Precise measurement of molecular phenotypes with barcode-based CRISPRi screens

Uncovering the genetic basis of molecular processes is essential for understanding a broad range of biological phenomena. CRIPSR-Cas9 approaches enable this discovery through programable and systematic profiling of regulatory genes underlying diverse cellular behaviors. A key challenge for dissecting genetic networks is expanding CRISPR-based screens to interrogate specific phenotypes with high precision. Here, we use a quantitative, sequencing-based CRISPRi platform to enhance the scope and sensitivity of genome-wide screens. We first systematically explore how technical variations distort guide effects and correct for these factors by using RNA reporters and normalizers expressed from closely matched promoters. We then combine this platform with a recombinase-based integration system to interrogate protein and RNA-level phenotypes. We find our approach accurately captures known regulators of protein or RNA quality control with high accuracy and minimal background. These barcode-based CRISPR systems provide a powerful and generalizable platform for dissecting critical cellular regulatory pathways. Overall design: We perform barcode-based CRISPRi screens across various conditions and identify methods to reduce background