Deciphering essential cistromes using genome-wide CRISPR screens

Proc Natl Acad Sci U S A. 2019 Dec 10;116(50):25186-25195. doi: 10.1073/pnas.1908155116. Epub 2019 Nov 14.


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.

Keywords: CRISPR screen; CTCF; FOXA1; cistrome; enhancer.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Breast Neoplasms / genetics
  • Breast Neoplasms / metabolism
  • CCCTC-Binding Factor / genetics
  • CCCTC-Binding Factor / metabolism*
  • CRISPR-Cas Systems
  • Cell Line, Tumor
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Female
  • Genome, Human
  • Hepatocyte Nuclear Factor 3-alpha / genetics
  • Hepatocyte Nuclear Factor 3-alpha / metabolism*
  • Humans
  • Male
  • Promoter Regions, Genetic
  • Prostatic Neoplasms / genetics
  • Prostatic Neoplasms / metabolism
  • Regulatory Elements, Transcriptional*


  • CCCTC-Binding Factor
  • CTCF protein, human
  • FOXA1 protein, human
  • Hepatocyte Nuclear Factor 3-alpha