A tissue dissociation method optimized for ATAC-seq and CUT&RUN inDrosophilapupal tissues

Chromatin accessibility, histone modifications and transcription factor binding are highly dynamic duringDrosophilametamorphosis and drive global changes in gene expression as larval tissues differentiate into adult structures. Unfortunately, the presence of pupa cuticle on manyDrosophilatissues during metamorphosis prevents enzyme access to cells and has limited the use of enzymaticin situmethods for assessing chromatin accessibility and histone modifications. Here, we present a dissociation method for cuticle-bound pupal tissues that is optimized for use with ATAC-Seq and CUT&RUN to interrogate chromatin accessibility and histone modifications. We show this method provides comparable chromatin accessibility data to the non-enzymatic approach FAIRE-seq, with only a fraction of the amount of input tissue required. This approach is also compatible with CUT&RUN, which allows genome-wide mapping of histone modifications with less than 1/10thof the tissue input required for more conventional approaches such as Chromatin Immunoprecipitation Sequencing (ChIP-seq). Our protocol makes it possible to use newer, more sensitive enzymaticin situapproaches to interrogate gene regulatory networks duringDrosophilametamorphosis.