ATAC-seq of TNF-alpha activation in HEK cells with or without TRAFTAC against NfkB

TRAnscription Factor TArgeting Chimeras (TRAFTACs) can downregulated specific transcription factors at the protein-level through their DNA-binding affinity. We tested a previously validated TRAFTAC (Samarasinghe et al., 2021) against NFkB in the context of TNF-alpha activation in HEK cells, and profiled DNA accessibility using ATAC-seq. Overall design: Replicating the experiments from (Samarasinghe et al., 2021), we transfected HEK cells with the dCas9-HT7 plasmid and DNA-RNA hybrids (NFkB or scrambled TRAFTAC, in duplicates) for 6h, before treating the cells with TNF-alpha (which triggers NFkB activation) and the PROTAC against the Halo tag (HP14) for 19h. We confirmed a 37% reduction in NFkB1/p50 levels before collecting the four samples for ATAC profiling.