Daniel Armendariz

Keywords Perturb-seq CRISPR/Cas9 human pluripotent stem cells single-cell genomics cardiomyocytes neural progenitor cells Introduction CRISPR interference (CRISPRi) Perturb-seq is a high-throughput phenotypic assay that combines CRISPRi using a library of single guide RNAs (sgRNAs) with single-cell RNA sequencing (scRNA-seq) to analyze the effects of thousands of genetic perturbations in a single experiment (Replogle et al., 2022; Adamson et al., 2016).

Abstract Genetic studies have associated thousands of enhancers with breast cancer. However, the vast majority have not been functionally characterized. Thus, it remains unclear how variant-associated enhancers contribute to cancer. Here, we perform single-cell CRISPRi screens of 3,512 regulatory elements associated with breast cancer to measure the impact of these regions on transcriptional phenotypes.

Since there are millions of regulatory elements in the human genome and many more sequence variants, it is not feasible to experimentally test all of them for their impact on developmental disorders. Computational models that can accurately predict the regulatory activity of sequence variants will be an essential component to close this gap. Several recent advances highlight the promise of this nascent field.