Zebrafish Epigenetics Project

Welcome to our zebrafish chromatin factor screen database. To generate a complete compendium of chromatin factors that establish the genetic code during developmental hematopoiesis, we conducted a large-scale reverse genetic screen targeting orthologues of 425 human chromatin factors that contain chromatin binding, modifying, or remodeling domains in zebrafish. All the results from the screen are compiled in this database, including the gene list, morpholino sequences, and in situ data.

Morpholinos for each chromatin factor were injected into single cell embryos, and each morpholino was injected at three concentrations to give a range of phenotypes from a hypomorph to a near complete knockdown for most mRNA products, similar to an allelic series. Post-injection, the embryos were grown to the proper developmental stage and collected to assay for hematopoietic defects by whole-mount in situ hybridization (WISH). Two screens were conducted simultaneously for primitive and definitive blood formation. For the primitive screen, developing erythrocytes were assayed by ß-globin e3 expression at the 16 somite stage (ss), or 17 hours post-fertilization (hpf), in the posterior tail of the embryo. For the definitive screen, the establishment of hematopoietic stem and progenitor cells (HSPCs) in the aorta-gonad-mesonephros (AGM) region was detected with c-myb and runx1 expression at 36 hpf.

According to the expression phenotypes observed, the morphants were divided into three major categories: no change, decrease, or increase. Due to the range of decreased staining from subtle reduction to complete absence of staining, we further subdivided the decrease category into mild, intermediate, and strong. Morphants with developmental abnormalities were also noted. Click links below to access the database.

Chromatin Factor and Experiment Results

Nature Cell Biology (2013) doi:10.1038/ncb2870