We will create a resource for the investigation of chromatin structure, epigenetic modifications, and transcriptional regulators in early zebrafish development. The resource will be named CZECH, the Center for Zebrafish Epigenetics and CHromatin. Chromatin regulates gene expression, and impacts development by influencing the transcriptional programs that drive cell growth and fate decisions. DNA methylation and other chromatin marks (defined as the epigenome) strongly influence the timing and strength of expression of particular genes during development, but a systematic study has not been performed in any organism. Furthermore, misregulation of transcription via chromatin underlies many developmental defects and certain cancers. Thus, we must understand how chromatin dynamics help guide development. The Center will address this issue using a combination of genomic and genetic approaches, will provide detailed protocols for genomic approaches, and will deploy and manage a database for the community to view and submit datasets. Here, we will define the basic epigenome of germ cells and the early embryo of the zebrafish, both before and during organ specification. We will combine chromatin immunoprecipitation (ChIP) with high-density genome tiling arrays (to examine chromatin), and also perform gene expression profiling. We will initially limit our examination to the chromatin modifications most closely associated with transcriptional repression (DNA methylation, H3K9me3, and H3K27me3), or transcriptional activation (H3K4me3), which include the `bivalent'modifications important for poising genes in stem cells. Notably, our preliminary studies suggest the poising of early developmental regulators in sperm chromatin by DNA hypomethylation. In later stage embryos, we will use FACS to isolate developing tissues and then determine their epigenome.

Public Health Relevance

This project addresses how chromosomes and their resident genes are packaged in germ cells and then change their packaging following fertilization to regulate gene expression during early development. This process is central to understanding how cells differentiate, how organs develop, and how cell growth is regulated. The misregulation of chromosome and gene packaging leads to problems such as birth defects, retardation, or cancer, depending on the particular chromosome(s) or gene(s) affected.

National Institute of Health (NIH)
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Research Project (R01)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-BDA-F (50))
Program Officer
Coulombe, James N
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Utah
Internal Medicine/Medicine
Schools of Medicine
Salt Lake City
United States
Zip Code
Potok, Magdalena E; Nix, David A; Parnell, Timothy J et al. (2013) Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern. Cell 153:759-72
Wu, Shan-Fu; Zhang, Haiying; Hammoud, Saher Sue et al. (2011) DNA methylation profiling in zebrafish. Methods Cell Biol 104:327-39
Wu, Shan-Fu; Zhang, Haiying; Cairns, Bradley R (2011) Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm. Genome Res 21:578-89
Rai, Kunal; Sarkar, Sharmistha; Broadbent, Talmage J et al. (2010) DNA demethylase activity maintains intestinal cells in an undifferentiated state following loss of APC. Cell 142:930-42
Rai, Kunal; Jafri, Itrat F; Chidester, Stephanie et al. (2010) Dnmt3 and G9a cooperate for tissue-specific development in zebrafish. J Biol Chem 285:4110-21
Rai, Kunal; Huggins, Ian J; James, Smitha R et al. (2008) DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and gadd45. Cell 135:1201-12