PUBLICATION
Chromatin immunoprecipitation and an open chromatin assay in zebrafish erythrocytes
- Authors
- Yang, S., Ott, C.J., Rossmann, M.P., Superdock, M., Zon, L.I., Zhou, Y.
- ID
- ZDB-PUB-160725-16
- Date
- 2016
- 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
- MeSH Terms
-
- Animals
- Chromatin/genetics*
- Chromatin Immunoprecipitation/methods*
- Erythrocytes/metabolism
- Gene Expression Profiling/methods*
- Genome
- Genomics/methods*
- High-Throughput Nucleotide Sequencing
- Sequence Analysis, DNA/methods
- Zebrafish/genetics
- PubMed
- 27443937 Full text @ Meth. Cell. Biol.
Citation
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.
Abstract
Zebrafish 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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping