Pub Date : 2025-03-20DOI: 10.1016/j.molcel.2025.02.020
Zhifu Han, Yu Cao, Jijie Chai
In a recent Cell study, Yirmiya et al.,1 using AlphaFold2-Multimer co-folding analyses, identify multiple phage inhibitors of bacterial defense systems on a proteome-wide scale and uncover a novel inhibition mechanism of these anti-defense proteins. The study significantly promotes our understanding of phage-bacteria interactions.
{"title":"Proteome-wide discovery of phage anti-defense proteins by Alphafold2","authors":"Zhifu Han, Yu Cao, Jijie Chai","doi":"10.1016/j.molcel.2025.02.020","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.02.020","url":null,"abstract":"In a recent <em>Cell</em> study, Yirmiya et al.,<span><span><sup>1</sup></span></span> using AlphaFold2-Multimer co-folding analyses, identify multiple phage inhibitors of bacterial defense systems on a proteome-wide scale and uncover a novel inhibition mechanism of these anti-defense proteins. The study significantly promotes our understanding of phage-bacteria interactions.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"34 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143660421","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 : 2025-03-20DOI: 10.1016/j.molcel.2025.02.029
Andrew E.H. Elia, Snehanshu Chowdhury, William R. DeNight
A recent study in Molecular Cell by Ogawa et al.1 demonstrates that the protein SLFN11, which is a potent biomarker for sensitivity to DNA damage, induces p53-independent apoptosis through inhibition of protein translation.
{"title":"Lost in translation: SLFN11 induces p53-independent apoptosis","authors":"Andrew E.H. Elia, Snehanshu Chowdhury, William R. DeNight","doi":"10.1016/j.molcel.2025.02.029","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.02.029","url":null,"abstract":"A recent study in <em>Molecular Cell</em> by Ogawa et al.<span><span><sup>1</sup></span></span> demonstrates that the protein SLFN11, which is a potent biomarker for sensitivity to DNA damage, induces p53-independent apoptosis through inhibition of protein translation.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"183 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143660305","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 : 2025-03-20DOI: 10.1016/j.molcel.2025.02.022
Min Tang, Yingfeng Tu, Yanqiu Gong, Qin Yang, Jinrui Wang, Zhenzhen Zhang, Junhong Qin, Shenghui Niu, Jiamin Yi, Zehua Shang, Hongyu Chen, Yingying Tang, Qian Huang, Yanmei Liu, Daniel D. Billadeau, Xingguo Liu, Lunzhi Dai, Da Jia
Mitochondrial dynamics and metabolites reciprocally influence each other. Mitochondrial-derived vesicles (MDVs) transport damaged mitochondrial components to lysosomes or the extracellular space. While many metabolites are known to modulate mitochondrial dynamics, it is largely unclear whether they are involved in MDV generation. Here, we discovered that the major component of ketone body, β-hydroxybutyrate (BHB), improved mitochondrial functions by facilitating the biogenesis of MDVs. Mechanistically, BHB drove specific lysine β-hydroxybutyrylation (Kbhb) of sorting nexin-9 (SNX9), a key regulator of MDV biogenesis. Kbhb increased SNX9 interaction with inner mitochondrial membrane (IMM)/matrix proteins and promoted the formation of IMM/matrix MDVs. SNX9 Kbhb was not only critical for maintaining mitochondrial homeostasis in cells but also protected mice from alcohol-induced liver injury. Altogether, our research uncovers the fact that metabolites influence the formation of MDVs by directly engaging in post-translational modifications of key protein machineries and establishes a framework for understanding how metabolites regulate mitochondrial functions.
{"title":"β-hydroxybutyrate facilitates mitochondrial-derived vesicle biogenesis and improves mitochondrial functions","authors":"Min Tang, Yingfeng Tu, Yanqiu Gong, Qin Yang, Jinrui Wang, Zhenzhen Zhang, Junhong Qin, Shenghui Niu, Jiamin Yi, Zehua Shang, Hongyu Chen, Yingying Tang, Qian Huang, Yanmei Liu, Daniel D. Billadeau, Xingguo Liu, Lunzhi Dai, Da Jia","doi":"10.1016/j.molcel.2025.02.022","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.02.022","url":null,"abstract":"Mitochondrial dynamics and metabolites reciprocally influence each other. Mitochondrial-derived vesicles (MDVs) transport damaged mitochondrial components to lysosomes or the extracellular space. While many metabolites are known to modulate mitochondrial dynamics, it is largely unclear whether they are involved in MDV generation. Here, we discovered that the major component of ketone body, β-hydroxybutyrate (BHB), improved mitochondrial functions by facilitating the biogenesis of MDVs. Mechanistically, BHB drove specific lysine β-hydroxybutyrylation (Kbhb) of sorting nexin-9 (SNX9), a key regulator of MDV biogenesis. Kbhb increased SNX9 interaction with inner mitochondrial membrane (IMM)/matrix proteins and promoted the formation of IMM/matrix MDVs. SNX9 Kbhb was not only critical for maintaining mitochondrial homeostasis in cells but also protected mice from alcohol-induced liver injury. Altogether, our research uncovers the fact that metabolites influence the formation of MDVs by directly engaging in post-translational modifications of key protein machineries and establishes a framework for understanding how metabolites regulate mitochondrial functions.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"20 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143660406","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 : 2025-03-20DOI: 10.1016/j.molcel.2025.02.023
Mark Hochstrasser
Pathogenic or symbiotic bacteria residing inside eukaryotic cells often foil attempts to eliminate them by secreting deubiquitinases into the host. In this issue of Molecular Cell, Hermanns et al.1 uncover an unexpected “clippase” activity in certain bacterial deubiquitinases, which cleaves substrate-linked ubiquitin within the ubiquitin C terminus, thereby inactivating it.
{"title":"A cut above: Bacterial deubiquitinases with ubiquitin clippase activity","authors":"Mark Hochstrasser","doi":"10.1016/j.molcel.2025.02.023","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.02.023","url":null,"abstract":"Pathogenic or symbiotic bacteria residing inside eukaryotic cells often foil attempts to eliminate them by secreting deubiquitinases into the host. In this issue of <em>Molecular Cell</em>, Hermanns et al.<span><span><sup>1</sup></span></span> uncover an unexpected “clippase” activity in certain bacterial deubiquitinases, which cleaves substrate-linked ubiquitin within the ubiquitin C terminus, thereby inactivating it.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"19 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143666216","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 : 2025-03-20DOI: 10.1016/j.molcel.2025.02.010
Arne Elofsson
In this issue of Molecular Cell, Schmid and Walter present “Predictomes,”1 a machine-learning-based platform that utilizes AlphaFold-Multimer (AF-M) to identify high-confidence protein-protein interactions (PPIs). Their SPOC classifier is better than existing methods at separating true and false interactions.
{"title":"Unlocking protein networks with Predictomes: The SPOC advantage","authors":"Arne Elofsson","doi":"10.1016/j.molcel.2025.02.010","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.02.010","url":null,"abstract":"In this issue of <em>Molecular Cell</em>, Schmid and Walter present “Predictomes,”<span><span><sup>1</sup></span></span> a machine-learning-based platform that utilizes AlphaFold-Multimer (AF-M) to identify high-confidence protein-protein interactions (PPIs). Their SPOC classifier is better than existing methods at separating true and false interactions.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"14 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143660418","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}
PIWI-interacting RNAs (piRNAs) are crucial for silencing transposable elements (TEs). In many species, piRNAs are generated via a complex process known as the ping-pong pathway, coupling TE cleavage with piRNA amplification. However, the biological significance of this complexity remains unclear. Here, we systematically compared piRNA profiles in two related silkworm cell lines and found significant changes in their sequence repertoire. Importantly, the changeability of this repertoire negatively correlated with the piRNA biogenesis efficiency, a trend also observed in Drosophila stocks and single silkworm eggs. This can be explained by competition between adjacent ping-pong sites, supported by our mathematical modeling. Moreover, this competition can rationalize how piRNAs autonomously avoid deleterious mismatches to target TEs in silkworms, flies, and mice. These findings unveil the intrinsic plasticity and adaptability of the piRNA system to combat diverse TE sequences and highlight the universal power of competition and self-amplification to drive autonomous optimization.
PIWI-interacting RNA（piRNA）是沉默转座元件（TE）的关键。在许多物种中，piRNA 是通过一种被称为 "乒乓途径 "的复杂过程产生的，它将 TE 的裂解与 piRNA 的扩增结合在一起。然而，这种复杂性的生物学意义仍不清楚。在这里，我们系统地比较了两种相关家蚕细胞系的 piRNA 图谱，发现它们的序列库发生了显著变化。重要的是，这种序列的可变性与 piRNA 的生物发生效率呈负相关，果蝇种群和单个蚕卵中也观察到了这种趋势。这可以用相邻乒乓位点之间的竞争来解释，我们的数学建模也支持这一观点。此外，这种竞争还能合理解释 piRNA 如何在家蚕、苍蝇和小鼠中自主避免目标 TE 的有害错配。这些发现揭示了 piRNA 系统对抗不同 TE 序列的内在可塑性和适应性，并强调了竞争和自我扩增推动自主优化的普遍力量。
{"title":"Autonomous shaping of the piRNA sequence repertoire by competition between adjacent ping-pong amplification sites","authors":"Jie Yu, Fumiko Kawasaki, Natsuko Izumi, Takashi Kiuchi, Susumu Katsuma, Yukihide Tomari, Keisuke Shoji","doi":"10.1016/j.molcel.2025.02.015","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.02.015","url":null,"abstract":"PIWI-interacting RNAs (piRNAs) are crucial for silencing transposable elements (TEs). In many species, piRNAs are generated via a complex process known as the ping-pong pathway, coupling TE cleavage with piRNA amplification. However, the biological significance of this complexity remains unclear. Here, we systematically compared piRNA profiles in two related silkworm cell lines and found significant changes in their sequence repertoire. Importantly, the changeability of this repertoire negatively correlated with the piRNA biogenesis efficiency, a trend also observed in <em>Drosophila</em> stocks and single silkworm eggs. This can be explained by competition between adjacent ping-pong sites, supported by our mathematical modeling. Moreover, this competition can rationalize how piRNAs autonomously avoid deleterious mismatches to target TEs in silkworms, flies, and mice. These findings unveil the intrinsic plasticity and adaptability of the piRNA system to combat diverse TE sequences and highlight the universal power of competition and self-amplification to drive autonomous optimization.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"61 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143660405","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 : 2025-03-20DOI: 10.1016/j.molcel.2025.02.014
Jackson B. Trotman, Elizabeth W. Abrash, McKenzie M. Murvin, Aki K. Braceros, Shuang Li, Samuel P. Boyson, Ryan T. Salcido, Rachel E. Cherney, Steven R. Bischoff, Kyle Kaufmann, Quinn E. Eberhard, Zhiyue Zhang, Dale O. Cowley, J. Mauro Calabrese
The mechanisms and biological roles of Polycomb repressive complex (PRC) recruitment by long noncoding RNAs (lncRNAs) remain unclear. To gain insight, we expressed two lncRNAs that recruit PRCs to multi-megabase domains, Airn and Xist, from an ectopic locus in mouse stem cells and compared effects. Unexpectedly, ectopic Airn recruited PRC1 and PRC2 to chromatin with a potency resembling Xist yet did not repress genes. Compared with PRC2, PRC1 was more proximal to Airn and Xist, where its enrichment over C-rich elements required the RNA-binding protein HNRNPK. Fusing Airn to Repeat A, the domain required for gene silencing by Xist, enabled gene silencing and altered local patterns but not relative levels of PRC-directed modifications. Our data suggest that, endogenously, Airn recruits PRCs to maintain rather than initiate gene silencing, that PRC recruitment occurs independently of Repeat A, and that protein-bridged interactions, not direct RNA contacts, underlie PRC recruitment by Airn, Xist, and other lncRNAs.
{"title":"Isogenic comparison of Airn and Xist reveals core principles of Polycomb recruitment by lncRNAs","authors":"Jackson B. Trotman, Elizabeth W. Abrash, McKenzie M. Murvin, Aki K. Braceros, Shuang Li, Samuel P. Boyson, Ryan T. Salcido, Rachel E. Cherney, Steven R. Bischoff, Kyle Kaufmann, Quinn E. Eberhard, Zhiyue Zhang, Dale O. Cowley, J. Mauro Calabrese","doi":"10.1016/j.molcel.2025.02.014","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.02.014","url":null,"abstract":"The mechanisms and biological roles of Polycomb repressive complex (PRC) recruitment by long noncoding RNAs (lncRNAs) remain unclear. To gain insight, we expressed two lncRNAs that recruit PRCs to multi-megabase domains, <em>Airn</em> and <em>Xist</em>, from an ectopic locus in mouse stem cells and compared effects. Unexpectedly, ectopic <em>Airn</em> recruited PRC1 and PRC2 to chromatin with a potency resembling <em>Xist</em> yet did not repress genes. Compared with PRC2, PRC1 was more proximal to <em>Airn</em> and <em>Xist</em>, where its enrichment over C-rich elements required the RNA-binding protein HNRNPK. Fusing <em>Airn</em> to Repeat A, the domain required for gene silencing by <em>Xist</em>, enabled gene silencing and altered local patterns but not relative levels of PRC-directed modifications. Our data suggest that, endogenously, <em>Airn</em> recruits PRCs to maintain rather than initiate gene silencing, that PRC recruitment occurs independently of Repeat A, and that protein-bridged interactions, not direct RNA contacts, underlie PRC recruitment by <em>Airn</em>, <em>Xist</em>, and other lncRNAs.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"70 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143660409","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 : 2025-03-20DOI: 10.1016/j.molcel.2025.02.018
Jordan D. Lin, Ami S. Bhatt
In a recent issue of Molecular Cell, Fesenko et al.1 report a systematic investigation of intergenic regions within Enterobacteriaceae, shedding light on a vast, unexplored microprotein landscape that has been overlooked in well-characterized bacterial genomes.
{"title":"Mind the gap: Intergenic regions in bacteria encode numerous small proteins","authors":"Jordan D. Lin, Ami S. Bhatt","doi":"10.1016/j.molcel.2025.02.018","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.02.018","url":null,"abstract":"In a recent issue of <em>Molecular Cell</em>, Fesenko et al.<span><span><sup>1</sup></span></span> report a systematic investigation of intergenic regions within Enterobacteriaceae, shedding light on a vast, unexplored microprotein landscape that has been overlooked in well-characterized bacterial genomes.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"28 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143660346","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 : 2025-03-20DOI: 10.1016/j.molcel.2025.02.005
Frank Uhlmann
The ring-shaped cohesin complex topologically entraps two DNAs to establish sister chromatid cohesion. Cohesin also shapes the interphase chromatin landscape by forming DNA loops, which it is thought to achieve using an in vitro-observed loop extrusion mechanism. However, recent studies revealed that loop-extrusion-deficient cohesin retains its ability to form chromatin loops, suggesting a divergence of in vitro and in vivo loop formation. Instead of loop extrusion, we examine whether cohesin forms chromatin loops by a mechanism akin to sister chromatid cohesion establishment: sequential topological capture of two DNAs. We explore similarities and differences between the “loop capture” and the “loop extrusion” model, how they compare at explaining experimental observations, and how future approaches can delineate their possible respective contributions. We extend our DNA-DNA capture model for cohesin function to related structural maintenance of chromosomes (SMC) family members, condensin, the Smc5-Smc6 complex, and bacterial SMC complexes.
{"title":"A unified model for cohesin function in sisterchromatid cohesion and chromatin loop formation","authors":"Frank Uhlmann","doi":"10.1016/j.molcel.2025.02.005","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.02.005","url":null,"abstract":"The ring-shaped cohesin complex topologically entraps two DNAs to establish sister chromatid cohesion. Cohesin also shapes the interphase chromatin landscape by forming DNA loops, which it is thought to achieve using an <em>in vitro</em>-observed loop extrusion mechanism. However, recent studies revealed that loop-extrusion-deficient cohesin retains its ability to form chromatin loops, suggesting a divergence of <em>in vitro</em> and <em>in vivo</em> loop formation. Instead of loop extrusion, we examine whether cohesin forms chromatin loops by a mechanism akin to sister chromatid cohesion establishment: sequential topological capture of two DNAs. We explore similarities and differences between the “loop capture” and the “loop extrusion” model, how they compare at explaining experimental observations, and how future approaches can delineate their possible respective contributions. We extend our DNA-DNA capture model for cohesin function to related structural maintenance of chromosomes (SMC) family members, condensin, the Smc5-Smc6 complex, and bacterial SMC complexes.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"91 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143660404","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 : 2025-03-19DOI: 10.1016/j.molcel.2025.02.019
Yaoyi Li, Yingliang Sheng, Chao Di, Hongjie Yao
R-loops are pervasive triplex nucleic acid structures across diverse organisms, yet their biological functions remain incompletely understood. Here, we develop R-loop identification assisted by nucleases and sequencing (RIAN-seq), a nuclease-assisted, antibody-free sequencing technology, to map R-loops at base-pair resolution. By digesting single-stranded RNA (ssRNA), single-stranded DNA (ssDNA), and double-stranded DNA (dsDNA) with nuclease P1, T5 exonuclease, and lambda exonuclease while preserving RNA:DNA hybrids, RIAN-seq achieves unprecedented precision in identifying the position and size of R-loops, detecting an order of magnitude more R-loops than existing methods. Approximately 50% of RNA:DNA hybrids span between 60 and 130 bp, with many forming previously undetectable clusters. Clustered R-loops at promoters recruit zinc-finger proteins VEZF1 and SP5, enhancing transcription in a number-dependent manner and resisting transcriptional perturbation. Conversely, R-loops featuring the Y(C/T)M(A/C)CAG motif at both ends contribute to DNA damage, a phenomenon conserved from yeast to mammalian cells. Our findings reveal a dual role for R-loops: clustered R-loops promote gene expression, while YMCAG-associated R-loops compromise genome stability.
{"title":"Base-pair resolution reveals clustered R-loops and DNA damage-susceptible R-loops","authors":"Yaoyi Li, Yingliang Sheng, Chao Di, Hongjie Yao","doi":"10.1016/j.molcel.2025.02.019","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.02.019","url":null,"abstract":"R-loops are pervasive triplex nucleic acid structures across diverse organisms, yet their biological functions remain incompletely understood. Here, we develop R-loop identification assisted by nucleases and sequencing (RIAN-seq), a nuclease-assisted, antibody-free sequencing technology, to map R-loops at base-pair resolution. By digesting single-stranded RNA (ssRNA), single-stranded DNA (ssDNA), and double-stranded DNA (dsDNA) with nuclease P1, T5 exonuclease, and lambda exonuclease while preserving RNA:DNA hybrids, RIAN-seq achieves unprecedented precision in identifying the position and size of R-loops, detecting an order of magnitude more R-loops than existing methods. Approximately 50% of RNA:DNA hybrids span between 60 and 130 bp, with many forming previously undetectable clusters. Clustered R-loops at promoters recruit zinc-finger proteins VEZF1 and SP5, enhancing transcription in a number-dependent manner and resisting transcriptional perturbation. Conversely, R-loops featuring the Y(C/T)M(A/C)CAG motif at both ends contribute to DNA damage, a phenomenon conserved from yeast to mammalian cells. Our findings reveal a dual role for R-loops: clustered R-loops promote gene expression, while YMCAG-associated R-loops compromise genome stability.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"49 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143653794","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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