Abstract
Although millions of transcription factor binding sites, or cistromes, have been identified across the human genome, defining which of these sites is functional in a given condition remains challenging. Using CRISPR/Cas9 knockout screens and gene essentiality or fitness as the readout, we systematically investigated the essentiality of over 10,000 FOXA1 and CTCF binding sites in breast and prostate cancer cells. We found that essential FOXA1 binding sites act as enhancers to orchestrate the expression of nearby essential genes through the binding of lineage-specific transcription factors. In contrast, CRISPR screens of the CTCF cistrome revealed 2 classes of essential binding sites. The first class of essential CTCF binding sites act like FOXA1 sites as enhancers to regulate the expression of nearby essential genes, while a second class of essential CTCF binding sites was identified at topologically associated domain (TAD) boundaries and display distinct characteristics. Using regression methods trained on our screening data and public epigenetic profiles, we developed a model to predict essential cis-elements with high accuracy. The model for FOXA1 essentiality correctly predicts noncoding variants associated with cancer risk and progression. Taken together, CRISPR screens of cis-regulatory elements can define the essential cistrome of a given factor and can inform the development of predictive models of cistrome function.
Highlights
Millions of transcription factor binding sites, or cistromes, have been identified across the human genome, defining which of these sites is functional in a given condition remains challenging
Based on the screening data, we further evaluated genomic and epigenomic features associated with essential enhancers, and built machine-learning models that predict the functions of sites that are not included in the screen
Our study demonstrated genome-wide cistrome screens as a promising technology to characterize the functions of transcription factor binding in detail
Summary
Millions of transcription factor binding sites, or cistromes, have been identified across the human genome, defining which of these sites is functional in a given condition remains challenging. Using genome-wide CRISPR screens, we profiled over 10,000 FOXA1 and CTCF binding sites for their roles in regulating the fitness of breast and prostate cancer cells, and developed a model to predict essentiality for cis-elements. These efforts reveal how the key transcription factors and their cistromes regulate cell essentiality in hormone-dependent cancers and highlight an efficient approach to investigate the functions of noncoding regions of the genome. M.B. has served as a consultant to GTx, Inc. and Aleta Biotherapeutics
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