Dynamic network-guided CRISPRi screen reveals CTCF loop-constrained nonlinear enhancer-gene regulatory activity in cell state transitions.

   June 8th, 2023 at 6:36pm

Note: Replaced Biorxiv  

This biorxiv set was replaced by PMID:37488417.



Comprehensive enhancer discovery is challenging because most enhancers, especially those affected in complex diseases, have weak effects on gene expression. Our network modeling revealed that nonlinear enhancer-gene regulation during cell state transitions can be leveraged to improve the sensitivity of enhancer discovery. Utilizing hESC definitive endoderm differentiation as a dynamic transition system, we conducted a mid-transition CRISPRi-based enhancer screen. The screen discovered a comprehensive set of enhancers (4 to 9 per locus) for each of the core endoderm lineage-specifying transcription factors, and many enhancers had strong effects mid-transition but weak effects post-transition. Through integrating enhancer activity measurements and three-dimensional enhancer-promoter interaction information, we were able to develop a CTCF loop-constrained Interaction Activity (CIA) 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 more comprehensive enhancer discovery in both normal and pathological cell state transitions.


Luo R  •  Yan J  •  Oh JW  •  Xi W  •  Shigaki D  •  Wong W  •  Cho H  •  Murphy D  •  Cutler R  •  Rosen BP  •  Pulecio J  •  Yang D  •  Glenn R  •  Chen T  •  Li QV  •  Vierbuchen T  •  Sidoli S  •  Apostolou E  •  Huangfu D  •  Beer MA



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March 9th, 2023