Pub Date : 2026-02-02DOI: 10.1038/s41594-025-01742-y
Daniel Scholl, Tumara Boyd, Andrew P. Latham, Alexandra Salazar, Asma M. A. M. Khan, Steven Boeynaems, Alex S. Holehouse, Gabriel C. Lander, Andrej Sali, Donghyun Park, Ashok A. Deniz, Keren Lasker
Biomolecular condensates have key roles in regulating cellular processes. Yet, the relationship between atomic features and condensate function remains poorly understood. We studied this relationship using the polar organizing protein Z (PopZ). Here, we revealed hierarchical assembly of PopZ into a filamentous condensate by integrating cryo-electron tomography, biochemistry, single-molecule techniques and molecular dynamics simulations. The PopZ helical domain drives filamentation and condensation, while the disordered region inhibits them. Phase-dependent conformational changes prevent interfilament contacts in the dilute phase and expose client-binding sites in the dense phase. Perturbing filament formation in vitro alters the dynamics of scaffold and client proteins and the condensate’s wetting behavior. In cells, perturbing either filament formation or the ability of filaments to condense impairs PopZ function and leads to growth phenotypes. These findings establish a multiscale framework linking molecular interactions and condensate ultrastructure to cellular function.
{"title":"The filamentous ultrastructure of the PopZ condensate is required for its cellular function","authors":"Daniel Scholl, Tumara Boyd, Andrew P. Latham, Alexandra Salazar, Asma M. A. M. Khan, Steven Boeynaems, Alex S. Holehouse, Gabriel C. Lander, Andrej Sali, Donghyun Park, Ashok A. Deniz, Keren Lasker","doi":"10.1038/s41594-025-01742-y","DOIUrl":"https://doi.org/10.1038/s41594-025-01742-y","url":null,"abstract":"Biomolecular condensates have key roles in regulating cellular processes. Yet, the relationship between atomic features and condensate function remains poorly understood. We studied this relationship using the polar organizing protein Z (PopZ). Here, we revealed hierarchical assembly of PopZ into a filamentous condensate by integrating cryo-electron tomography, biochemistry, single-molecule techniques and molecular dynamics simulations. The PopZ helical domain drives filamentation and condensation, while the disordered region inhibits them. Phase-dependent conformational changes prevent interfilament contacts in the dilute phase and expose client-binding sites in the dense phase. Perturbing filament formation in vitro alters the dynamics of scaffold and client proteins and the condensate’s wetting behavior. In cells, perturbing either filament formation or the ability of filaments to condense impairs PopZ function and leads to growth phenotypes. These findings establish a multiscale framework linking molecular interactions and condensate ultrastructure to cellular function.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"103 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146102122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
RNA-guided DNA nucleases Cas9 and IscB (insertion sequences Cas9-like OrfB) are components of type II CRISPR-Cas adaptive immune systems and transposon-associated OMEGA (obligate mobile element-guided activity) systems, respectively. Sequence and structural comparisons indicate that IscB (~500 residues) evolved into Cas9 (~700-1,600 residues) through protein expansion coupled with guide RNA miniaturization. However, the specific sequence of events in this evolutionary transition remains unknown. Here, we report cryo-electron microscopy structures of four phylogenetically diverse RNA-guided nucleases-two IscBs and two Cas9s-each in complex with its cognate guide RNA and target DNA. Comparisons of these four complex structures to previously reported IscB and Cas9 structures indicate that evolution from IscB to Cas9 involved the loss of the N-terminal PLMP domain and the acquisition of the zinc-finger-containing REC3 domain, followed by bridge helix extension and REC1 domain acquisition. These structural changes led to expansion of the REC lobe, increasing the target DNA cleavage specificity. Additionally, the structural conservation of the RNA scaffolds indicates that the dual CRISPR RNA (crRNA) and trans-activating crRNA guides of CRISPR-Cas9 evolved from the single ωRNA guides of OMEGA systems. Our findings provide insights into the succession of structural changes involved in the exaptation of transposon-associated RNA-guided nucleases for the role of effector nucleases in adaptive immune systems.
{"title":"Structural visualization of the molecular evolution of CRISPR-Cas9.","authors":"Naoto Nagahata,Kazuki Kato,Sota Yamada,Soumya Kannan,Sae Okazaki,Yukari Isayama,Masahiro Hiraizumi,Keitaro Yamashita,Eugene V Koonin,Feng Zhang,Hiroshi Nishimasu","doi":"10.1038/s41594-025-01743-x","DOIUrl":"https://doi.org/10.1038/s41594-025-01743-x","url":null,"abstract":"RNA-guided DNA nucleases Cas9 and IscB (insertion sequences Cas9-like OrfB) are components of type II CRISPR-Cas adaptive immune systems and transposon-associated OMEGA (obligate mobile element-guided activity) systems, respectively. Sequence and structural comparisons indicate that IscB (~500 residues) evolved into Cas9 (~700-1,600 residues) through protein expansion coupled with guide RNA miniaturization. However, the specific sequence of events in this evolutionary transition remains unknown. Here, we report cryo-electron microscopy structures of four phylogenetically diverse RNA-guided nucleases-two IscBs and two Cas9s-each in complex with its cognate guide RNA and target DNA. Comparisons of these four complex structures to previously reported IscB and Cas9 structures indicate that evolution from IscB to Cas9 involved the loss of the N-terminal PLMP domain and the acquisition of the zinc-finger-containing REC3 domain, followed by bridge helix extension and REC1 domain acquisition. These structural changes led to expansion of the REC lobe, increasing the target DNA cleavage specificity. Additionally, the structural conservation of the RNA scaffolds indicates that the dual CRISPR RNA (crRNA) and trans-activating crRNA guides of CRISPR-Cas9 evolved from the single ωRNA guides of OMEGA systems. Our findings provide insights into the succession of structural changes involved in the exaptation of transposon-associated RNA-guided nucleases for the role of effector nucleases in adaptive immune systems.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146088952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-22DOI: 10.1038/s41594-025-01737-9
Nataliya Petryk
{"title":"ADAR1 is an editor of DNA replication forks.","authors":"Nataliya Petryk","doi":"10.1038/s41594-025-01737-9","DOIUrl":"https://doi.org/10.1038/s41594-025-01737-9","url":null,"abstract":"","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"38 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146021570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-21DOI: 10.1038/s41594-026-01748-0
Ben L Carty,Danilo Dubocanin,Marina Murillo-Pineda,Marie Dumont,Emilia Volpe,Pawel Mikulski,Julia Humes,Oliver Whittingham,Daniele Fachinetti,Simona Giunta,Nicolas Altemose,Lars E T Jansen
{"title":"Author Correction: Heterochromatin boundaries maintain centromere position, size and number.","authors":"Ben L Carty,Danilo Dubocanin,Marina Murillo-Pineda,Marie Dumont,Emilia Volpe,Pawel Mikulski,Julia Humes,Oliver Whittingham,Daniele Fachinetti,Simona Giunta,Nicolas Altemose,Lars E T Jansen","doi":"10.1038/s41594-026-01748-0","DOIUrl":"https://doi.org/10.1038/s41594-026-01748-0","url":null,"abstract":"","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"112 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146015328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-20DOI: 10.1038/s41594-025-01738-8
Stefano Annunziato,Chao Quan,Etienne J Donckele,Ilaria Lamberto,Richard D Bunker,Mary Zlotosch,Laura Schwander,Anastasia Murthy,Lars Wiedmer,Camille Staehly,Michelle Matysik,Samuel Gilberto,Despina Kapsitidou,Daric Wible,Gian Marco De Donatis,Peter Trenh,Rohitha SriRamaratnam,Vaik Strande,Raphael Lieberherr,David Lyon,Danielle Steiner,Joao Silva,Reinaldo Almeida,Elena Dolgikh,Bradley DeMarco,Jennifer Tsai,Amine Sadok,Vladislav Zarayskiy,Magnus Walter,Ralph Tiedt,Kevin J Lumb,Debora Bonenfant,Bernhard Fasching,John C Castle,Sharon A Townson,Pablo Gainza,Georg Petzold
Molecular glue degraders (MGDs) are small-molecule compounds that divert E3 ligases to degrade nonnatural substrates called neosubstrates. Clinically effective MGDs bind cereblon (CRBN), a substrate receptor of the Cullin 4-RING E3 ubiquitin ligase (CRL4CRBN), and recruit neosubstrates to an MGD-induced neosurface on the CRBN CULT domain through molecular mimicry of a natural CRBN degron. Here, we identify G3BP2 (Ras-GAP SH3 domain-binding protein 2), a neosubstrate that bypasses canonical interactions with CRBN by engaging an unconventional binding site on the CRBN LON domain. The ternary complex interface does not resemble known interactions with CRBN. Instead, CRBN leverages a preexisting protein-protein interaction (PPI) hotspot on the target protein by mimicking an endogenous binding partner of G3BP2. Our findings suggest that composite neosurfaces that mimic and stabilize the footprint of natural PPIs (in short, 'glueprints') could become a viable strategy for the rational expansion of the MGD target repertoire.
{"title":"Cereblon induces G3BP2 neosubstrate degradation using molecular surface mimicry.","authors":"Stefano Annunziato,Chao Quan,Etienne J Donckele,Ilaria Lamberto,Richard D Bunker,Mary Zlotosch,Laura Schwander,Anastasia Murthy,Lars Wiedmer,Camille Staehly,Michelle Matysik,Samuel Gilberto,Despina Kapsitidou,Daric Wible,Gian Marco De Donatis,Peter Trenh,Rohitha SriRamaratnam,Vaik Strande,Raphael Lieberherr,David Lyon,Danielle Steiner,Joao Silva,Reinaldo Almeida,Elena Dolgikh,Bradley DeMarco,Jennifer Tsai,Amine Sadok,Vladislav Zarayskiy,Magnus Walter,Ralph Tiedt,Kevin J Lumb,Debora Bonenfant,Bernhard Fasching,John C Castle,Sharon A Townson,Pablo Gainza,Georg Petzold","doi":"10.1038/s41594-025-01738-8","DOIUrl":"https://doi.org/10.1038/s41594-025-01738-8","url":null,"abstract":"Molecular glue degraders (MGDs) are small-molecule compounds that divert E3 ligases to degrade nonnatural substrates called neosubstrates. Clinically effective MGDs bind cereblon (CRBN), a substrate receptor of the Cullin 4-RING E3 ubiquitin ligase (CRL4CRBN), and recruit neosubstrates to an MGD-induced neosurface on the CRBN CULT domain through molecular mimicry of a natural CRBN degron. Here, we identify G3BP2 (Ras-GAP SH3 domain-binding protein 2), a neosubstrate that bypasses canonical interactions with CRBN by engaging an unconventional binding site on the CRBN LON domain. The ternary complex interface does not resemble known interactions with CRBN. Instead, CRBN leverages a preexisting protein-protein interaction (PPI) hotspot on the target protein by mimicking an endogenous binding partner of G3BP2. Our findings suggest that composite neosurfaces that mimic and stabilize the footprint of natural PPIs (in short, 'glueprints') could become a viable strategy for the rational expansion of the MGD target repertoire.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"77 4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146005287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-13DOI: 10.1038/s41594-025-01708-0
Minji Kim, Ping Wang, Patricia A. Clow, Eli Chien, Xiaotao Wang, Jianhao Peng, Haoxi Chai, Xiyuan Liu, Byoungkoo Lee, Chew Yee Ngan, Olgica Milenkovic, Jeffrey H. Chuang, Chia-Lin Wei, Rafael Casellas, Albert W. Cheng, Yijun Ruan
Cohesin is required for chromatin loop formation. However, its precise role in regulating gene transcription remains largely debated. Here we investigated the relationship between cohesin and RNA polymerase II (RNAPII) using single-molecule mapping and live-cell imaging methods in human cells. Cohesin-mediated transcriptional loops were highly correlated with those of RNA polymerase II and followed the direction of gene transcription. Depleting RAD21, a subunit of cohesin, resulted in the loss of long-range (>100 kb) loops between distal (super-)enhancers and promoters of cell-type-specific downregulated genes. By contrast, short-range (<50 kb) loops were insensitive to RAD21 depletion and connected genes that are mostly constitutively expressed. This result explains why only a small fraction of genes are affected by the loss of long-range chromatin interactions in cohesin-depleted cells. Remarkably, RAD21 depletion appeared to upregulate genes that were involved in initiating DNA replication and disrupted DNA replication timing. Our results elucidate the multifaceted roles of cohesin in establishing transcriptional loops, preserving long-range chromatin interactions for cell-specific genes and maintaining timely DNA replication.
{"title":"Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription","authors":"Minji Kim, Ping Wang, Patricia A. Clow, Eli Chien, Xiaotao Wang, Jianhao Peng, Haoxi Chai, Xiyuan Liu, Byoungkoo Lee, Chew Yee Ngan, Olgica Milenkovic, Jeffrey H. Chuang, Chia-Lin Wei, Rafael Casellas, Albert W. Cheng, Yijun Ruan","doi":"10.1038/s41594-025-01708-0","DOIUrl":"https://doi.org/10.1038/s41594-025-01708-0","url":null,"abstract":"Cohesin is required for chromatin loop formation. However, its precise role in regulating gene transcription remains largely debated. Here we investigated the relationship between cohesin and RNA polymerase II (RNAPII) using single-molecule mapping and live-cell imaging methods in human cells. Cohesin-mediated transcriptional loops were highly correlated with those of RNA polymerase II and followed the direction of gene transcription. Depleting RAD21, a subunit of cohesin, resulted in the loss of long-range (>100 kb) loops between distal (super-)enhancers and promoters of cell-type-specific downregulated genes. By contrast, short-range (<50 kb) loops were insensitive to RAD21 depletion and connected genes that are mostly constitutively expressed. This result explains why only a small fraction of genes are affected by the loss of long-range chromatin interactions in cohesin-depleted cells. Remarkably, RAD21 depletion appeared to upregulate genes that were involved in initiating DNA replication and disrupted DNA replication timing. Our results elucidate the multifaceted roles of cohesin in establishing transcriptional loops, preserving long-range chromatin interactions for cell-specific genes and maintaining timely DNA replication.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145956332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-08DOI: 10.1038/s41594-025-01736-w
Bin Chen, Guangchao Sun, Jake A. Kloeber, Huaping Xiao, Yaobin Ouyang, Fei Zhao, Ya Li, Shilin Xu, Sonja Dragojevic, Zheming Wu, Shouhai Zhu, Yiqun Han, Ping Yin, Xinyi Tu, Hongran Qin, Xiang Zhou, Kuntian Luo, Kevin L. Peterson, Jinzhou Huang, Taro Hitosugi, Haiming Dai, Min Deng, Robert W. Mutter, Zhenkun Lou
Okazaki fragment maturation requires efficient removal of RNA primers to form a continuous lagging strand, yet how mismatched primers introduced by error-prone primase are corrected remains unresolved. Here, we show that physiological levels of reactive oxygen species (ROS) initiate a redox-dependent mechanism that drives ADAR1-mediated adenosine-to-inosine (A-to-I) editing. Oxidation triggers ADAR1 dimerization at replication forks, enhancing RNA editing of mismatched primers—particularly those caused by ATP misincorporation on d(T+C)-rich centromeric DNA. This A-to-I editing step facilitates more efficient RNA primer degradation by RNase H2, thereby ensuring proper Okazaki fragment maturation. Disruption of ADAR1 oxidation results in increased unligated Okazaki fragments, single-stranded gaps and double-strand breaks, most prominently at centromeres. These findings reveal a role for ROS in safeguarding lagging-strand synthesis by coupling ADAR1 oxidation-induced A-to-I RNA editing to replication fork stability.
Okazaki片段成熟需要有效地去除RNA引物以形成连续的滞后链，但如何纠正易出错引物引入的不匹配引物仍未解决。在这里，我们表明生理水平的活性氧（ROS）启动氧化还原依赖机制，驱动adar1介导的腺苷到肌苷（a -to-i）编辑。氧化触发复制叉上的ADAR1二聚化，增强错配引物的RNA编辑，特别是那些由富含d（T+C）的着丝粒DNA上ATP错误结合引起的引物。这一A-to-I编辑步骤有助于RNase H2更有效地降解RNA引物，从而确保适当的Okazaki片段成熟。ADAR1氧化的破坏导致未结扎的冈崎片段，单链间隙和双链断裂增加，最显著的是在着丝粒处。这些发现揭示了ROS通过将ADAR1氧化诱导的a -to- i RNA编辑与复制叉稳定性耦合，在保护滞后链合成方面的作用。
{"title":"Redox-driven ADAR1 activation promotes Okazaki fragment maturation and DNA replication integrity","authors":"Bin Chen, Guangchao Sun, Jake A. Kloeber, Huaping Xiao, Yaobin Ouyang, Fei Zhao, Ya Li, Shilin Xu, Sonja Dragojevic, Zheming Wu, Shouhai Zhu, Yiqun Han, Ping Yin, Xinyi Tu, Hongran Qin, Xiang Zhou, Kuntian Luo, Kevin L. Peterson, Jinzhou Huang, Taro Hitosugi, Haiming Dai, Min Deng, Robert W. Mutter, Zhenkun Lou","doi":"10.1038/s41594-025-01736-w","DOIUrl":"https://doi.org/10.1038/s41594-025-01736-w","url":null,"abstract":"Okazaki fragment maturation requires efficient removal of RNA primers to form a continuous lagging strand, yet how mismatched primers introduced by error-prone primase are corrected remains unresolved. Here, we show that physiological levels of reactive oxygen species (ROS) initiate a redox-dependent mechanism that drives ADAR1-mediated adenosine-to-inosine (A-to-I) editing. Oxidation triggers ADAR1 dimerization at replication forks, enhancing RNA editing of mismatched primers—particularly those caused by ATP misincorporation on d(T+C)-rich centromeric DNA. This A-to-I editing step facilitates more efficient RNA primer degradation by RNase H2, thereby ensuring proper Okazaki fragment maturation. Disruption of ADAR1 oxidation results in increased unligated Okazaki fragments, single-stranded gaps and double-strand breaks, most prominently at centromeres. These findings reveal a role for ROS in safeguarding lagging-strand synthesis by coupling ADAR1 oxidation-induced A-to-I RNA editing to replication fork stability.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145919892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-15DOI: 10.1038/s41594-025-01718-y
Alexandra G. Chivu, Brent A. Basso, Abderhman Abuhashem, Michelle M. Leger, Gilad Barshad, Edward J. Rice, Albert C. Vill, Wilfred Wong, Shao-Pei Chou, Gopal Chovatiya, Rebecca Brady, Jeramiah J. Smith, Athula H. Wikramanayake, César Arenas-Mena, Ilana L. Brito, Iñaki Ruiz-Trillo, Anna-Katerina Hadjantonakis, John T. Lis, James J. Lewis, Charles G. Danko
Promoter-proximal pausing of RNA polymerase (Pol) II is a key regulatory step during transcription. Despite the central role of pausing in gene regulation, we do not understand the evolutionary processes that led to the emergence of Pol II pausing or its transition to a rate-limiting step actively controlled by transcription factors. Here, we analyzed transcription in species across the tree of life. Unicellular eukaryotes display an accumulation of Pol II near transcription start sites, which we propose transitioned to the longer-lived, focused pause observed in metazoans. This transition coincided with the evolution of new subunits in the negative elongation factor (NELF) and 7SK complexes. Depletion of NELF in mammals shifted the promoter-proximal buildup of Pol II from the pause site into the early gene body and compromised transcriptional activation for a set of heat-shock genes. Our work details the evolutionary history of Pol II pausing and sheds light on how new transcriptional regulatory mechanisms evolve.
{"title":"Evolution of promoter-proximal pausing enabled a new layer of transcription control","authors":"Alexandra G. Chivu, Brent A. Basso, Abderhman Abuhashem, Michelle M. Leger, Gilad Barshad, Edward J. Rice, Albert C. Vill, Wilfred Wong, Shao-Pei Chou, Gopal Chovatiya, Rebecca Brady, Jeramiah J. Smith, Athula H. Wikramanayake, César Arenas-Mena, Ilana L. Brito, Iñaki Ruiz-Trillo, Anna-Katerina Hadjantonakis, John T. Lis, James J. Lewis, Charles G. Danko","doi":"10.1038/s41594-025-01718-y","DOIUrl":"https://doi.org/10.1038/s41594-025-01718-y","url":null,"abstract":"Promoter-proximal pausing of RNA polymerase (Pol) II is a key regulatory step during transcription. Despite the central role of pausing in gene regulation, we do not understand the evolutionary processes that led to the emergence of Pol II pausing or its transition to a rate-limiting step actively controlled by transcription factors. Here, we analyzed transcription in species across the tree of life. Unicellular eukaryotes display an accumulation of Pol II near transcription start sites, which we propose transitioned to the longer-lived, focused pause observed in metazoans. This transition coincided with the evolution of new subunits in the negative elongation factor (NELF) and 7SK complexes. Depletion of NELF in mammals shifted the promoter-proximal buildup of Pol II from the pause site into the early gene body and compromised transcriptional activation for a set of heat-shock genes. Our work details the evolutionary history of Pol II pausing and sheds light on how new transcriptional regulatory mechanisms evolve.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145759744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-08DOI: 10.1038/s41594-025-01723-1
Tao Li,Ji Chen,Hao Li,Hong Cao,Sheng-You Huang
Cryo-electron microscopy (cryo-EM) has become the mainstream technique for macromolecular structure determination. However, because of intrinsic resolution heterogeneity, accurate modeling of all-atom structure from cryo-EM maps remains challenging even for maps at near-atomic resolution. Addressing the challenge, we present EMProt, a fully automated method for accurate protein structure determination from cryo-EM maps by efficiently integrating map information and structure prediction with a three-track attention network. EMProt is extensively evaluated on a diverse test set of 177 experimental cryo-EM maps with up to 54 chains in a case at <4-Å resolution, and compared to state-of-the-art methods including DeepMainmast, ModelAngelo, phenix.dock_and_rebuild and AlphaFold3. It is shown that EMProt greatly outperforms the existing methods in recovering the protein structure and building the complete structure. In addition, the built models by EMrot exhibit a high accuracy in model-to-map fit and structure validations.
{"title":"EMProt improves structure determination from cryo-EM maps.","authors":"Tao Li,Ji Chen,Hao Li,Hong Cao,Sheng-You Huang","doi":"10.1038/s41594-025-01723-1","DOIUrl":"https://doi.org/10.1038/s41594-025-01723-1","url":null,"abstract":"Cryo-electron microscopy (cryo-EM) has become the mainstream technique for macromolecular structure determination. However, because of intrinsic resolution heterogeneity, accurate modeling of all-atom structure from cryo-EM maps remains challenging even for maps at near-atomic resolution. Addressing the challenge, we present EMProt, a fully automated method for accurate protein structure determination from cryo-EM maps by efficiently integrating map information and structure prediction with a three-track attention network. EMProt is extensively evaluated on a diverse test set of 177 experimental cryo-EM maps with up to 54 chains in a case at <4-Å resolution, and compared to state-of-the-art methods including DeepMainmast, ModelAngelo, phenix.dock_and_rebuild and AlphaFold3. It is shown that EMProt greatly outperforms the existing methods in recovering the protein structure and building the complete structure. In addition, the built models by EMrot exhibit a high accuracy in model-to-map fit and structure validations.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145704660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：