Min Duan, Pan Gao, Yi-Zhou Zhang, Yu-Long Hu, Lei Zhou, Zhong-Chen Xu, Hou-Yuan Qiu, Xiao-Han Tong, Rui-Jin Ji, Xin-Lin Lei, Hao Yin, Cun-Lan Guo, Ying Zhang
{"title":"TOPO-seq reveals DNA topology-induced off-target activity by Cas9 and base editors","authors":"Min Duan, Pan Gao, Yi-Zhou Zhang, Yu-Long Hu, Lei Zhou, Zhong-Chen Xu, Hou-Yuan Qiu, Xiao-Han Tong, Rui-Jin Ji, Xin-Lin Lei, Hao Yin, Cun-Lan Guo, Ying Zhang","doi":"10.1038/s41589-025-01867-7","DOIUrl":"https://doi.org/10.1038/s41589-025-01867-7","url":null,"abstract":"<p>With the increasing use of CRISPR–Cas9, detecting off-target events is essential for safety. Current methods primarily focus on guide RNA (gRNA) sequence mismatches, often overlooking the impact of DNA topology in regulating off-target activity. Here we present TOPO-seq, a high-throughput and sensitive method that identifies genome-wide off-target effects of Cas9 and base editors while accounting for DNA topology. TOPO-seq revealed that topology-induced off-target sites frequently harbor higher mismatches than the relaxed DNA sequence, with over 50% of off-target sites containing six mismatches, which are usually overlooked using previous methods. Applying TOPO-seq to three therapeutic gRNAs in hematopoietic stem cells identified 47 bona fide off-target loci, six of which are specifically induced by DNA topology. These findings highlight DNA topology as a regulator of off-target editing rates, establish TOPO-seq as a robust method for capturing DNA topology-induced off-target events and underscore its importance in off-target detection for developing safe genome-editing therapies.</p><figure></figure>","PeriodicalId":18832,"journal":{"name":"Nature chemical biology","volume":"106 1","pages":""},"PeriodicalIF":14.8,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143758450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yaqing Zhang, Yuan Jiang, David Kuster, Qiwei Ye, Wenhao Huang, Simon Fürbacher, Jingye Zhang, Pia Doll, Wenjun Lin, Siwei Dong, Hui Wang, Zhipeng Tang, David Ibberson, Klemens Wild, Irmgard Sinning, Anthony A. Hyman, Andres Jäschke
{"title":"Single-step discovery of high-affinity RNA ligands by UltraSelex","authors":"Yaqing Zhang, Yuan Jiang, David Kuster, Qiwei Ye, Wenhao Huang, Simon Fürbacher, Jingye Zhang, Pia Doll, Wenjun Lin, Siwei Dong, Hui Wang, Zhipeng Tang, David Ibberson, Klemens Wild, Irmgard Sinning, Anthony A. Hyman, Andres Jäschke","doi":"10.1038/s41589-025-01868-6","DOIUrl":"https://doi.org/10.1038/s41589-025-01868-6","url":null,"abstract":"<p>Aptamers, nucleic acid ligands targeting specific molecules, have emerged as drug candidates, sensors, imaging tools and nanotechnology building blocks. The predominant method for their discovery, systematic evolution of ligands by exponential enrichment, while successful, is laborious, time-consuming and often results in candidates enriched for unintended criteria. Here we present UltraSelex, a noniterative method that combines biochemical partitioning, high-throughput sequencing and computational signal-to-background rank modeling for discovering RNA aptamers in about 1 day. UltraSelex identified high-affinity RNA aptamers capable of binding a fluorogenic silicon rhodamine dye and two protein targets, the SARS-CoV-2 RNA-dependent RNA polymerase and HIV reverse transcriptase, enabling live-cell RNA imaging and efficient enzyme inhibition, respectively. From the ranked sequences, minimal aptamer motifs could be easily inferred. UltraSelex provides a rapid route to reveal new drug candidates and diagnostic tools.</p><figure></figure>","PeriodicalId":18832,"journal":{"name":"Nature chemical biology","volume":"1 1","pages":""},"PeriodicalIF":14.8,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143736722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fangting Zuo, Li Jiang, Ni Su, Yaqiang Zhang, Bingkun Bao, Limei Wang, Yajie Shi, Huimin Yang, Xinyi Huang, Ruilong Li, Qingmei Zeng, Zhengda Chen, Qiuning Lin, Yingping Zhuang, Yuzheng Zhao, Xianjun Chen, Linyong Zhu, Yi Yang
{"title":"Author Correction: Imaging the dynamics of messenger RNA with a bright and stable green fluorescent RNA","authors":"Fangting Zuo, Li Jiang, Ni Su, Yaqiang Zhang, Bingkun Bao, Limei Wang, Yajie Shi, Huimin Yang, Xinyi Huang, Ruilong Li, Qingmei Zeng, Zhengda Chen, Qiuning Lin, Yingping Zhuang, Yuzheng Zhao, Xianjun Chen, Linyong Zhu, Yi Yang","doi":"10.1038/s41589-025-01892-6","DOIUrl":"https://doi.org/10.1038/s41589-025-01892-6","url":null,"abstract":"<p>Correction to: <i>Nature Chemical Biology</i> https://doi.org/10.1038/s41589-024-01629-x, published online 23 May 2024.</p>","PeriodicalId":18832,"journal":{"name":"Nature chemical biology","volume":"59 1","pages":""},"PeriodicalIF":14.8,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xiaowei Zhang, Luis S. Mille-Fragoso, K. Eerik Kaseniit, Arden P. Lee, Meng Zhang, Connor C. Call, Yixin Hu, Yunxin Xie, Xiaojing J. Gao
{"title":"Post-transcriptional modular synthetic receptors","authors":"Xiaowei Zhang, Luis S. Mille-Fragoso, K. Eerik Kaseniit, Arden P. Lee, Meng Zhang, Connor C. Call, Yixin Hu, Yunxin Xie, Xiaojing J. Gao","doi":"10.1038/s41589-025-01872-w","DOIUrl":"https://doi.org/10.1038/s41589-025-01872-w","url":null,"abstract":"<p>Inspired by the power of transcriptional synthetic receptors and hoping to complement them to expand the toolbox for cell engineering, we establish LIDAR (Ligand-Induced Dimerization-Activating RNA editing), a modular post-transcriptional synthetic receptor platform that harnesses RNA editing by adenosine deaminases acting on RNA. LIDAR is compatible with various receptor architectures in different cellular contexts and enables the sensing of diverse ligands and the production of functional outputs. Furthermore, LIDAR can sense orthogonal signals in the same cell and produce synthetic spatial patterns, potentially enabling the programming of complex multicellular behaviors. Lastly, LIDAR is compatible with compact encoding and can be delivered as synthetic mRNA. Thus, LIDAR expands the family of synthetic receptors, holding the promise to empower basic research and therapeutic applications.</p><figure></figure>","PeriodicalId":18832,"journal":{"name":"Nature chemical biology","volume":"15 1","pages":""},"PeriodicalIF":14.8,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143723133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Trans-splicing for gene regulation","authors":"Samat Bayakhmetov, Mahan Naseri, Xiao Wang","doi":"10.1038/s41589-025-01871-x","DOIUrl":"https://doi.org/10.1038/s41589-025-01871-x","url":null,"abstract":"Trans-splicing enables the ligation of exons from different pre-mRNAs into a single transcript. A recent study harnesses this process and develops riboregulators that, upon binding programmable external guide sequences (EGSs), allow customizable, orthogonal and predictable gene circuit construction.","PeriodicalId":18832,"journal":{"name":"Nature chemical biology","volume":"61 1","pages":""},"PeriodicalIF":14.8,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143712831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Takeshi Tsusaka, Mohd. Altaf Najar, Benjamin Schwarz, Eric Bohrnsen, Juan A. Oses-Prieto, Helena Neudorf, Christina Lee, Jonathan P. Little, Alma L. Burlingame, Catharine M. Bosio, George M. Burslem, Emily L. Goldberg
{"title":"Reversible histone deacetylase activity catalyzes lysine acylation","authors":"Takeshi Tsusaka, Mohd. Altaf Najar, Benjamin Schwarz, Eric Bohrnsen, Juan A. Oses-Prieto, Helena Neudorf, Christina Lee, Jonathan P. Little, Alma L. Burlingame, Catharine M. Bosio, George M. Burslem, Emily L. Goldberg","doi":"10.1038/s41589-025-01869-5","DOIUrl":"https://doi.org/10.1038/s41589-025-01869-5","url":null,"abstract":"<p>The dynamic modification of proteins by many metabolites suggests an intimate link between energy metabolism and post-translational modifications (PTMs). For instance, starvation and low-carbohydrate diets lead to the accumulation of β-hydroxybutyrate (BHB), whose blood concentrations can reach millimolar levels, concomitant with the accumulation of lysine β-hydroxybutyrylation (Kbhb) of proteins. Here we report that class I histone deacetylases (HDACs) unexpectedly catalyze the formation of Kbhb. Through mutational analysis, we show a shared reliance on key active site amino acids for classical deacetylation and noncanonical HDAC-catalyzed β-hydroxybutyrylation. On the basis of these data, we propose that HDACs catalyze a condensation reaction between the free amine group on lysine and the BHB carboxylic acid, thereby generating an amide bond. This reversible HDAC activity is not limited to BHB and extends to multiple short-chain fatty acids, representing a novel mechanism of PTM deposition relevant to metabolically sensitive proteome modifications.</p><figure></figure>","PeriodicalId":18832,"journal":{"name":"Nature chemical biology","volume":"71 1","pages":""},"PeriodicalIF":14.8,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143702901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hua Pu, Laura C. Bailey, Ludwig G. Bauer, Maria Voronkov, Matthew Baxter, Kilian V. M. Huber, Sepideh Khorasanizadeh, David Ray, Fraydoon Rastinejad
{"title":"Pharmacological targeting of BMAL1 modulates circadian and immune pathways","authors":"Hua Pu, Laura C. Bailey, Ludwig G. Bauer, Maria Voronkov, Matthew Baxter, Kilian V. M. Huber, Sepideh Khorasanizadeh, David Ray, Fraydoon Rastinejad","doi":"10.1038/s41589-025-01863-x","DOIUrl":"https://doi.org/10.1038/s41589-025-01863-x","url":null,"abstract":"<p>The basic helix–loop–helix PER-ARNT-SIM (bHLH-PAS) proteins BMAL1 and CLOCK heterodimerize to form the master transcription factor governing rhythmic gene expression. Owing to connections between circadian regulation and numerous physiological pathways, targeting the BMAL1–CLOCK complex pharmacologically is an attractive entry point for intervening in circadian-related processes. In this study, we developed a small molecule, Core Circadian Modulator (CCM), that targets the cavity in the PASB domain of BMAL1, causing it to expand, leading to conformational changes in the PASB domain and altering the functions of BMAL1 as a transcription factor. Biochemical, structural and cellular investigations validate the high level of selectivity of CCM in engaging BMAL1, enabling direct access to BMAL1–CLOCK cellular activities. CCM induces dose-dependent alterations in PER2–Luc oscillations and orchestrates the downregulation of inflammatory and phagocytic pathways in macrophages. These findings collectively reveal that the BMAL1 protein architecture is inherently configured to enable the binding of chemical ligands for functional modulation.</p><figure></figure>","PeriodicalId":18832,"journal":{"name":"Nature chemical biology","volume":"97 1","pages":""},"PeriodicalIF":14.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143695536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Learning from CoQ10 history","authors":"Francesco Zamberlan","doi":"10.1038/s41589-025-01877-5","DOIUrl":"10.1038/s41589-025-01877-5","url":null,"abstract":"","PeriodicalId":18832,"journal":{"name":"Nature chemical biology","volume":"21 4","pages":"465-465"},"PeriodicalIF":12.9,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143677726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}