Multimodal CRISPR screens uncover DDX39B as a global repressor of A-to-I RNA editing
Summary: Adenosine-to-inosine (A-to-I) RNA editing is a critical post-transcriptional modification that diversifies the transcriptome and influences various cellular processes, yet its regulatory mechanisms remain largely unknown. Here, we present two complementary CRISPR-based genetic screening pla...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-07-01
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| Series: | Cell Reports |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211124725007806 |
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| author | Tianzi Wei Jiaxuan Li Xiang Lei Risheng Lin Qingyan Wu Zhenfeng Zhang Shimin Shuai Ruilin Tian |
| author_facet | Tianzi Wei Jiaxuan Li Xiang Lei Risheng Lin Qingyan Wu Zhenfeng Zhang Shimin Shuai Ruilin Tian |
| author_sort | Tianzi Wei |
| collection | DOAJ |
| description | Summary: Adenosine-to-inosine (A-to-I) RNA editing is a critical post-transcriptional modification that diversifies the transcriptome and influences various cellular processes, yet its regulatory mechanisms remain largely unknown. Here, we present two complementary CRISPR-based genetic screening platforms: CREDITS (CRISPR-based RNA editing regulator screening), which enables genome-scale identification of editing regulators using an RNA recorder-based reporter system, and scCREDIT-seq (single-cell CRISPR-based RNA editing sequencing), which provides multiplexed single-cell characterization of transcriptome and editome changes for pooled perturbations. By screening 1,350 RNA-binding proteins, we identified a series of A-to-I editing regulators. Mechanistic investigation revealed DDX39B as a global repressor of A-to-I editing, which functions by preventing double-stranded RNA accumulation through its helicase activity. Targeting DDX39B significantly enhances the efficiency of RNA-editing-based tools, such as CellREADR (cell access through RNA sensing by endogenous ADAR) and LEAPER (leveraging endogenous ADAR for programmable editing of RNA), and disrupts hepatitis D virus (HDV) RNA editing homeostasis. These technological advances not only expand our understanding of RNA editing regulation but also provide powerful tools for exploring tissue-specific and context-dependent RNA modification mechanisms, with broad implications for therapeutic development. |
| format | Article |
| id | doaj-art-623e094d75bc48eb9dcbdaab350acabe |
| institution | DOAJ |
| issn | 2211-1247 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Reports |
| spelling | doaj-art-623e094d75bc48eb9dcbdaab350acabe2025-08-20T03:17:03ZengElsevierCell Reports2211-12472025-07-0144711600910.1016/j.celrep.2025.116009Multimodal CRISPR screens uncover DDX39B as a global repressor of A-to-I RNA editingTianzi Wei0Jiaxuan Li1Xiang Lei2Risheng Lin3Qingyan Wu4Zhenfeng Zhang5Shimin Shuai6Ruilin Tian7Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; SUSTech Homeostatic Medicine Institute, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong 518055, ChinaSUSTech Homeostatic Medicine Institute, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, ChinaDepartment of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; SUSTech Homeostatic Medicine Institute, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong 518055, ChinaDepartment of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; SUSTech Homeostatic Medicine Institute, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong 518055, ChinaSchool of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen, Guangdong 518055, ChinaSchool of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen, Guangdong 518055, ChinaSUSTech Homeostatic Medicine Institute, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Corresponding authorDepartment of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; SUSTech Homeostatic Medicine Institute, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Corresponding authorSummary: Adenosine-to-inosine (A-to-I) RNA editing is a critical post-transcriptional modification that diversifies the transcriptome and influences various cellular processes, yet its regulatory mechanisms remain largely unknown. Here, we present two complementary CRISPR-based genetic screening platforms: CREDITS (CRISPR-based RNA editing regulator screening), which enables genome-scale identification of editing regulators using an RNA recorder-based reporter system, and scCREDIT-seq (single-cell CRISPR-based RNA editing sequencing), which provides multiplexed single-cell characterization of transcriptome and editome changes for pooled perturbations. By screening 1,350 RNA-binding proteins, we identified a series of A-to-I editing regulators. Mechanistic investigation revealed DDX39B as a global repressor of A-to-I editing, which functions by preventing double-stranded RNA accumulation through its helicase activity. Targeting DDX39B significantly enhances the efficiency of RNA-editing-based tools, such as CellREADR (cell access through RNA sensing by endogenous ADAR) and LEAPER (leveraging endogenous ADAR for programmable editing of RNA), and disrupts hepatitis D virus (HDV) RNA editing homeostasis. These technological advances not only expand our understanding of RNA editing regulation but also provide powerful tools for exploring tissue-specific and context-dependent RNA modification mechanisms, with broad implications for therapeutic development.http://www.sciencedirect.com/science/article/pii/S2211124725007806CP: GenomicsCP: Molecular biology |
| spellingShingle | Tianzi Wei Jiaxuan Li Xiang Lei Risheng Lin Qingyan Wu Zhenfeng Zhang Shimin Shuai Ruilin Tian Multimodal CRISPR screens uncover DDX39B as a global repressor of A-to-I RNA editing Cell Reports CP: Genomics CP: Molecular biology |
| title | Multimodal CRISPR screens uncover DDX39B as a global repressor of A-to-I RNA editing |
| title_full | Multimodal CRISPR screens uncover DDX39B as a global repressor of A-to-I RNA editing |
| title_fullStr | Multimodal CRISPR screens uncover DDX39B as a global repressor of A-to-I RNA editing |
| title_full_unstemmed | Multimodal CRISPR screens uncover DDX39B as a global repressor of A-to-I RNA editing |
| title_short | Multimodal CRISPR screens uncover DDX39B as a global repressor of A-to-I RNA editing |
| title_sort | multimodal crispr screens uncover ddx39b as a global repressor of a to i rna editing |
| topic | CP: Genomics CP: Molecular biology |
| url | http://www.sciencedirect.com/science/article/pii/S2211124725007806 |
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