Nature ProtocolsPub Date : 2026-04-23DOI: 10.1038/s41596-026-01355-9
Longjiang Ding, Sisi Fan, Na Liu
{"title":"Morphology-coupled formation and reversible gating of membrane channels in synthetic cells using reconfigurable DNA nanorafts.","authors":"Longjiang Ding, Sisi Fan, Na Liu","doi":"10.1038/s41596-026-01355-9","DOIUrl":"https://doi.org/10.1038/s41596-026-01355-9","url":null,"abstract":"<p><p>Membrane reshaping and channel formation often emerge from the coordinated interplay between membranes and their associated proteins. Reconstituting such integrated behaviors in synthetic systems remains challenging, especially when seeking reversible and programmable control. Here we present a protocol for the construction and application of reconfigurable DNA nanorafts that couple membrane morphology modulation with the formation of large, gated membrane channels in synthetic cells. These nanorafts are DNA origami structures that are functionalized with cholesterol anchors and undergo reversible shape transformations. Upon membrane binding, conformational changes drive their self-arrangement into locally ordered domains that deform giant unilamellar vesicles (GUVs). During GUV shape recovery, aided by protein nanopores, the nanorafts interact with the membrane to form synthetic channels capable of transporting large biomolecules (~70 kDa). These channels can be reversibly sealed, allowing programmable control over membrane permeability. Unlike conventional DNA-based nanopores that require pre-assembly and membrane insertion, this protocol supports stepwise, membrane-coupled channel formation with reversible gating. The protocol details the preparation of DNA nanorafts, membrane-bound conformational control, GUV formation, membrane remodeling, morphology-coupled large channel formation and sealing, as well as quantitative fluorescence microscopy assays to analyze vesicle morphology changes and cargo transport. Standard DNA nanotechnology tools and fluorescence microscopy techniques are sufficient to perform the workflow, which can be completed in ~4 d. The system's modularity makes it broadly applicable for constructing artificial cellular systems with programmable structure and function.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":16.0,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776790","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}
Nature ProtocolsPub Date : 2026-04-22DOI: 10.1038/s41596-026-01349-7
Yafeng Zhu, Olena Berkovska, Lingshuo Wang, Mei Yang, Henrik J Johansson, Georgios Mermelekas, Mahshid Zarrineh, Dong Yin, Lukas M Orre, Janne Lehtiö
{"title":"Differential protein expression analysis of quantitative mass spectrometry data using DEqMS.","authors":"Yafeng Zhu, Olena Berkovska, Lingshuo Wang, Mei Yang, Henrik J Johansson, Georgios Mermelekas, Mahshid Zarrineh, Dong Yin, Lukas M Orre, Janne Lehtiö","doi":"10.1038/s41596-026-01349-7","DOIUrl":"https://doi.org/10.1038/s41596-026-01349-7","url":null,"abstract":"<p><p>DEqMS is an R package-based statistical tool for differential protein expression analysis in quantitative mass spectrometry-based proteomics. It implements a robust Bayesian method for accurate variance estimation that accounts for the number of mass spectrometry features used for protein quantification (number of peptide precursors or peptide spectrum matches). Originally validated for data-dependent acquisition proteomics, DEqMS now extends to data-independent acquisition workflows, as demonstrated using both spike-in and real-world datasets. Given a peptide- or protein-level quantification table with mass spectrometry feature count as inputs, DEqMS outputs a protein- or gene-level results table containing fold changes and multiple statistics (t-values, P value, among others) adjusted according to mass spectrometry feature count. Here we detail the use of the DEqMS R package. This updated workflow broadens DEqMS's applicability, enabling researchers with basic R programming knowledge to identify proteins with significantly altered abundance between sample groups across diverse quantitative proteomics datasets. DEqMS is available to install at https://bioconductor.org/packages/DEqMS/ .</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":16.0,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776667","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}
Nature ProtocolsPub Date : 2026-04-22DOI: 10.1038/s41596-026-01354-w
Keyun Wang, Kejia Li, Jiayang Yan, Lianji Xue, Yanni Ma, Haiyang Zhu, Ting Yu, Yan Wang, Mikhail Savitski, Mingliang Ye
{"title":"Peptide-centric local stability assay (PELSA) for sensitive identification of ligand-targeting proteins and binding sites at proteome scale.","authors":"Keyun Wang, Kejia Li, Jiayang Yan, Lianji Xue, Yanni Ma, Haiyang Zhu, Ting Yu, Yan Wang, Mikhail Savitski, Mingliang Ye","doi":"10.1038/s41596-026-01354-w","DOIUrl":"https://doi.org/10.1038/s41596-026-01354-w","url":null,"abstract":"<p><p>The peptide-centric local stability assay (PELSA) was developed to identify the protein targets and binding regions of diverse ligands at a proteome-wide scale. In this approach, the ligand is added to a cell lysate, and the proteins are digested for a short, defined time period using 0.5 mg ml<sup>-1</sup> trypsin. Protein regions involved in ligand binding show less digestion, making it possible to identify binding sites and even quantify binding activity by dose-dependent analysis. In contrast to modification-based techniques that require chemical modification of ligands, the ligand modification-free property of the PELSA offers a key advantage by avoiding derivatization, thereby enabling proteome-wide identification of target proteins across diverse ligand types and biological contexts. The PELSA is broadly applicable for identifying protein targets of diverse ligands such as drugs and antibodies as well as endogenous metabolites and metal ions. However, performing PELSA experiments and subsequent data analysis to extract protein-ligand interaction details, including the binding protein, binding region and binding affinity, is not a trivial task. To address this, we present a detailed protocol for the experimental and computational PELSA workflow, including raw data processing and result visualization with the PELSA-Decipher software ( https://zenodo.org/records/18266507 ). Key points, such as selection of ligand concentrations, timing of trypsinization and quality control between different replicates, are discussed. Finally, we demonstrate the application of the protocol for identifying targets of staurosporine and 5-methyltetrahydrofolate, as well as for the dose-dependent PELSA analysis of inhibitors targeting the HSP90 family. The full PELSA protocol can be finished in 2 days, 1 day for sample preparation and 1 day for liquid chromatography-tandem mass spectrometry analysis and data processing. PELSA-Decipher can be downloaded from GitHub ( https://github.com/DICP-1809/ ).</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":16.0,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776835","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}
Nature ProtocolsPub Date : 2026-04-20DOI: 10.1038/s41596-026-01346-w
Sarah Ahannach, Sandra Condori-Catachura, Jelle Dillen, Caroline Dricot, Thies Gehrmann, Stijn Wittouck, Josiane Marie Kenfack, Wannes Van Beeck, Ilke De Boeck, Tom Eilers, Monica Ticlla, Agustina Santullo Latorre, Wenke Smets, Jari Temmermans, Enya Arconada Nuin, Sandra Van Puyvelde, Irina Spacova, Veronique Verhoeven, Sarah Lebeer
{"title":"Considerations for the design of impactful citizen-science projects in microbiome research.","authors":"Sarah Ahannach, Sandra Condori-Catachura, Jelle Dillen, Caroline Dricot, Thies Gehrmann, Stijn Wittouck, Josiane Marie Kenfack, Wannes Van Beeck, Ilke De Boeck, Tom Eilers, Monica Ticlla, Agustina Santullo Latorre, Wenke Smets, Jari Temmermans, Enya Arconada Nuin, Sandra Van Puyvelde, Irina Spacova, Veronique Verhoeven, Sarah Lebeer","doi":"10.1038/s41596-026-01346-w","DOIUrl":"https://doi.org/10.1038/s41596-026-01346-w","url":null,"abstract":"<p><p>Citizen science offers a transformative approach to microbiome research. It allows the collection of rich, context-specific data from diverse sources, such as varying human populations and environments. Here, we describe guidelines that cover the design and implementation of community-engaged citizen-science projects focused on microbiome research. We outline essential research steps, beginning with defining the objectives and forming a transdisciplinary team, and continuing with community interaction, standardized self-sampling protocols, strategies for data processing, analysis and communication of results to community members and policymakers, as well as the implementation of robust data management practices that uphold participant privacy and data sovereignty. The guidelines highlight culturally-sensitive outreach strategies and capacity building in research teams and communities, emphasizing ethical considerations and tailored recruitment strategies. Community engagement may help reduce sampling bias but does not automatically ensure participant diversity: intentional inclusion strategies are essential. They cover culturally sensitive outreach, ethical considerations and tailored recruitment approaches that support inclusive participation and meaningful collaboration. These recommendations draw inspiration from a range of health and environment-related citizen-science projects in Belgium, Peru and Cameroon, and collaborative projects across the world. Specific examples highlight the importance of adapting methodologies to diverse cultural contexts and logistical constraints. While wet-laboratory sample processing and downstream analyses are detailed elsewhere, this Perspective focuses on the unique considerations and best practices needed for designing impactful cocreative citizen-science projects that combine scientific discovery with community, environmental health and well-being. It can serve as a blueprint for future citizen-science initiatives that aim to expand access to microbiome research, foster global collaboration and promote long-term research equity and environmental sustainability.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":16.0,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147729534","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}
Nature ProtocolsPub Date : 2026-04-13DOI: 10.1038/s41596-026-01341-1
Maobin Xie, Liming Lian, Zhenrui Zhang, Zeng Lin, Emilio Mireles Guajardo, Jugal Kishore Sahoo, Guosheng Tang, Gang Li, Khoon S Lim, David L Kaplan, Yu Shrike Zhang
{"title":"Rapid volumetric bioprinting of pristine protein-based (bio)inks.","authors":"Maobin Xie, Liming Lian, Zhenrui Zhang, Zeng Lin, Emilio Mireles Guajardo, Jugal Kishore Sahoo, Guosheng Tang, Gang Li, Khoon S Lim, David L Kaplan, Yu Shrike Zhang","doi":"10.1038/s41596-026-01341-1","DOIUrl":"https://doi.org/10.1038/s41596-026-01341-1","url":null,"abstract":"<p><p>Volumetric bioprinting (VBP) enables the rapid photopolymerization of 3D constructs by modifying the illumination patterns within a build volume. However, only a few unmodified, pristine protein-based bioinks can be used for VBP, making the resulting (bio)printed volumes sometimes incompatible with further modification steps required for extended applications and thus limiting the wider adoption of VBP. We have recently developed new methods for VBP, in which unmodified protein-based (bio)inks with tyrosine groups, including those based on silk, decellularized extracellular matrix (dECM) and gelatin, can be (bio)printed, in their pristine state, by using the tris(2,2-bipyridyl)dichlororuthenium(II) hexahydrate/sodium persulfate photoinitiator system to form sophisticated shapes and architectures. Here, we provide step-by-step instructions to complete the VBP process and include the characterization of these bioinks. After treatment, the volumetrically printed silk sericin constructs show properties including reversible shrinkage and expansion, or shape-memory, whereas the volumetrically printed silk fibroin constructs exhibit broadly tunable mechanical performances ranging from a few hundred pascals to hundreds of megapascals. Both types of silk-based (bio)inks as well as dECM (bio)inks are cytocompatible. We further cover several demonstrations that show the potential uses of volumetrically (bio)printed silk and dECM constructs in clinical and biomedical applications.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":16.0,"publicationDate":"2026-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147675144","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}
Nature ProtocolsPub Date : 2026-04-10DOI: 10.1038/s41596-026-01340-2
Fan Cao, Sheng Wang, Zhixin Chen, Shizheng Zhang, Qianqian Wu, Jiaqi Zhang, Xuyong Yang
{"title":"Preparation of homogeneous ZnSeTeS quantum dots.","authors":"Fan Cao, Sheng Wang, Zhixin Chen, Shizheng Zhang, Qianqian Wu, Jiaqi Zhang, Xuyong Yang","doi":"10.1038/s41596-026-01340-2","DOIUrl":"https://doi.org/10.1038/s41596-026-01340-2","url":null,"abstract":"<p><p>Quantum dots (QDs) have emerged as promising candidates for next-generation display owing to their exceptional optoelectronic properties. However, despite substantial advancements in QD synthesis, the blue-emitting QDs, especially heavy-metal-free blue ones, still underperform compared with their red and green counterparts. ZnSeTe QDs offer a viable ecofriendly alternative for blue emissions, but their performance is limited by spectrum broadening (linewidth >20 nm) and structural instability. These issues stem from compositional inhomogeneity, which is primarily induced by Te aggregation during synthesis. Recently, we realized the synthesis of homogeneous quaternary-alloyed ZnSeTeS QDs through a synergistic strategy of reactivity modulation and isoelectronic control. This Protocol enables precise bandgap tuning in the blue spectral region (450-475 nm) by controlling the Te ratio, while ensuring high color purity and stability of QDs. Furthermore, the as-prepared ZnSeTeS QDs exhibit outstanding electroluminescence performance, with a peak external quantum efficiency of 24.7% and half-life of 29,600 h at 100 cd cm<sup>-2</sup>, and demonstrate strong potential for applications such as solid-state lighting and bioimaging owing to their high stability and low toxicity. Here we detail a synthesis Protocol for ZnSe<sub>0.94</sub>Te<sub>0.03</sub>S<sub>0.03</sub>/ZnSe/ZnS core/shell/shell QDs via a hot-injection method using zinc carboxylate and anionic phosphine precursor, systematically outlining the design and preparation of precursors and QDs, post treatments (including purifications) and characterization methods, including time-resolved photoluminescence spectroscopy. The entire process typically requires 11-12 h for QD synthesis and 6 h for characterizations, demanding only accessible chemistry knowledge and routine colloidal synthesis techniques.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":16.0,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147654744","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}
Nature ProtocolsPub Date : 2026-04-08DOI: 10.1038/s41596-026-01356-8
Wenkai Wang, Xiaocheng Liu, Zhenling Peng, Jianyi Yang
{"title":"The trRosettaRNA server for RNA structure prediction.","authors":"Wenkai Wang, Xiaocheng Liu, Zhenling Peng, Jianyi Yang","doi":"10.1038/s41596-026-01356-8","DOIUrl":"https://doi.org/10.1038/s41596-026-01356-8","url":null,"abstract":"<p><p>Similar to proteins, many RNAs fold into three-dimensional (3D) structures to perform biological functions. Here we present the trRosettaRNA server, a web-based platform for automated RNA 3D structure prediction using deep learning. The primary input is the nucleotide sequence of a target RNA, with the option to upload custom multiple sequence alignments and secondary structures. The server uses an end-to-end neural network for automated 3D structure prediction, followed by an energy optimization step to resolve structural violations. As an automated server, trRosettaRNA is distinguished by its state-of-the-art modeling accuracy, flexible input options and comprehensive visualization of prediction results. trRosettaRNA has been successfully applied in various contexts, including predicting structures for Rfam families lacking known 3D structures, where representative cases of high-confidence structure predictions were found to align well with subsequent experimental observations. Utilizing up to 5 central processing unit (CPU) cores in parallel on our computer cluster, the server takes a median time of about 1 h to predict structures for RNA sequences with about 200 nucleotides. The standalone package for trRosettaRNA offers distinct advantages such as enhanced data privacy for sensitive sequences, the ability to bypass server queues and integration into high-throughput automated pipelines. Importantly, the open-source nature of the package empowers researchers to directly modify the codebase for specialized research needs or to develop derivative tools by fine-tuning the underlying neural network. The web server and standalone package of trRosettaRNA are available at https://yanglab.qd.sdu.edu.cn/trRosettaRNA/ and https://github.com/YangLab-SDU/trRosettaRNA2 , respectively.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":16.0,"publicationDate":"2026-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147639378","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}
Nature ProtocolsPub Date : 2026-04-07DOI: 10.1038/s41596-026-01344-y
Kamal Jouad, Marisa Hom, Ashtyn McAdoo, J Oliver McIntyre, Eben L Rosenthal, Adam J Rosenberg
{"title":"Automated cGMP optical labeling of FDA-approved antibodies for human use.","authors":"Kamal Jouad, Marisa Hom, Ashtyn McAdoo, J Oliver McIntyre, Eben L Rosenthal, Adam J Rosenberg","doi":"10.1038/s41596-026-01344-y","DOIUrl":"10.1038/s41596-026-01344-y","url":null,"abstract":"<p><p>Monoclonal antibodies are commonly used as targeted therapies for autoimmune, infectious and oncologic diseases. Here, we describe a simple protocol to optically label monoclonal antibodies for use as molecular imaging agents for clinical investigation. In preclinical settings, optical imaging has complemented the strengths of nuclear imaging while offering higher resolution and a safer method for antibody-ligand engagement. However, translation of optically labeled monoclonal antibodies to the clinic has been slow because antibodies require a manual process in current good manufacturing practices (cGMP)-compliant facilities; the cost barriers to establish the investigational new drug application by using the traditional contract research organization pathway (>US$1 million) exceed the resources of academic institutions and early-phase pharmaceutical companies. To address these challenges, we repurposed an existing radiolabeling cGMP method for optical labeling that uses an automated, self-contained synthesis module. This method depends on commercially available, single-use, cassette-based production, which simplifies the workflow and does not require a clean room facility. This automated production method reduces both the cost and time required to produce a clinical dose of near-IR fluorescently labeled monoclonal antibody-IRDye800CW, decreasing the development costs for pilot and initial batches by almost 90%, as well as the production time by 40% to 4 h plus quality control (~10 h total). Our cGMP manufacturing method can optically label any compatible monoclonal antibodies at any dedicated radiochemistry facility. We provide the detailed protocol for production of panitumumab-IRDye800CW and nivolumab-IRDye800CW under cGMP regulations, achieving excellent yield, optimal degree of labeling and high purity.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":16.0,"publicationDate":"2026-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147632765","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}
Nature ProtocolsPub Date : 2026-04-02DOI: 10.1038/s41596-025-01305-x
Jeremy Koob, Kaiyi Jiang, Samantha R Sgrizzi, Fei Chen, Omar O Abudayyeh, Jonathan S Gootenberg
{"title":"Sensing and perturbing mammalian cell states with reprogrammable ADAR sensors (RADARS).","authors":"Jeremy Koob, Kaiyi Jiang, Samantha R Sgrizzi, Fei Chen, Omar O Abudayyeh, Jonathan S Gootenberg","doi":"10.1038/s41596-025-01305-x","DOIUrl":"https://doi.org/10.1038/s41596-025-01305-x","url":null,"abstract":"<p><p>Reprogrammable Adenosine Deaminase Acting on RNA (ADAR) Sensors (RADARS) control RNA translation in mammalian cells, allowing for noninvasive sensing or perturbation of specific cell types based on transcriptional signatures. Upon base-pairing between a target RNA and a sensor RNA, RADARS leverages ADAR to edit a premature stop codon upstream of a gene of interest, thereby releasing translation of the desired cargo. These design principles enable sequence programmability, allowing RADARS to adapt more easily to new contexts than existing tools for targeting cell types. We describe a detailed protocol for performing experiments with RADARS, including designing, cloning and validating RADARS constructs targeting a transcript of interest. RADARS guide sequences can be designed with an intuitive web interface and cloned into existing constructs for downstream applications including imaging, sorting and sequencing. We outline recommendations for cargo choice, sensor design and ADAR system selection, enabling users to choose the best workflow depending on the desired application. Beginning with sensor design, the selection of top-performing RADARS guides can be completed in ~2 weeks, followed by a desired use case. Convenient engineering and application of RADARS for various applications enable the design and execution of various cell-targeting experiments.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":16.0,"publicationDate":"2026-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147609000","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}
Nature ProtocolsPub Date : 2026-04-02DOI: 10.1038/s41596-026-01342-0
Surbhi Sharma, Madeline E Rasband, Xuemei Wang, Karen Tolentino, Sharon S Huang, Furqan M Fazal
{"title":"APEX-seq maps transcriptome-wide subcellular RNA localization in living cells.","authors":"Surbhi Sharma, Madeline E Rasband, Xuemei Wang, Karen Tolentino, Sharon S Huang, Furqan M Fazal","doi":"10.1038/s41596-026-01342-0","DOIUrl":"10.1038/s41596-026-01342-0","url":null,"abstract":"<p><p>Although we know a great deal about the subcellular locations of most proteins, our knowledge of where most RNAs localize within cells remains limited. As RNA subcellular localization determines the fate, function and regulation of both coding and noncoding RNAs, there has been substantial interest in developing new scalable approaches to study the location of RNAs in their native context. Furthermore, many locations, such as membrane-bound and membrane-less organelles, have traditionally been challenging to study owing to lack of suitable tools to interrogate their constituents. Here we describe a detailed protocol for APEX sequencing (APEX-seq) that yields transcriptome-wide information of the subcellular address of RNAs that can, in principle, be applied to any subcellular location, membrane or condensate. APEX-seq utilizes a genetically encoded engineered ascorbate peroxidase (APEX2) tagged to a specific protein that localizes it to a region of interest. In the presence of biotin-phenol and hydrogen peroxide, APEX2 catalyzes the biotinylation of RNAs in its vicinity, which can be purified using streptavidin beads and sequenced to reveal the RNA repertoire at that subcellular location. APEX-seq experiments can be carried out by laboratory personnel trained in molecular biology. The analysis of APEX-seq data requires familiarity with standard RNA sequencing workflows. With APEX2-expressing cell lines in hand, the entire procedure from labeling reaction to analysis can be completed in 1 week. We expect this proximity labeling approach to facilitate the unbiased discovery of RNAs localizing to different organelles and to generate hypotheses for the mechanisms and pathways involved in regulating these processes.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":16.0,"publicationDate":"2026-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147608939","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}