Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions
Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions
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DOI：
10.1038/s41588-023-01450-7
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发表时间：
2023-07-24
期刊：
影响因子：
30.8
通讯作者：
Beer，Michael A. A.
中科院分区：
文献类型：
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作者：
Luo，Renhe;Yan，Jielin;Beer，Michael A. A.
发现全面的增强子是具有挑战性的，因为大多数增强子，特别是那些导致复杂疾病的增强子，对基因表达的影响很弱。我们的基因调控网络模型发现，细胞状态转换过程中的非线性增强子基因调控可以被用来提高增强子发现的敏感性。以人胚胎干细胞明确的内胚层分化为动态转化系统，我们进行了基于CRISPRi的中期转化增强子筛选。我们发现了一套全面的增强剂，用于每个核心内胚层特定的转录因子。许多增强剂在跃迁中期有较强的作用，而在相变后的作用较弱，这与模型预测的对增强子扰动的非线性时间响应是一致的。结合三维基因组信息，我们能够开发出一个CTCF环约束的相互作用活性模型，与依赖基于Hi-C的增强子-启动子接触频率的模型相比，该模型可以更好地预测功能增强子。我们的研究为在正常和病理细胞状态转变中发现敏感和系统的增强子提供了可推广的策略。
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.