title: Chromatin immunoprecipitation and an open chromatin assay in zebrafish erythrocytes.
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.
authors.affiliation: Boston Children's Hospital, Boston, MA, United States; Dana Farber Cancer Institute, Harvard Stem Cell Institute, Boston, MA, United States; Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, United States.
authors.forename: S
authors.initials: S
authors.lastname: Yang
authors.affiliation: Dana Farber Cancer Institute, Harvard Stem Cell Institute, Boston, MA, United States.
authors.forename: C J
authors.initials: CJ
authors.lastname: Ott
authors.affiliation: Harvard University, Harvard, Cambridge, MA, United States.
authors.forename: M P
authors.initials: MP
authors.lastname: Rossmann
authors.affiliation: Boston Children's Hospital, Boston, MA, United States; Dana Farber Cancer Institute, Harvard Stem Cell Institute, Boston, MA, United States; Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, United States.
authors.forename: M
authors.initials: M
authors.lastname: Superdock
authors.affiliation: Boston Children's Hospital, Boston, MA, United States; Dana Farber Cancer Institute, Harvard Stem Cell Institute, Boston, MA, United States; Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, United States; Harvard University, Harvard, Cambridge, MA, United States.
authors.forename: L I
authors.initials: LI
authors.lastname: Zon
authors.affiliation: Boston Children's Hospital, Boston, MA, United States; Dana Farber Cancer Institute, Harvard Stem Cell Institute, Boston, MA, United States; Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, United States; Harvard University, Harvard, Cambridge, MA, United States.
authors.forename: Y
authors.initials: Y
authors.lastname: Zhou
mesh_terms: D000818:Animals; D002843:Chromatin / Q000235:genetics*; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004912:Erythrocytes / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D016678:Genome; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D017422:Sequence Analysis, DNA / Q000379:methods; D015027:Zebrafish / Q000235:genetics
chemical_list: D002843:Chromatin
keywords: ATAC-seq; ChIP-seq; Chromatin; Epigenetics; Erythrocytes; Immunoprecipitation; Transcription