Journal Article

Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions

Cutler, Ronald, Cho, Hyein S., Li, Qing V., Luo, Renhe, Murphy, Dylan, Vierbuchen, Thomas, Oh, Jin Woo, Huangfu, Danwei, Yang, Dapeng, Yan, Jielin, Wong, Wilfred, Chen, Tingxu, Sidoli, Simone, Apostolou, Effie, Pulecio, Julian, Beer, Michael A., Shigaki, Dustin, Glenn, Rachel A., Xi, Wang, Rosen, Bess P.

2023

Overview

Comprehensive enhancer discovery is challenging because most enhancers, especially those contributing to complex diseases, have weak effects on gene expression. Our gene regulatory network modeling identified that nonlinear enhancer gene regulation during cell state transitions can be leveraged to improve the sensitivity of enhancer discovery. Using human embryonic stem cell definitive endoderm differentiation as a dynamic transition system, we conducted a mid-transition CRISPRi-based enhancer screen. We discovered a comprehensive set of enhancers for each of the core endoderm-specifying transcription factors. Many enhancers had strong effects mid-transition but weak effects post-transition, consistent with the nonlinear temporal responses to enhancer perturbation predicted by the modeling. Integrating three-dimensional genomic information, we were able to develop a CTCF-loop-constrained Interaction Activity model that can better predict functional enhancers compared to models that rely on Hi-C-based enhancer–promoter contact frequency. Our study provides generalizable strategies for sensitive and systematic enhancer discovery in both normal and pathological cell state transitions. CRISPRi-based screen identifies enhancers that nonlinearly regulate lineage-specifying transcription factors during definitive endoderm differentiation. A new CTCF-loop-constrained Interaction Activity (CIA) model is better at predicting functional enhancers than previous Hi-C-based enhancer–promoter contact frequency models.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 13/1 / 13/100 / 13/106 / 13/44 / 631/114/2163 / 631/136/532 / 631/208/191/1908 / 631/208/200 / 631/553/1833 / 82/58 / Agriculture / Animal Genetics and Genomics / Binding sites / Biomedical and Life Sciences / Biomedicine / Cancer Research / Cell differentiation / Cell Differentiation - genetics / Chromatin - genetics / CRISPR / Embryo cells / Endoderm / Enhancer Elements, Genetic - genetics / Enhancers / Gene expression / Gene Expression Regulation / Gene Function / Gene regulation / Gene Regulatory Networks - genetics / Human Genetics / Humans / Modelling / Perturbation / Sensitivity enhancement / Simulation / Stem cells / Three dimensional models / Transcription factors / Transcription Factors - genetics