Poshen B Chen, Patrick C Fiaux, Kai Zhang, Bin Li, Naoki Kubo et al.
A scarcity of functionally validated enhancers in the human genome presents a significant hurdle to understanding how these cis-regulatory elements contribute to human diseases. We carry out highly multiplexed CRISPR-based perturbation and sequencing to identify enhancers required for cell proliferation and fitness in 10 human cancer cell lines. Our results suggest that the cell fitness enhancers, unlike their target genes, display high cell-type specificity of chromatin features. They typically adopt a modular structure, comprised of activating elements enriched for motifs of oncogenic transcription factors, surrounded by repressive elements enriched for motifs recognized by transcription factors with tumor suppressor functions. We further identify cell fitness enhancers that are selectively accessible in clinical tumor samples, and the levels of chromatin accessibility are associated with patient survival. These results reveal functional enhancers across multiple cancer cell lines, characterize their context-dependent chromatin organization, and yield insights into altered transcription programs in cancer cells.
Poshen B Chen, Patrick C Fiaux, Kai Zhang, Bin Li, Naoki Kubo, Shan Jiang, Rong Hu, Emma Rooholfada, Sihan Wu, Mengchi Wang, Wei Wang, Graham McVicker, Paul S Mischel, Bing Ren. Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation. 2022-11-08. https://doi.org/10.1016/j.celrep.2022.111630
An episomal hSTARR-seq library comprising 12,833 190-bp fragments tiled across HCT116 essential-enhancer windows, 60 positive-control oligos for known MYC/SV40 enhancers, and 2,095 yeast ORF negative controls was electroporated into HCT116 cells in triplicate. Matched plasmid DNA and poly(A)+ reporter-RNA counts from Table S3 were used to quantify per-oligo enhancer activity.
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