Dynamic network-guided CRISPRi screen reveals CTCF loop constrained enhancer function in cell state transitions. Dynamic network-guided CRISPRi screen reveals CTCF loop constrained enhancer function in cell state transitions

We performed CRISPRi enhancer screens during differentiation of human embryonic stem cells (hESC) to definitive endoderm (DE) in genomic windows surrounding ten lineage-specifying core TFs. We also generated scRNA-seq, ATAC-seq, and TF ChIP-seq data and show that CTCF loops constrain the interactions between enhancers and their promoter targets. Overall design: Single-cell scRNA-seq gene expression profiling of differentiating idCas9-KRAB SOX17eGFP/+ HUES8 hESC line at 7 time points from 0hr to 72hr post-differentiation ATAC-seq chromatin accessibility profiling of differentiating idCas9-KRAB SOX17eGFP/+ HUES8 hESC line at 7 time points from 0hr to 72hr post-differentiation gRNA sequencing data of CRISPRi experiment at 36hr post differentiation in idCas9-KRAB SOX17eGFP/+ HUES8 hESC line Hi-C chromatin interaction profiling in hESC and DE HUES8 hESC cell line. TF ChIP-seq for GATA6, EOMES, SOX17, H3K27ac, and CTCF in HUES8 hESC line