效应器
生物
增强子
计算生物学
染色质
转录因子
抄写(语言学)
抑制因子
遗传学
发起人
背景(考古学)
基因
细胞生物学
基因表达
古生物学
语言学
哲学
作者
Josh Tycko,Mike V. Van,Aradhana Aradhana,Nicole DelRosso,David Yao,Xiaoshu Xu,Connor Ludwig,Kaitlyn Spees,Katherine Liu,Gaelen T. Hess,Mingxin Gu,Adi Mukund,Peter Suzuki,Roarke A. Kamber,Lei S. Qi,Lacramioara Bintu,Michael C. Bassik
标识
DOI:10.1101/2023.05.12.540558
摘要
Abstract Human nuclear proteins contain >1000 transcriptional effector domains that can activate or repress transcription of target genes. We lack a systematic understanding of which effector domains regulate transcription robustly across genomic, cell-type, and DNA-binding domain (DBD) contexts. Here, we developed dCas9-mediated high-throughput recruitment (HT-recruit), a pooled screening method for quantifying effector function at endogenous targets, and tested effector function for a library containing 5092 nuclear protein Pfam domains across varied contexts. We find many effectors depend on target and DBD contexts, such as HLH domains that can act as either activators or repressors. We then confirm these findings and further map context dependencies of effectors drawn from unannotated protein regions using a larger library containing 114,288 sequences tiling chromatin regulators and transcription factors. To enable efficient perturbations, we select effectors that are potent in diverse contexts, and engineer (1) improved ZNF705 KRAB CRISPRi tools to silence promoters and enhancers, and (2) a compact human activator combination NFZ for better CRISPRa and inducible circuit delivery. Together, this effector-by-context functional map reveals context-dependence across human effectors and guides effector selection for robustly manipulating transcription.
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