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.
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.
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.