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SmartImpute is a targeted imputation framework for single-cell transcriptome data. SmartImpute是一个针对单细胞转录组数据的目标输入框架。
IF 4.5
Cell Reports Methods Pub Date : 2025-08-18 Epub Date: 2025-08-04 DOI: 10.1016/j.crmeth.2025.101122
Sijie Yao, Tingyi Li, Joshua T Davis, Timothy I Shaw, Xiaoqing Yu, Xuefeng Wang
{"title":"SmartImpute is a targeted imputation framework for single-cell transcriptome data.","authors":"Sijie Yao, Tingyi Li, Joshua T Davis, Timothy I Shaw, Xiaoqing Yu, Xuefeng Wang","doi":"10.1016/j.crmeth.2025.101122","DOIUrl":"10.1016/j.crmeth.2025.101122","url":null,"abstract":"<p><p>In this study, we present SmartImpute, a targeted imputation framework for single-cell RNA sequencing (scRNA-seq) data. SmartImpute focuses on predefined marker genes to improve biological relevance and computational efficiency. It employs a modified generative adversarial imputation network (GAIN) with a multi-task discriminator that imputes missing values while preserving true biological zeros. We applied SmartImpute to scRNA-seq datasets from head and neck squamous cell carcinoma, human bone marrow, and lung cancer. Across these datasets, SmartImpute improved clustering, cell type annotation, and trajectory inference and successfully scaled to datasets with over one million cells. In addition, SmartImpute was applied to spatial transcriptomics data, where it improved spatial gene expression patterns and clustering. These results demonstrate that SmartImpute facilitates deeper insights into cellular heterogeneity and disease progression.</p>","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101122"},"PeriodicalIF":4.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461658/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144790141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Fluorescence recovery in the super-resolution regime reveals subcompartments of 53BP1 foci. 超分辨率下的荧光恢复显示53BP1病灶的亚区室。
IF 4.5
Cell Reports Methods Pub Date : 2025-08-18 Epub Date: 2025-08-04 DOI: 10.1016/j.crmeth.2025.101118
Chengchen Wu, Janeth Catalina Manjarrez-González, Muntaqa Choudhury, Noor Shamkhi, Siwen Ding, Vishnu M Nair, Viji M Draviam
{"title":"Fluorescence recovery in the super-resolution regime reveals subcompartments of 53BP1 foci.","authors":"Chengchen Wu, Janeth Catalina Manjarrez-González, Muntaqa Choudhury, Noor Shamkhi, Siwen Ding, Vishnu M Nair, Viji M Draviam","doi":"10.1016/j.crmeth.2025.101118","DOIUrl":"10.1016/j.crmeth.2025.101118","url":null,"abstract":"<p><p>Double-strand break (DSB) repair protein 53BP1 (p53 binding protein-1) mediates long-range DNA end-joining and heterochromatin maintenance. We exploit lattice structured illumination microscopy (SIM) (dual iterative SIM [diSIM, also called SIM<sup>2</sup>]; ∼60 nm lateral resolution) alongside lattice light-sheet microscopy and fluorescence recovery after photobleaching (FRAP) and reveal differences in 53BP1 foci contour and composition. Compact 53BP1 foci remain stationary, while amorphous foci undergo dynamic shape changes. Using FRAP in the super-resolution (SR) regime (FRAP-SR), we show that amorphous 53BP1 foci recover 53BP1-EGFP signals rapidly exhibiting subcompartments, indicating differential protein mobilities and functions within a single foci. In contrast, compact foci recover 53BP1-EGFP uniformly as a single compartment but show heterogeneous recovery rates. In cells released from a DNA replication block, 53BP1-EGFP shows increased mobility in amorphous foci compared to compact foci. We discuss the conceptual implications of different 53BP1 mobilities and foci contours and how the FRAP-SR method transforms studies of dynamic 60-100 nm structures.</p>","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101118"},"PeriodicalIF":4.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461648/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144790138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
MR1-ligand cross-linking identifies vitamin B6 metabolites as TCR-reactive antigens. mr1配体交联鉴定维生素B6代谢物作为tcr反应性抗原。
IF 4.5
Cell Reports Methods Pub Date : 2025-08-18 Epub Date: 2025-08-04 DOI: 10.1016/j.crmeth.2025.101120
Thierry Schmidlin, Enas Behiry, Hannah Thomas, Garry Dolton, Fabio Marino, Samiul Hasan, Magdalena von Essen, Rose M Gathungu, Barbara A Steigenberger, Hayden Selvadurai, Joseph Dukes, Paul E Brennan, Owen B Spiller, Jonathan D Silk, Andrew K Sewell, Nicola Ternette
{"title":"MR1-ligand cross-linking identifies vitamin B6 metabolites as TCR-reactive antigens.","authors":"Thierry Schmidlin, Enas Behiry, Hannah Thomas, Garry Dolton, Fabio Marino, Samiul Hasan, Magdalena von Essen, Rose M Gathungu, Barbara A Steigenberger, Hayden Selvadurai, Joseph Dukes, Paul E Brennan, Owen B Spiller, Jonathan D Silk, Andrew K Sewell, Nicola Ternette","doi":"10.1016/j.crmeth.2025.101120","DOIUrl":"10.1016/j.crmeth.2025.101120","url":null,"abstract":"<p><p>Major histocompatibility complex class I-related protein 1 (MR1) plays a central role in the immune recognition of infected cells and can mediate T cell detection of cancer. Knowledge of the nature of the ligands presented by MR1 is still sparse and has been limited by a lack of efficient approaches for MR1 ligand discovery. Here, we present a cross-linking strategy to investigate Schiff base-bound MR1 ligands. Our methodology employs reductive amination to stabilize the labile Schiff base bond between MR1 and its ligand, allowing for the detection of ligands as covalent MR1 adducts by mass spectrometry-based proteomics. We apply our approach to identifying vitamin B6 vitamers pyridoxal and pyridoxal 5'-phosphate (PLP) as MR1 ligands and show that both compounds are recognized by T cells expressing either A-F7, a mucosal-associated invariant T (MAIT) cell T cell receptor (TCR), or MC.7.G5, an MR1-restricted TCR reported to recognize cancer cells, highlighting them as immunogenic MR1 ligands.</p>","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101120"},"PeriodicalIF":4.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461623/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144790139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
High-throughput measurement of Drosophila feeding behavior. 果蝇摄食行为的高通量测量。
IF 4.5
Cell Reports Methods Pub Date : 2025-08-18 Epub Date: 2025-07-18 DOI: 10.1016/j.crmeth.2025.101109
Huai-Zheng Zheng, Shuo Song, Jing-Hao Tang, Hong-Shan Liu, Man Song, Zhen-Xia Chen
{"title":"High-throughput measurement of Drosophila feeding behavior.","authors":"Huai-Zheng Zheng, Shuo Song, Jing-Hao Tang, Hong-Shan Liu, Man Song, Zhen-Xia Chen","doi":"10.1016/j.crmeth.2025.101109","DOIUrl":"10.1016/j.crmeth.2025.101109","url":null,"abstract":"<p><p>Accurate measurement of Drosophila feeding is vital for metabolic and aging studies, but current assays lack the throughput and sensitivity needed for large-scale screens. We introduce FlyPlate-BCA, a 96-well platform that combines automated single-fly tracking with BCA protein quantification for high-resolution, longitudinal intake measurements. FlyPlate-BCA detects a 0.1× nutrient dilution with 90% power using just four replicates, three times fewer than the capillary feeder (CAFE) assay. It uncovers sucrose-driven hyperphagia independent of osmotic stress and preserved lipid-satiety responses, while extended monitoring reveals a female-specific metabolic adaptation. By delivering individual-level data at scale, FlyPlate-BCA establishes a benchmark for nutritional genomics and appetite neurobiology and streamlines nutraceutical and genetic screening.</p>","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101109"},"PeriodicalIF":4.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461584/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Recent advances and future prospects for blockchain in biomedicine. 区块链在生物医学上的研究进展及前景展望。
IF 4.5
Cell Reports Methods Pub Date : 2025-08-18 Epub Date: 2025-07-25 DOI: 10.1016/j.crmeth.2025.101114
Eric Ni, Xiangru Tang, Xiao Zhou, Danielle Lee, Ahmed Elhussein, Elizabeth Knight, Gamze Gürsoy, Mark Gerstein
{"title":"Recent advances and future prospects for blockchain in biomedicine.","authors":"Eric Ni, Xiangru Tang, Xiao Zhou, Danielle Lee, Ahmed Elhussein, Elizabeth Knight, Gamze Gürsoy, Mark Gerstein","doi":"10.1016/j.crmeth.2025.101114","DOIUrl":"10.1016/j.crmeth.2025.101114","url":null,"abstract":"<p><p>Healthcare data are rapidly evolving with the introduction of new modalities and an exponential increase in volume. Current health data storage and communication services face major obstacles in terms of privacy, security, and operational efficiency in the face of this new data landscape. Blockchain technology, characterized by its immutability, auditability, and decentralization, is emerging as a promising solution. However, integrating blockchain into existing systems presents significant challenges, particularly regarding data privacy and scalability. This review aims to provide a comprehensive understanding of how blockchain technology can transform the biomedical sector, potentially making healthcare data management more secure and efficient.</p>","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101114"},"PeriodicalIF":4.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461581/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144718789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An integrative assay for measuring social aversion and motivation in freely behaving mice. 一种测量自由行为小鼠社会厌恶和动机的综合分析。
IF 4.5
Cell Reports Methods Pub Date : 2025-08-18 Epub Date: 2025-07-17 DOI: 10.1016/j.crmeth.2025.101108
Jordan Grammer, Rene Valles, Alexis Bowles, Moriel Zelikowsky
{"title":"An integrative assay for measuring social aversion and motivation in freely behaving mice.","authors":"Jordan Grammer, Rene Valles, Alexis Bowles, Moriel Zelikowsky","doi":"10.1016/j.crmeth.2025.101108","DOIUrl":"10.1016/j.crmeth.2025.101108","url":null,"abstract":"<p><p>Social aversion is a key feature of numerous mental health disorders, yet we lack adequate behavioral tools to interrogate social aversion in model systems. Here, we developed a behavioral task-selective access to unrestricted social interaction (SAUSI)-that integrates elements of social motivation, hesitancy, and free interaction to enable a multiplexed assessment of social aversion. Using SAUSI, we discovered that prolonged social isolation induces social aversion in mice-an effect largely driven by increases in social fear coupled with decreases in social motivation. Application of deep learning approaches revealed unique behavioral motifs underlying the socially aversive state produced by isolation, demonstrating the compatibility of modern computational pipelines with SAUSI. Last, we demonstrated that unique forms of social aversion can be induced by distinct stressors, highlighting the versatility of SAUSI. Our findings debut a fresh task for the behavioral toolbox-one that offers an integrative approach for assessing social aversion.</p>","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101108"},"PeriodicalIF":4.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461583/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Anticlustering for sample allocation to minimize batch effects. 反聚类的样本分配，以尽量减少批量影响。
IF 4.5
Cell Reports Methods Pub Date : 2025-08-18 DOI: 10.1016/j.crmeth.2025.101137
Martin Papenberg, Cheng Wang, Maïgane Diop, Syed Hassan Bukhari, Boris Oskotsky, Brittany R Davidson, Kim Chi Vo, Binya Liu, Juan C Irwin, Alexis J Combes, Brice Gaudilliere, Jingjing Li, David K Stevenson, Gunnar W Klau, Linda C Giudice, Marina Sirota, Tomiko T Oskotsky
{"title":"Anticlustering for sample allocation to minimize batch effects.","authors":"Martin Papenberg, Cheng Wang, Maïgane Diop, Syed Hassan Bukhari, Boris Oskotsky, Brittany R Davidson, Kim Chi Vo, Binya Liu, Juan C Irwin, Alexis J Combes, Brice Gaudilliere, Jingjing Li, David K Stevenson, Gunnar W Klau, Linda C Giudice, Marina Sirota, Tomiko T Oskotsky","doi":"10.1016/j.crmeth.2025.101137","DOIUrl":"10.1016/j.crmeth.2025.101137","url":null,"abstract":"<p><p>High-throughput sequencing enables efficient processing of DNA and RNA samples in batches, but batch effects can obscure true biological signal. We propose using anticlustering as an automated method to assign samples to balanced batches, minimizing covariate imbalance and supporting user-defined constraints such as batch size, number of batches, and \"must-link\" assignments. In simulations, anticlustering outperforms existing methods in assigning balanced batches. We illustrate its utility using a real-life example from the University of California, San Francisco (UCSF)-Stanford Endometriosis Center for Discovery, Innovation, Training and Community Engagement (ENACT) Center, where multiple samples per individual required processing within the same batch to avoid confounding. The Two-Phase Must-Link (2PML) anticlustering algorithm realized the must-link restrictions while balancing disease stage, menstrual cycle phase, case vs. control, and clinical site. All methods are accessible via the free, open-source R package anticlust, with a companion RShiny web app for visualization and interactive batch assignment.</p>","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"5 8","pages":"101137"},"PeriodicalIF":4.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461633/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144883900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategy. Graft-seq通过位点特异性化学嫁接策略精确地映射RNA修饰。
IF 4.5
Cell Reports Methods Pub Date : 2025-07-21 Epub Date: 2025-07-10 DOI: 10.1016/j.crmeth.2025.101103
Ting Li, Ke Ding, Ziming Bao, Quan Ma, Chenyang Huang, Jie Cao, Xiao Shu, Minsong Gao, Zisheng Luo, Xushen Xiong, Jianzhao Liu
{"title":"Graft-seq precisely maps RNA modifications via site-specific chemical grafting strategy.","authors":"Ting Li, Ke Ding, Ziming Bao, Quan Ma, Chenyang Huang, Jie Cao, Xiao Shu, Minsong Gao, Zisheng Luo, Xushen Xiong, Jianzhao Liu","doi":"10.1016/j.crmeth.2025.101103","DOIUrl":"10.1016/j.crmeth.2025.101103","url":null,"abstract":"<p><p>The current expansion of RNA epitranscriptomics calls for direct and high-precision mapping tools to characterize the intrinsically low abundant RNA modifications. Here, we developed a strategy, termed Graft-seq, which harnesses specific enzymatic and chemical reactions on an RNA modification site to covalently graft a known RNA branch and further utilizes the branch-to-main-chain or main-chain-to-branch landing/jumping site signal during reverse transcription to determine the locations of RNA modifications at single-base resolution. We developed a matched bioinformatics analysis pipeline for Graft-seq and successfully mapped internal N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) and cap N<sup>6</sup>,2'-O-dimethyladenosine (m<sup>6</sup>Am), as well as nicotinamide adenine dinucleotide (NAD) on transcriptome-wide mRNAs and/or nuclear non-coding RNAs in different cell lines. Paralleled comparisons of Graft-seq with available techniques confirmed the effectiveness of the RNA grafting strategy. Graft-seq represents a direct and enrichment-free technique for characterizing RNA modifications at base resolution and offers the potential to discover new RNA modifications and RNA-RNA interactions.</p>","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101103"},"PeriodicalIF":4.5,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12296446/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144620806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Fragment dispersity index analysis of cfDNA fragments reveals chromatin accessibility and enables early cancer detection. 片段分散指数分析cfDNA片段揭示染色质可及性和早期癌症检测。
IF 4.5
Cell Reports Methods Pub Date : 2025-07-21 Epub Date: 2025-06-18 DOI: 10.1016/j.crmeth.2025.101083
Yunze Wang, Yuying Hou, Zhankun Xiong, Libo Lu, Zhanxiang Zong, Bo Wang, Hebing Chen, Wen Zhang, Xionghui Zhou
{"title":"Fragment dispersity index analysis of cfDNA fragments reveals chromatin accessibility and enables early cancer detection.","authors":"Yunze Wang, Yuying Hou, Zhankun Xiong, Libo Lu, Zhanxiang Zong, Bo Wang, Hebing Chen, Wen Zhang, Xionghui Zhou","doi":"10.1016/j.crmeth.2025.101083","DOIUrl":"10.1016/j.crmeth.2025.101083","url":null,"abstract":"<p><p>We introduce a cell-free DNA (cfDNA) fragmentation pattern: the fragment dispersity index (FDI), which integrates information on the distribution of cfDNA fragment ends with the variation in fragment coverage, enabling precise characterization of chromatin accessibility in specific regions. The FDI shows a strong correlation with chromatin accessibility and gene expression, and regions with high FDI are enriched in active regulatory elements. Using whole-genome cfDNA data from five datasets, we developed and validated the FDI-oncology model, which demonstrates robust performance in early cancer diagnosis, subtyping, and prognosis. Case studies reveal that key cancer genes such as HER2 and TP53 exhibit significantly different FDIs between cancer and control samples. Simulation experiments suggest that deep targeted sequencing of a small number of regions can achieve high diagnostic efficiency.</p>","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"5 7","pages":"101083"},"PeriodicalIF":4.5,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12296511/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145024279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
TAS-seq enables subcellular single-stranded adenosine profiling by signal peptide-assisted adenosine deamination. TAS-seq通过信号肽辅助的腺苷脱胺，实现亚细胞单链腺苷谱分析。
IF 4.5
Cell Reports Methods Pub Date : 2025-07-21 Epub Date: 2025-06-25 DOI: 10.1016/j.crmeth.2025.101087
Lixia Wang, Yangfan Zhou, Zhenxing Yu, Panfeng Wu, Zhike Lu, Lijia Ma
{"title":"TAS-seq enables subcellular single-stranded adenosine profiling by signal peptide-assisted adenosine deamination.","authors":"Lixia Wang, Yangfan Zhou, Zhenxing Yu, Panfeng Wu, Zhike Lu, Lijia Ma","doi":"10.1016/j.crmeth.2025.101087","DOIUrl":"10.1016/j.crmeth.2025.101087","url":null,"abstract":"<p><p>RNA structure plays a crucial role in its function and undergoes dynamic changes throughout its life cycle. To study these dynamics, we developed TAS sequencing (TAS-seq), which expresses the deaminase TadA-8e in specific subcellular compartments to modify single-stranded adenosines, particularly within hairpin loops. We applied TAS-seq to the nucleus, cytosol, and endoplasmic reticulum membrane, identifying adenosine structural variations and compartment-specific regulation of RNA stability. Single-cell TAS-seq revealed structural heterogeneity of cytosolic RNAs. Additionally, adenosines labeled by TAS-seq contribute to guide RNA optimization in the CRISPR-Cas13d system. Our method provides insights into compartment-specific RNA structural dynamics, cell-specific heterogeneity, and their functional implications.</p>","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101087"},"PeriodicalIF":4.5,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12296453/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144508679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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