Seminar: Nick Ingolia, UC Berkeley

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“Dissecting gene regulatory networks with CiBER-Seq”

Nicholas Ingolia, PhD
Assistant Professor
Department of Molecular & Cell Biology
University of California, Berkeley

Faculty host:
Kristin Koutmou, Ph.D.
Seyhan N. Ege Assistant Professor of Chemistry
Department of Chemistry

Department of Chemistry Seminar

ABSTRACT: Cells integrate environmental signals and internal physiology to dynamically control gene expression. We have developed a technique to dissect this regulatory logic by linking targeted, genome-wide genetic perturbations with a deep-sequencing readout that quantitatively measures the expression phenotype induced by each perturbation. Our approach combines CRISPR interference (CRISPRi) with barcoded expression reporters (CiBER-seq) to profile transcriptional, translational, and posttranslational regulatory responses, connecting each guide in a genome-scale library with its individual phenotypic consequences. Applying CiBER-Seq to the well-studied integrated stress response (ISR) pathway recapitulated the known biology of this pathway and uncovered further triggers for ISR activation that were not previously appreciated. The quantitative phenotypic measurements from CiBER-Seq are well suited to epistasis analysis, and we measure dual-perturbation phenotypes and compare patterns of genetic interaction to gain further insight into regulatory pathways. CiBER-Seq is an incisive tool for dissecting genetic networks, and can be applied to study a wide range of biological processes, using gene expression regulation as a sensitive and specific readout of the state of the cell.