|ZFIN ID: ZDB-PUB-160725-16|
Chromatin immunoprecipitation and an open chromatin assay in zebrafish erythrocytes
Yang, S., Ott, C.J., Rossmann, M.P., Superdock, M., Zon, L.I., Zhou, Y.
|Source:||Methods in cell biology 135: 387-412 (Chapter)|
|Registered Authors:||Zhou, Yi, Zon, Leonard I.|
|Keywords:||ATAC-seq, ChIP-seq, Chromatin, Epigenetics, Erythrocytes, Immunoprecipitation, Transcription|
|PubMed:||27443937 Full text @ Meth. Cell. Biol.|
Yang, S., Ott, C.J., Rossmann, M.P., Superdock, M., Zon, L.I., Zhou, Y. (2016) Chromatin immunoprecipitation and an open chromatin assay in zebrafish erythrocytes. Methods in cell biology. 135:387-412.
ABSTRACTZebrafish is an excellent genetic and developmental model for the study of vertebrate development and disease. Its ability to produce an abundance of transparent, externally developed embryos has facilitated large-scale genetic and chemical screens for the identification of critical genes and chemical factors that modulate developmental pathways. These studies can have profound implications for the diagnosis and treatment of a variety of human diseases. Recent advancements in molecular and genomic studies have provided valuable tools and resources for comprehensive and high-resolution analysis of epigenomes during cell specification and lineage differentiation throughout development. In this chapter, we describe two simple methods to evaluate protein-DNA interaction and chromatin architecture in erythrocytes from adult zebrafish. These are chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) and an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). These techniques, together with gene expression profiling, are useful for analyzing epigenomic regulation of cell specification, differentiation, and function during zebrafish development in both normal and disease models.
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