Rosalind Franklin Society Proudly Announces the 2022 Award Recipient for Zebrafish

Genome-wide profiling of the eukaryotic genome has powered the identification of critical regulatory genomic regions and transcription factor targeted genes that impact all areas of biology and medicine. However, analyses in rare cell populations have been challenging, in particular in the stem cell biology field. Cleavage Under Targets and Release Using Nuclease (CUT&RUN), first developed by Skene and Henikoff, has emerged as a chromatin profiling strategy that excels traditional methods. Cross-linkage with formaldehyde is not necessary in CUT&RUN, increasing the resolution and reducing the number of cells needed. Nevertheless, CUT&RUN is at its early stages, and standards for quality, reproducibility, validation and usage in different animal organisms are lacking. We have developed a method to successfully perform CUT&RUN to map transcription factor (TF) binding sites in embryonic, adult tissues, and fluorescence activated cell sorted zebrafish cells. We also provide a detailed workflow for the identification and validation of predicted TF binding sites that can be utilized in any animal species. Altogether, our strategy provides the necessary standardized workflow to apply this invaluable technique to many species, as well as expanding this tool to the zebrafish community, improving the epigenetic resolution that can be achieved in small cell numbers.