Pub Date : 2025-12-19DOI: 10.1016/j.molcel.2025.11.028
Rongrong Du, Michael J. Flynn, Karan Mahe, Monique Honsa, Bo Gu, Dongyang Li, Sean E. McGeary, Viviana Gradinaru, Ralf Jungmann, Michael B. Elowitz
Accurate control of transgene expression is important for research and therapy but is challenging to achieve in most settings. MicroRNA (miRNA)-based regulatory circuits can be incorporated within transgenes for improved control. However, the design principles, performance limits, and applications of these circuits in research and biotechnology have not been systematically determined. Here, combining modeling and experiments, we introduce miRNA-based circuit modules, termed “dosage invariant miRNA-mediated expression regulators” (DIMMERs), that establish precise, tunable control of transgene expression across diverse cell types to facilitate imaging, editing, and gene therapy. The circuits use multivalent miRNA regulatory interactions to achieve nearly uniform, tunable protein expression over two orders of magnitude variation in gene dosage. They function across diverse cell types and can be multiplexed for the independent regulation of multiple genes. DIMMERs reduce off-target CRISPR base editing, improve single-molecule imaging, and allow live tracking of adeno-associated virus (AAV)-delivered transgene expression in mouse cortical neurons. DIMMERs thus enable accurate regulation for research and biotechnology applications.
{"title":"miRNA modules for precise, tunable control of gene expression","authors":"Rongrong Du, Michael J. Flynn, Karan Mahe, Monique Honsa, Bo Gu, Dongyang Li, Sean E. McGeary, Viviana Gradinaru, Ralf Jungmann, Michael B. Elowitz","doi":"10.1016/j.molcel.2025.11.028","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.11.028","url":null,"abstract":"Accurate control of transgene expression is important for research and therapy but is challenging to achieve in most settings. MicroRNA (miRNA)-based regulatory circuits can be incorporated within transgenes for improved control. However, the design principles, performance limits, and applications of these circuits in research and biotechnology have not been systematically determined. Here, combining modeling and experiments, we introduce miRNA-based circuit modules, termed “dosage invariant miRNA-mediated expression regulators” (DIMMERs), that establish precise, tunable control of transgene expression across diverse cell types to facilitate imaging, editing, and gene therapy. The circuits use multivalent miRNA regulatory interactions to achieve nearly uniform, tunable protein expression over two orders of magnitude variation in gene dosage. They function across diverse cell types and can be multiplexed for the independent regulation of multiple genes. DIMMERs reduce off-target CRISPR base editing, improve single-molecule imaging, and allow live tracking of adeno-associated virus (AAV)-delivered transgene expression in mouse cortical neurons. DIMMERs thus enable accurate regulation for research and biotechnology applications.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"116 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145777700","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}
Pub Date : 2025-12-19DOI: 10.1016/j.molcel.2025.11.025
Catherine H. Freudenreich
{"title":"Time and space: How the circadian clock controls DNA break repair location and pathway choice","authors":"Catherine H. Freudenreich","doi":"10.1016/j.molcel.2025.11.025","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.11.025","url":null,"abstract":"","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"35 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145784405","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}
Pub Date : 2025-12-19DOI: 10.1016/j.molcel.2025.11.029
Ron Kelley, Sagar Khavnekar, Ricardo D. Righetto, Jessica Heebner, Martin Obr, Xianjun Zhang, Saikat Chakraborty, Grigory Tagiltsev, Alicia K. Michael, Sofie van Dorst, Florent Waltz, Caitlyn L. McCafferty, Lorenz Lamm, Simon Zufferey, Philippe Van der Stappen, Hugo van den Hoek, Wojciech Wietrzynski, Pavol Harar, William Wan, John A.G. Briggs, Abhay Kotecha
In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate the structures of biomolecules in their native context. However, challenges remain for the efficient production and sharing of large-scale cryo-ET datasets. Here, we combined cryogenic plasma-based focused ion beam (cryo-PFIB) milling with recent advances in cryo-ET acquisition and processing to generate a dataset of 1,829 annotated tomograms of the green alga Chlamydomonas reinhardtii, which we provide as a community resource to drive method development and inspire biological discovery. To assay data quality, we performed subtomogram averaging of both soluble and membrane-bound complexes ranging in size from >3 MDa to ∼200 kDa, including 80S ribosomes, Rubisco, nucleosomes, microtubules, clathrin, photosystem II, and mitochondrial ATP synthase. The majority of these density maps reached sub-nanometer resolution, demonstrating the potential of this C. reinhardtii dataset as well as the promise of modern cryo-ET workflows and open data sharing to empower visual proteomics.
{"title":"Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii","authors":"Ron Kelley, Sagar Khavnekar, Ricardo D. Righetto, Jessica Heebner, Martin Obr, Xianjun Zhang, Saikat Chakraborty, Grigory Tagiltsev, Alicia K. Michael, Sofie van Dorst, Florent Waltz, Caitlyn L. McCafferty, Lorenz Lamm, Simon Zufferey, Philippe Van der Stappen, Hugo van den Hoek, Wojciech Wietrzynski, Pavol Harar, William Wan, John A.G. Briggs, Abhay Kotecha","doi":"10.1016/j.molcel.2025.11.029","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.11.029","url":null,"abstract":"<em>In situ</em> cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate the structures of biomolecules in their native context. However, challenges remain for the efficient production and sharing of large-scale cryo-ET datasets. Here, we combined cryogenic plasma-based focused ion beam (cryo-PFIB) milling with recent advances in cryo-ET acquisition and processing to generate a dataset of 1,829 annotated tomograms of the green alga <em>Chlamydomonas reinhardtii</em>, which we provide as a community resource to drive method development and inspire biological discovery. To assay data quality, we performed subtomogram averaging of both soluble and membrane-bound complexes ranging in size from >3 MDa to ∼200 kDa, including 80S ribosomes, Rubisco, nucleosomes, microtubules, clathrin, photosystem II, and mitochondrial ATP synthase. The majority of these density maps reached sub-nanometer resolution, demonstrating the potential of this <em>C. reinhardtii</em> dataset as well as the promise of modern cryo-ET workflows and open data sharing to empower visual proteomics.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"31 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145777701","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}
Pub Date : 2025-12-19DOI: 10.1016/j.molcel.2025.11.026
Erdem M. Terzi, Richard Possemato
{"title":"Transporting the transporter: TIM22 translocates mitoferrins to enable mitochondrial iron-sulfur cluster synthesis","authors":"Erdem M. Terzi, Richard Possemato","doi":"10.1016/j.molcel.2025.11.026","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.11.026","url":null,"abstract":"","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"10 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145784784","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}
Pub Date : 2025-12-19DOI: 10.1016/j.molcel.2025.11.030
Sandra Nitsch, Aria E. Coraor, Tamas Schauer, Yiheng Wu, Jianfeng Sun, Natalie Möritz, Jonas Funke, Harsh Nagpal, Gabriella N.L. Chua, Federica Battistini, Shannon M. Lauberth, Eva Richard, Modesto Orozco, Shixin Liu, Lourdes R. Desviat, Beat Fierz, Hendrik Dietz, Robert G. Roeder, Juan J. de Pablo, Robert Schneider
{"title":"H4K16 acylations destabilize chromatin architecture and facilitate transcriptional response during metabolic perturbations","authors":"Sandra Nitsch, Aria E. Coraor, Tamas Schauer, Yiheng Wu, Jianfeng Sun, Natalie Möritz, Jonas Funke, Harsh Nagpal, Gabriella N.L. Chua, Federica Battistini, Shannon M. Lauberth, Eva Richard, Modesto Orozco, Shixin Liu, Lourdes R. Desviat, Beat Fierz, Hendrik Dietz, Robert G. Roeder, Juan J. de Pablo, Robert Schneider","doi":"10.1016/j.molcel.2025.11.030","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.11.030","url":null,"abstract":"","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"114 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145784785","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}
Pub Date : 2025-12-19DOI: 10.1016/j.molcel.2025.11.020
Zeshi Li, Bhagyashree S. Joshi, Hongbo Yin, Ruud H. Wijdeven, Azen Koç, Dick W. Zijlmans, Irene Santos-Barriopedro, Hailiang Mei, Wei Wu, Milad Shademan, Filip M. Zawisza, Eric Bos, Pradeep Chopra, Marvin E. Tanenbaum, Thomas H. Sharp, Michiel Vermeulen, Vered Raz, Chirlmin Joo
{"title":"Cell-surface RNA forms ternary complex with RNA-binding proteins and heparan sulfate to recruit immune receptors","authors":"Zeshi Li, Bhagyashree S. Joshi, Hongbo Yin, Ruud H. Wijdeven, Azen Koç, Dick W. Zijlmans, Irene Santos-Barriopedro, Hailiang Mei, Wei Wu, Milad Shademan, Filip M. Zawisza, Eric Bos, Pradeep Chopra, Marvin E. Tanenbaum, Thomas H. Sharp, Michiel Vermeulen, Vered Raz, Chirlmin Joo","doi":"10.1016/j.molcel.2025.11.020","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.11.020","url":null,"abstract":"","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"29 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145784781","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}
Pub Date : 2025-12-19DOI: 10.1016/j.molcel.2025.11.021
Saeid Parast, Simai Wang, Marta Iwanaszko, Yue He, Deniz G. Olgun, Sarah Gold, Jacob M. Zeidner, Yuki Aoi, Benjamin C. Howard, William R. Thakur, Vijay Ramani, Ali Shilatifard
{"title":"Defective RNA processing and ELOA-mediated transcriptional elongation in reversible cellular senescence suggest aging by transcription","authors":"Saeid Parast, Simai Wang, Marta Iwanaszko, Yue He, Deniz G. Olgun, Sarah Gold, Jacob M. Zeidner, Yuki Aoi, Benjamin C. Howard, William R. Thakur, Vijay Ramani, Ali Shilatifard","doi":"10.1016/j.molcel.2025.11.021","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.11.021","url":null,"abstract":"","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"1 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145784780","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}
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