Nature Structural & Molecular Biology最新文献

{"title":"MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy","authors":"Stephen P. Burr, Kathryn Auckland, Angelos Glynos, Abhilesh Dhawanjewar, Cameron Ryall, Wei Wei, Antony Hynes-Allen, Malwina Prater, Matylda Sczaniecka-Clift, Julien Prudent, Patrick F. Chinnery, Jelle van den Ameele","doi":"10.1038/s41594-026-01779-7","DOIUrl":"10.1038/s41594-026-01779-7","url":null,"abstract":"Mitochondria contain their own genome, mitochondrial DNA (mtDNA), which is under strict control by the cell nucleus. mtDNA occurs in many copies per cell and mutations often only affect a proportion of them, giving rise to heteroplasmy. mtDNA copy number and heteroplasmy level together shape the tissue-specific impact of mtDNA mutations, eventually giving rise to both rare mitochondrial and common neurodegenerative diseases. Here, we use MitoPerturb-Seq for CRISPR–Cas9-based, high-throughput single-cell interrogation of the nuclear genes and pathways that sense and control mtDNA copy number and heteroplasmy. We screened a panel of mtDNA maintenance genes in mouse cells with a heteroplasmic mtDNA mt-Ta mutation. This revealed both common and perturbation-specific aspects of the integrated stress response to mtDNA depletion caused by Tfam, Opa1 and Polg knockout. These responses are only partially mediated by ATF4 and cause cell-cycle stage-independent slowing of cell proliferation. MitoPerturb-Seq, thus, provides experimental insight into disease-relevant mitochondrial–nuclear interactions and may inform development of therapies targeting cell-type- and tissue-specific vulnerabilities to mitochondrial dysfunction. Burr and Auckland et. al develop MitoPerturb-Seq, which combines single-cell screening with multiomics to link nuclear genes to mitochondrial DNA (mtDNA) dynamics. They unveil core regulators of mtDNA copy number and characterize cell-cycle delays and transcriptional stress in response to mtDNA depletion.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"33 4","pages":"711-723"},"PeriodicalIF":10.1,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41594-026-01779-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147585940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Condensate protein aggregation in ALS/FTD is regulated by GGGGCC-repeat RNA scaffolds","authors":"Yu Liu, Minghui Song, Liqi Wan, Pei Guo, Da Han","doi":"10.1038/s41594-026-01785-9","DOIUrl":"10.1038/s41594-026-01785-9","url":null,"abstract":"Biomolecular condensates regulate essential biological processes relevant to health and disease. However, the mechanisms driving pathogenic condensate formation and their therapeutic targeting have not been fully elucidated. In amyotrophic lateral sclerosis and frontotemporal dementia caused by C9orf72 GGGGCC repeat expansions (c9ALS/FTD), the expanded repeat RNA and repeat-associated non-AUG translation products are key pathogenic factors. Here, we show that the GGGGCC-repeat RNA and poly(GR) form cocondensates in vitro and in cellulo. The G-quadruplex and hairpin structures of GGGGCC-repeat RNA act as scaffolds to accelerate liquid-to-solid phase transition and aggregation of poly(GR), with the hairpin structure promoting amorphous solid-like condensates in vitro and reducing poly(GR) mobility. The cocondensation of GGGGCC-repeat RNA and poly(GR) exacerbates nucleolar stress and cellular toxicity. Targeting both G-quadruplex and hairpin structures of GGGGCC-repeat RNA with small molecules diminishes poly(GR) aggregation and ameliorates cellular dysfunction. These findings expand our understanding of poly(GR) aggregation in c9ALS/FTD, highlight the importance of RNA structure in regulating protein aggregation and suggest that targeting the RNA scaffold may expand the druggable space of pathogenic condensates. Liu et al. show that the C9orf72 GGGGCC-repeat RNA drives liquid-to-solid phase transition of poly(GR) in ALS/FTD through forming G-quadruplex and hairpin scaffolds, whereas targeting the RNA structures with small molecules reduces poly(GR) aggregation and cellular dysfunction.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"33 4","pages":"641-651"},"PeriodicalIF":10.1,"publicationDate":"2026-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147584017","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":"Resolution of R-loops and transcription–replication conflicts by SETX–BRCA1–BARD1 complex","authors":"Arijit Dutta, Jae-Hoon Ji, Shahrez Syed, Qingming Fang, Pramiti Mukhopadhyay, Hanzhou Wang, Eva Loranc, Daisy Medina, Shahad Abdulsahib, Shuo Zhou, Miriam Tovar, Jeff Wang, Jane M. Benoit, Fengshan Liang, Nozomi Tomimatsu, Julius O. Nyalwidhe, Eloise Dray, Amy Verway-Cohen, Drew T. McDonald, Bárbara de la Peña Avalos, Wenjing Li, Ane Olazabal Herrero, O’Taveon Fitzgerald, Alexander B. Taylor, Youngho Kwon, Oliver J. Semmes, Miaw-Sheue Tsai, Manjeet Rao, Robert Hromas, Sandeep Burma, Yidong Chen, Alexander V. Mazin, Elizabeth Wasmuth, Shaun K. Olsen, Daohong Zhou, Alexander J. R. Bishop, Weixing Zhao, Gary M. Kupfer, Patrick Sung","doi":"10.1038/s41594-026-01778-8","DOIUrl":"10.1038/s41594-026-01778-8","url":null,"abstract":"Senataxin (SETX), an RNA–DNA helicase, accumulates at transcription pause sites through the tumor suppressor BRCA1. Here, we provide mechanistic insight into how SETX–BRCA1 resolves transcription-associated R-loops to prevent deleterious outcomes. Specifically, we show that full-length SETX unwinds R-loops with broad specificity and that the complex of BRCA1 and its obligatory partner BARD1 binds R-loops and stimulates R-loop unwinding by SETX. BRCA1–BARD1 alleviates the inhibitory effect of RAD52 on SETX-mediated R-loop unwinding. We also demonstrate that phosphorylation of Ser642 in SETX promotes its interaction with BRCA1 through the tandem BRCT domain of the latter. Accordingly, mutations impacting the catalytic domain or Ser642 in SETX lead to R-loop accumulation, transcription–replication conflicts, replication fork stalling and DNA double-strand breaks in human cells. Thus, our results delineate the molecular basis for functional synergy between SETX and BRCA1–BARD1 in R-loop resolution and the mitigation of transcription–replication conflicts to preserve genome integrity. Dutta et al. demonstrate that the tumor suppressor complex BRCA1–BARD1 physically interacts with the RNA–DNA helicase Senataxin (SETX) and upregulates the activity of SETX to resolve harmful R-loops crucial for the avoidance of transcription–replication conflicts.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"33 4","pages":"615-630"},"PeriodicalIF":10.1,"publicationDate":"2026-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147584018","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":"Structural insight into IscB’s RNA-lid-based inactivation mechanism","authors":"Feizuo Wang, Ruochen Guo, Senfeng Zhang, Yinuo Cui, Junlan Wang, Tao Hu, Kunming Liu, Qi Wang, Yao Liu, Ki Hyun Nam, Ziqing Winston Zhao, Quanquan Ji, Xin Xu, Ercheng Wang, Youyuan Zhu, Yao Yang, Min Luo, Peixiang Ma, Shengsheng Ma, Chunlong Xu, Chunyi Hu","doi":"10.1038/s41594-026-01761-3","DOIUrl":"10.1038/s41594-026-01761-3","url":null,"abstract":"IscB, a compact Cas9 ancestor from the obligate mobile element guided activity system, has attracted growing interest as a programmable genome editor because of its small size and therapeutic delivery potential. Despite its promise, structural insights into IscB’s regulation remain limited, with only a target-bound R-loop structure previously reported. Here, we present the structural trajectory of an engineered IscB, capturing its transition from a resting state to activation. Using cryo-electron microscopy, we resolve four high-resolution structures: the apo resting state, two intermediate complexes with 6-nt and 10-nt guide–target pairing and a fully paired 16-nt primed cleavage state. These structures uncover a dual inactivation mechanism mediated by RNA lids; the ωRNA lid blocks HNH domain access, while the guide RNA lid occludes the RuvC active site. As guide–target pairing progresses, the guide RNA undergoes a stepwise displacement, mimicking a ‘car pedal’ motion that triggers activation at 11-nt pairing. The HNH domain also contributes to R-loop stabilization through a positively charged R-wedge motif and undergoes a ~90° activation-driven rotation mediated by two hinge regions. In variants IscBHig1 and IscBHig2, engineering these hinge motifs to enhance conformational flexibility notably improved genome-editing efficiency in cells. In summary, our study reveals the molecular basis underlying IscB autoinhibition and activation, identifies previously uncharacterized regulatory features and establishes hinge elements as a target region for engineering compact, efficient genome editors. Wang, Guo, Zhang and colleagues obtain four cryo-electron microscopy snapshots that show how IscB is kept off by two RNA lids, with a car-pedal-like guide shift activating cleavage after ~11-nt pairing. They also engineer hinge regions that boost flexibility and improve genome editing in cells.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"33 4","pages":"603-614"},"PeriodicalIF":10.1,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41594-026-01761-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147506133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extending guide RNA length restores high-fidelity CRISPR–Cas9 activity","authors":"","doi":"10.1038/s41594-026-01765-z","DOIUrl":"10.1038/s41594-026-01765-z","url":null,"abstract":"High-fidelity CRISPR–Cas9 enzymes have fewer off-targets but often suffer from low editing efficiency. Here, we show that a simple extension of the guide RNA improves the activity of SuperFi-Cas9 while preserving its accuracy. This extension enhances SuperFi-Cas9’s genome editing performance by strengthening the interactions in the protospacer adjacent motif (PAM)-distal region.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"33 4","pages":"563-564"},"PeriodicalIF":10.1,"publicationDate":"2026-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147489980","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":"No stasis in proteostasis","authors":"","doi":"10.1038/s41594-026-01783-x","DOIUrl":"10.1038/s41594-026-01783-x","url":null,"abstract":"In this issue of Nature Structural & Molecular Biology, we focus on all things protein homeostasis, highlighting a variety of processes, from protein quality control in translation to autophagy.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"33 3","pages":"363-363"},"PeriodicalIF":10.1,"publicationDate":"2026-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41594-026-01783-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147481201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improving the efficiency of high-fidelity Cas9 by enhancing PAM-distal interactions","authors":"Rong Zheng, Zhike Lu, Rongwei Wei, Young-Cheul Shin, Jiang Du, Qingfeng Zhang, Jianbo Li, Xiaoqi Wang, Yi Wei, Botao Liu, Yang Chen, Lihong Ding, Heng Zhang, Hui Chen, Jing Huang, Lijia Ma","doi":"10.1038/s41594-026-01753-3","DOIUrl":"10.1038/s41594-026-01753-3","url":null,"abstract":"Engineering CRISPR enzymes for high fidelity often impairs cleavage activity. Meanwhile, a mechanistic understanding of why high-fidelity mutations reduce Cas9’s cleavage activity remains unclear, presenting a challenge in balancing nuclease specificity and efficiency for clinical applications. In this study, we show that extending the spacer region to 21 or 22 nucleotides restores the impaired cleavage activity of SuperFi-Cas9, a high-fidelity Cas9 variant with 7 mutations in the RuvC domain at the protospacer adjacent motif (PAM)-distal region. Cryo-electron microscopy structures and mutational analyses reveal that the negatively charged mutations in a protruding loop of the RuvC domain create repulsive forces that destabilize the nuclease–single guide (sg)RNA–DNA complex. Spacer extension enhances interactions in the PAM-distal region, effectively restoring cleavage activity and balancing editing efficiency with specificity. In addition, we develop a deep learning model, AIdit-SuperFi, to predict optimal sgRNA length for high-fidelity genome editing. Our findings introduce a straightforward strategy to enhance CRISPR complex stability and provide mechanistic insights into the impaired cleavage activity of engineered high-fidelity Cas9, presenting a pathway toward precise and efficient genome editing and clinical translation of CRISPR technologies. Zheng et al. show that extending the guide RNA restores the reduced activity of a high-fidelity CRISPR–Cas9 enzyme while preserving accuracy, revealing how strengthened PAM-distal interactions can improve genome-editing performance.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"33 4","pages":"590-602"},"PeriodicalIF":10.1,"publicationDate":"2026-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147478549","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":"Ribosome-associated quality control and related mechanisms","authors":"Toshifumi Inada","doi":"10.1038/s41594-026-01771-1","DOIUrl":"10.1038/s41594-026-01771-1","url":null,"abstract":"Ribosome-associated quality control (RQC) safeguards translation by detecting and resolving collided ribosomes and triaging their nascent chains. This Review outlines mechanisms, crosstalk and disease implications of RQC cascades and presents RQC as a ‘first responder’ that prevents escalation to global stress responses and provides protection against proteostasis collapse. Here the author highlights and summarizes the latest advances in ribosome-associated quality control and related mechanisms.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"33 3","pages":"394-407"},"PeriodicalIF":10.1,"publicationDate":"2026-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147471388","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":"Vitamin B2 metabolism promotes FSP1 stability to prevent ferroptosis","authors":"Kirandeep K. Deol, Cynthia A. Harris, Sydney J. Tomlinson, Colin J. Delaney, Amr Al-Farhan, Alyssa J. Mathiowetz, Cody E. Doubravsky, Derek A. Pratt, James A. Olzmann","doi":"10.1038/s41594-026-01759-x","DOIUrl":"10.1038/s41594-026-01759-x","url":null,"abstract":"Ferroptosis, a regulated form of cell death driven by excessive lipid peroxidation, has emerged as a promising therapeutic target in cancer. Ferroptosis suppressor protein 1 (FSP1) is a critical regulator of ferroptosis resistance, yet the mechanisms controlling its expression and stability remain mostly unexplored. To uncover regulators of FSP1 abundance, we conducted CRISPR–Cas9 screens using a genome-edited, dual-fluorescent FSP1 reporter cell line, identifying both transcriptional and post-translational mechanisms that determine FSP1 levels. Notably, we identified riboflavin kinase and flavin adenine dinucleotide (FAD) synthase, enzymes that are essential for synthesizing FAD from vitamin B2, as key contributors to FSP1 stability. Biochemical and cellular analyses revealed that FAD binding is critical for both FSP1 activity and stability. FAD deficiency and mutations blocking FSP1–FAD binding triggered FSP1 degradation through a ubiquitin–proteasome pathway involving the E3 ligase RNF8. Unlike other vitamins that inhibit ferroptosis by scavenging radicals, vitamin B2 supports ferroptosis resistance through FAD cofactor binding, ensuring proper FSP1 stability and function. This study provides a rich resource detailing mechanisms that regulate FSP1 abundance and highlights a novel connection between vitamin B2 metabolism and ferroptosis resistance, with implications for therapeutic strategies targeting FSP1 in cancer. Here, Deol et al. use genetic screens in gene-edited reporter cell lines to identify regulators of ferroptosis suppressor protein 1 (FSP1) expression and stability. They show that vitamin B2 metabolism stabilizes FSP1 through flavin adenine dinucleotide binding, preventing its degradation and ferroptosis sensitization.","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"33 3","pages":"525-536"},"PeriodicalIF":10.1,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41594-026-01759-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147454761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identifying factors regulating tauopathies","authors":"Dimitris Typas","doi":"10.1038/s41594-026-01781-z","DOIUrl":"10.1038/s41594-026-01781-z","url":null,"abstract":"","PeriodicalId":49141,"journal":{"name":"Nature Structural & Molecular Biology","volume":"33 3","pages":"372-372"},"PeriodicalIF":10.1,"publicationDate":"2026-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147458589","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}