[
International Worm Meeting,
2019]
The profiling of protein-DNA interactions, including transcription factors, has become increasingly important in genetics and genomics, to elucidate mechanisms of genome regulation. Some common strategies to view these interactions include ChIP-seq, ATAC-seq, MNase-seq, ChEC and ChIC. However, these methods have limitations, from large background noise, to lack of specificity or scalability. A new method, cleavage under targets and release using nuclease (CUT&RUN), allows for the profiling of specific DNA-protein complexes with low background noise in a short amount of time. CUT&RUN uses antibody-targeted controlled cleavage performed by a micrococcal nuclease in situ on permeabilized cells. C. elegans poses a specific challenge with CUT&RUN due to its cuticle, which prevents antibodies and nucleases from entering cells, and the release of protein-DNA complexes out of cells. To address these issues we have adapted CUT&RUN for larval C. elegans. This adapted CUT&RUN method includes a grinding protocol to break open the worm cuticle, without destroying cells, as evidenced by trypan blue staining. Our results show that we have successfully isolated an H3K27me3 histone ladder from C. elegans using an optimized version of CUT&RUN, not requiring nuclei purification, and are currently profiling the nuclear hormone receptor NHR-25 in L1s to adapt the protocol for endogenously tagged transcription factors.