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CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease.

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Title: CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease.
Authors: Green, Nicole F. O. (AUTHOR), Sutton, Gavin J. (AUTHOR), Pérez-Burillo, Javier (AUTHOR), Wang, Juli (AUTHOR), Bagot, Samuel (AUTHOR), Danon, Hannah G. (AUTHOR), Walsh, Kieran (AUTHOR), Gokool, Akira (AUTHOR), Miles, Samantha A. (AUTHOR), Yang, Guang (AUTHOR), Herring, Charles A. (AUTHOR), Liang, Yuheng (AUTHOR), Pfundstein, Grant (AUTHOR), Sytnyk, Vladimir (AUTHOR), Alinejad-Rokny, Hamid (AUTHOR), Lister, Ryan (AUTHOR), Rosenbluh, Joseph (AUTHOR), Gagnon-Bartsch, Johann A. (AUTHOR), Voineagu, Irina (AUTHOR)
Source: Nature Neuroscience. Mar2026, Vol. 29 Issue 3, p703-716. 14p.
Abstract: Genetic variants associated with complex traits often lie in distal enhancers. While candidate enhancers have been mapped genome wide, their functional state and gene targets in specific cell types remain unclear. Here we present AstroREG, a resource of enhancer–gene interactions in human primary astrocytes, generated by combining CRISPR inhibition (CRISPRi), single-cell RNA-seq and machine learning. By functionally testing nearly 1,000 PsychENCODE enhancers, we identified more than 150 regulatory interactions, revealing enhancers that control key astrocyte functions and genes implicated in Alzheimer's disease. The CRISPRi screen also provided valuable ground-truth data from a primary cell type for training and benchmarking prediction models of enhancer activity. We thus developed EGrf, a random forest (RF) model trained on these data, and applied it genome wide to predict regulatory interactions with high specificity. Together, our data provide a comprehensive functional map of enhancer-mediated regulation in a key glial cell type, shedding light on brain function and disease. This study reveals how distal DNA 'switches' control gene activity in human astrocytes. Using CRISPRi screens and single-cell RNA-seq, we map enhancer–gene links, highlight Alzheimer's disease-related targets and introduce a model that predicts additional regulatory interactions. [ABSTRACT FROM AUTHOR]
Copyright of Nature Neuroscience is the property of Springer Nature and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Psychology and Behavioral Sciences Collection
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  Data: CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease.
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  Data: Genetic variants associated with complex traits often lie in distal enhancers. While candidate enhancers have been mapped genome wide, their functional state and gene targets in specific cell types remain unclear. Here we present AstroREG, a resource of enhancer–gene interactions in human primary astrocytes, generated by combining CRISPR inhibition (CRISPRi), single-cell RNA-seq and machine learning. By functionally testing nearly 1,000 PsychENCODE enhancers, we identified more than 150 regulatory interactions, revealing enhancers that control key astrocyte functions and genes implicated in Alzheimer's disease. The CRISPRi screen also provided valuable ground-truth data from a primary cell type for training and benchmarking prediction models of enhancer activity. We thus developed EGrf, a random forest (RF) model trained on these data, and applied it genome wide to predict regulatory interactions with high specificity. Together, our data provide a comprehensive functional map of enhancer-mediated regulation in a key glial cell type, shedding light on brain function and disease. This study reveals how distal DNA 'switches' control gene activity in human astrocytes. Using CRISPRi screens and single-cell RNA-seq, we map enhancer–gene links, highlight Alzheimer's disease-related targets and introduce a model that predicts additional regulatory interactions. [ABSTRACT FROM AUTHOR]
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  Data: <i>Copyright of Nature Neuroscience is the property of Springer Nature and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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