Tissue-specific transcription footprinting using RNA PolII DamID (RAPID) in C. elegans [Blastomeres]

Gene expression is a major determinant of cell fate and physiology, yet it is notoriously difficult to characterize for the widely used model system C. elegans. By using a new method based on in vivo covalent modification of DNA by RNA polymerases, we determine genome-wide transcription patterns in single tissues of embryos or young adult animals. We show that the method is able to identify actively transcribed genes in tissues representing down to 0.2% of the somatic cells in adult animals. Additionally, this method can be fully performed in a single laboratory by using third generation sequencing methods (ONT). Overall design: DamID experiments with Dam fusions to GFP (control) and RPB-6 (RNA polymerases) in sorted embryonic blastomeres, nanopore amplicon sequencing