2. The results indicate that ChIP-Injection provides an efficient approach for identification of active enhancers in a potentially wide variety of developmental tissues and stages.

KEYWORDS:

Cis-regulatory element; Enhancer; Tailbud; Zebrafish

PMID:
27256877
DOI:
10.1016/j.ygeno.2016.05.005
[Indexed for MEDLINE]

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