Comprehensive Zebrafish Development Atlas Completed

Researchers at the Eunice Kennedy Shriver National Institute of Child Health and Human Development have released a detailed atlas of zebrafish development, outlining the gene expression programs activated in nearly every cell during the first five days of development. The study, published in Developmental Cell, provides valuable insights into human development and disease, as gene expression programs guiding embryonic growth are found to be similar across various species.

To create the atlas, the study team used single-cell RNA sequencing to identify gene expression programs over the course of five days, with samples taken every two to 12 hours. The resulting atlas follows nearly 490,000 cells continuously over 120 hours after fertilization, with an average of 8,621 transcripts and 1,745 genes detected per cell. The study team then sorted these data among known cell types and cell states during development. 

To highlight the atlas’ utility, the team focused on the development of understudied cells, including intestinal cells called BEST4+ cells, which are linked to gastrointestinal diseases and cancer in people. Little is known about how these cells develop because they are absent in other common model organisms, such as mice. By using the atlas, the team computationally predicted the full developmental program of BEST4+ cells, including signals that initiate the cells’ development and transcription factors that carry out the process. These findings can be evaluated in model organisms or clinical samples to better understand the role of BEST4+ cells in human disease.

Senior author Jeffrey A. Farrell, Ph.D., emphasized the thoroughness of the atlas, describing the expression programs of hundreds of cell types across 62 developmental stages. The findings offer a comprehensive resource for researchers, enabling them to uncover novel insights into various cells, including those involved in human diseases. The open-source atlas is accessible to the research community, fostering collaboration and further discoveries in the field.