Pub Date : 2025-02-20DOI: 10.1016/j.molcel.2025.01.026
Duo Pan, Mo-Fang Liu
The intron sequences of certain tRNAs are evolutionarily conserved among specific organisms, implying potential cellular functions of such tRNA introns. In this issue, Nostramo et al.1 identify free introns of tRNAs (fitRNAs) in S. cerevisiae as small regulatory RNAs that dynamically control mRNA levels in response to oxidative stress.
{"title":"tRNA intron-derived small regulatory RNAs fine-tune gene expression under oxidative stress","authors":"Duo Pan, Mo-Fang Liu","doi":"10.1016/j.molcel.2025.01.026","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.01.026","url":null,"abstract":"The intron sequences of certain tRNAs are evolutionarily conserved among specific organisms, implying potential cellular functions of such tRNA introns. In this issue, Nostramo et al.<span><span><sup>1</sup></span></span> identify free introns of tRNAs (fitRNAs) in <em>S. cerevisiae</em> as small regulatory RNAs that dynamically control mRNA levels in response to oxidative stress.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"13 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143451842","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 : 2025-02-20DOI: 10.1016/j.molcel.2025.01.033
Jessica J. Hawes, Alyson Ashe
In this issue, Fitz-James et al.1 use genetic manipulations to show that transient interchromosomal contacts between distant regulatory elements, mediated by the transcription factor GAF, can initiate transgenerational epigenetic inheritance in D. melanogaster.
{"title":"Moving epigenetic inheritance into the space age: Evidence that 3D genome organization is required for the establishment of epigenetic memory","authors":"Jessica J. Hawes, Alyson Ashe","doi":"10.1016/j.molcel.2025.01.033","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.01.033","url":null,"abstract":"In this issue, Fitz-James et al.<span><span><sup>1</sup></span></span> use genetic manipulations to show that transient interchromosomal contacts between distant regulatory elements, mediated by the transcription factor GAF, can initiate transgenerational epigenetic inheritance in <em>D. melanogaster</em>.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"12 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143452193","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 : 2025-02-20DOI: 10.1016/j.molcel.2025.01.028
Kenneth Wu, Zhen-Qiang Pan
In this issue of Molecular Cell, Sulter et al.1 describe a high-throughput method named COMET (combinatorial mapping of E3 targets) that enables direct screening for interactions between E3 ubiquitin ligases and their proteolytic substrate proteins.
{"title":"COMET enables direct screening for interactions between E3 ubiquitin ligases and their proteolytic target proteins","authors":"Kenneth Wu, Zhen-Qiang Pan","doi":"10.1016/j.molcel.2025.01.028","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.01.028","url":null,"abstract":"In this issue of <em>Molecular Cell</em>, Sulter et al.<span><span><sup>1</sup></span></span> describe a high-throughput method named COMET (combinatorial mapping of E3 targets) that enables direct screening for interactions between E3 ubiquitin ligases and their proteolytic substrate proteins.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"15 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143452228","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 : 2025-02-20DOI: 10.1016/j.molcel.2025.01.030
Xiaoqian Deng, Guoping Fan
In a recent Cell study,1 Quarto et al. uncovered a mechanism by which the METTL3-METTL14-DNMT1 axis fine-tunes gene expression during embryonic stem cell (ESC) differentiation. This work highlights the interplay between epigenetics and epitranscriptomics, shedding light on how methylation of DNA and RNA coordinately regulates a subset of differentiation genes.
{"title":"Tuning up gene transcription via direct crosstalk of DNA and RNA methylation","authors":"Xiaoqian Deng, Guoping Fan","doi":"10.1016/j.molcel.2025.01.030","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.01.030","url":null,"abstract":"In a recent <em>Cell</em> study,<span><span><sup>1</sup></span></span> Quarto et al. uncovered a mechanism by which the METTL3-METTL14-DNMT1 axis fine-tunes gene expression during embryonic stem cell (ESC) differentiation. This work highlights the interplay between epigenetics and epitranscriptomics, shedding light on how methylation of DNA and RNA coordinately regulates a subset of differentiation genes.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"2 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143451881","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 : 2025-02-20DOI: 10.1016/j.molcel.2025.01.027
Miao Shi, Tao Jiang, Mengfan Zhang, Quanjin Li, Kexin Liu, Ni Lin, Xinlu Wang, Amin Jiang, Yina Gao, Yong Wang, Songqing Liu, Liguo Zhang, Dong Li, Pu Gao
Retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs) and cyclic GMP-AMP synthase (cGAS) recognize aberrant nucleic acids and initiate antiviral responses. Host factor zinc finger CCHC domain-containing protein 3 (ZCCHC3) positively regulates both RLRs- and cGAS-mediated signaling through unknown mechanisms. Here, we show that ZCCHC3 employs a broad and unified strategy to promote these pathways in human cell lines. Rather than developing strong protein-protein interactions, ZCCHC3 harbors multiple nucleic-acid-binding modules and undergoes robust liquid phase condensation with nucleic acids. RNA-induced ZCCHC3 condensates enrich and activate RLRs, which then facilitate the interaction of RLRs with the downstream adaptor mitochondrial antiviral-signaling (MAVS). Direct and high-resolution structure determination of liquid condensates confirms the assembly of active-form MAVS filaments. Furthermore, ZCCHC3 efficiently promotes the condensation and enrichment of DNA, cGAS, ATP, and GTP, thereby enhancing cGAS signaling. ZCCHC3 mutants defective in RNA/DNA-induced condensation lost their regulatory efficiency in both pathways. These results highlight unexpectedly broad connections between biomolecular condensation and innate immunity.
{"title":"Nucleic-acid-induced ZCCHC3 condensation promotes broad innate immune responses","authors":"Miao Shi, Tao Jiang, Mengfan Zhang, Quanjin Li, Kexin Liu, Ni Lin, Xinlu Wang, Amin Jiang, Yina Gao, Yong Wang, Songqing Liu, Liguo Zhang, Dong Li, Pu Gao","doi":"10.1016/j.molcel.2025.01.027","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.01.027","url":null,"abstract":"Retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs) and cyclic GMP-AMP synthase (cGAS) recognize aberrant nucleic acids and initiate antiviral responses. Host factor zinc finger CCHC domain-containing protein 3 (ZCCHC3) positively regulates both RLRs- and cGAS-mediated signaling through unknown mechanisms. Here, we show that ZCCHC3 employs a broad and unified strategy to promote these pathways in human cell lines. Rather than developing strong protein-protein interactions, ZCCHC3 harbors multiple nucleic-acid-binding modules and undergoes robust liquid phase condensation with nucleic acids. RNA-induced ZCCHC3 condensates enrich and activate RLRs, which then facilitate the interaction of RLRs with the downstream adaptor mitochondrial antiviral-signaling (MAVS). Direct and high-resolution structure determination of liquid condensates confirms the assembly of active-form MAVS filaments. Furthermore, ZCCHC3 efficiently promotes the condensation and enrichment of DNA, cGAS, ATP, and GTP, thereby enhancing cGAS signaling. ZCCHC3 mutants defective in RNA/DNA-induced condensation lost their regulatory efficiency in both pathways. These results highlight unexpectedly broad connections between biomolecular condensation and innate immunity.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"25 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143451880","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 : 2025-02-19DOI: 10.1016/j.molcel.2025.01.024
Shirsha Saha, Fumiya K. Sano, Saloni Sharma, Manisankar Ganguly, Sudha Mishra, Annu Dalal, Hiroaki Akasaka, Takaaki A. Kobayashi, Nashrah Zaidi, Divyanshu Tiwari, Nabarun Roy, Manish K. Yadav, Nilanjana Banerjee, Sayantan Saha, Samanwita Mohapatra, Yuzuru Itoh, Andy Chevigné, Ramanuj Banerjee, Wataru Shihoya, Osamu Nureki, Arun K. Shukla
Selectivity of natural agonists for their cognate receptors is a hallmark of G-protein-coupled receptors (GPCRs); however, this selectivity often breaks down at the chemokine receptors. Chemokines often display promiscuous binding to chemokine receptors, but the underlying molecular determinants remain mostly elusive. Here, we perform a comprehensive transducer-coupling analysis, testing all known C-X-C chemokines on every C-X-C type chemokine receptor to generate a global fingerprint of the selectivity and promiscuity encoded within this system. Taking lead from this, we determine cryoelectron microscopy (cryo-EM) structures of the most promiscuous receptor, C-X-C chemokine receptor 2 (CXCR2), in complex with several chemokines. These structural snapshots elucidate the details of ligand-receptor interactions, including structural motifs, which are validated using mutagenesis and functional experiments. We also observe that most chemokines position themselves on CXCR2 as a dimer while CXCL6 exhibits a monomeric binding pose. Taken together, our findings provide the molecular basis of chemokine promiscuity at CXCR2 with potential implications for developing therapeutic molecules.
{"title":"Molecular basis of promiscuous chemokine binding and structural mimicry at the C-X-C chemokine receptor, CXCR2","authors":"Shirsha Saha, Fumiya K. Sano, Saloni Sharma, Manisankar Ganguly, Sudha Mishra, Annu Dalal, Hiroaki Akasaka, Takaaki A. Kobayashi, Nashrah Zaidi, Divyanshu Tiwari, Nabarun Roy, Manish K. Yadav, Nilanjana Banerjee, Sayantan Saha, Samanwita Mohapatra, Yuzuru Itoh, Andy Chevigné, Ramanuj Banerjee, Wataru Shihoya, Osamu Nureki, Arun K. Shukla","doi":"10.1016/j.molcel.2025.01.024","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.01.024","url":null,"abstract":"Selectivity of natural agonists for their cognate receptors is a hallmark of G-protein-coupled receptors (GPCRs); however, this selectivity often breaks down at the chemokine receptors. Chemokines often display promiscuous binding to chemokine receptors, but the underlying molecular determinants remain mostly elusive. Here, we perform a comprehensive transducer-coupling analysis, testing all known C-X-C chemokines on every C-X-C type chemokine receptor to generate a global fingerprint of the selectivity and promiscuity encoded within this system. Taking lead from this, we determine cryoelectron microscopy (cryo-EM) structures of the most promiscuous receptor, C-X-C chemokine receptor 2 (CXCR2), in complex with several chemokines. These structural snapshots elucidate the details of ligand-receptor interactions, including structural motifs, which are validated using mutagenesis and functional experiments. We also observe that most chemokines position themselves on CXCR2 as a dimer while CXCL6 exhibits a monomeric binding pose. Taken together, our findings provide the molecular basis of chemokine promiscuity at CXCR2 with potential implications for developing therapeutic molecules.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"15 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143451891","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 : 2025-02-19DOI: 10.1016/j.molcel.2025.01.022
Varun Sood, Ronald Holewinski, Thorkell Andresson, Daniel R. Larson, Tom Misteli
Stochastic transcriptional bursting is a universal property of active genes. While different genes exhibit distinct bursting patterns, the molecular mechanisms that govern gene-specific stochastic bursting are largely unknown. We have developed a high-throughput-imaging-based screening strategy to identify cellular factors that determine the bursting patterns of native genes in human cells. We identify protein acetylation as a prominent effector of burst frequency and burst size acting via decreasing off-times and gene-specific changes in the on-time. These effects are not correlated with promoter acetylation. Instead, we demonstrate acetylation of the Integrator complex as a key determinant of gene bursting that alters Integrator interactions with transcription elongation and RNA processing factors but without affecting pausing. Our results suggest a prominent role for non-histone acetylation of a transcription cofactors as a mechanism for modulation of bursting via a far-downstream checkpoint.
{"title":"Identification of molecular determinants of gene-specific bursting patterns by high-throughput imaging screens","authors":"Varun Sood, Ronald Holewinski, Thorkell Andresson, Daniel R. Larson, Tom Misteli","doi":"10.1016/j.molcel.2025.01.022","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.01.022","url":null,"abstract":"Stochastic transcriptional bursting is a universal property of active genes. While different genes exhibit distinct bursting patterns, the molecular mechanisms that govern gene-specific stochastic bursting are largely unknown. We have developed a high-throughput-imaging-based screening strategy to identify cellular factors that determine the bursting patterns of native genes in human cells. We identify protein acetylation as a prominent effector of burst frequency and burst size acting via decreasing off-times and gene-specific changes in the on-time. These effects are not correlated with promoter acetylation. Instead, we demonstrate acetylation of the Integrator complex as a key determinant of gene bursting that alters Integrator interactions with transcription elongation and RNA processing factors but without affecting pausing. Our results suggest a prominent role for non-histone acetylation of a transcription cofactors as a mechanism for modulation of bursting via a far-downstream checkpoint.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"1 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143451890","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}
Current RNA editing techniques are predominantly limited to single-base edits. Here, we introduce selective cleavages and intramolecular stitches of RNA (SCISSOR) for selective cleavage and intramolecular stitches of RNA. Building on the principle that type III CRISPR complex determines target cleavage positions based on gRNA length in 6-nt increments, we hypothesized that engineering gRNAs with bulge loops could circumvent this rule, allowing for flexible RNA excision. Through systematic evaluation of gRNAs with various bulge loops, we established the rules for precise non-6-nt target cleavage and repair. We observed that the complex tolerates 1- or 2-nt bulge loops and accommodates large bulge loops ranging from 6 to 24 nt. Consequently, SCISSOR could accomplish nearly any length of short fragment excision. With its capability to modify open reading frames, we demonstrate the potential of SCISSOR in repairing frameshift mutations and introducing frameshifts to create immunogenic poly-epitopes in human cells. SCISSOR holds promise in RNA therapy and biomedical research.
{"title":"Type III CRISPR-mediated flexible RNA excision with engineered guide RNAs","authors":"Yuanfan Sun, Yingyin Wu, Zihua He, Yiying Wang, Wenhao Hou, Yong Cao, Qihao Zhou, Rui Zhang","doi":"10.1016/j.molcel.2025.01.021","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.01.021","url":null,"abstract":"Current RNA editing techniques are predominantly limited to single-base edits. Here, we introduce selective cleavages and intramolecular stitches of RNA (SCISSOR) for selective cleavage and intramolecular stitches of RNA. Building on the principle that type III CRISPR complex determines target cleavage positions based on gRNA length in 6-nt increments, we hypothesized that engineering gRNAs with bulge loops could circumvent this rule, allowing for flexible RNA excision. Through systematic evaluation of gRNAs with various bulge loops, we established the rules for precise non-6-nt target cleavage and repair. We observed that the complex tolerates 1- or 2-nt bulge loops and accommodates large bulge loops ranging from 6 to 24 nt. Consequently, SCISSOR could accomplish nearly any length of short fragment excision. With its capability to modify open reading frames, we demonstrate the potential of SCISSOR in repairing frameshift mutations and introducing frameshifts to create immunogenic poly-epitopes in human cells. SCISSOR holds promise in RNA therapy and biomedical research.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"47 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143451889","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 : 2025-02-19DOI: 10.1016/j.molcel.2025.01.025
Igor Fesenko, Harutyun Sahakyan, Rajat Dhyani, Svetlana A. Shabalina, Gisela Storz, Eugene V. Koonin
Microproteins encoded by small open reading frames comprise the “dark matter” of proteomes. Although microproteins have been detected in diverse organisms from all three domains of life, many more remain to be identified, and only a few have been functionally characterized. In this comprehensive study of intergenic small open reading frames (ismORFs, 15–70 codons) in 5,668 bacterial genomes of the family Enterobacteriaceae, we identify 67,297 clusters of ismORFs subject to purifying selection. Expression of tagged Escherichia coli microproteins is detected for 11 of the 16 tested, validating the predictions. Although the ismORFs mainly code for hydrophobic, potentially transmembrane, unstructured, or minimally structured microproteins, some globular folds, oligomeric structures, and possible interactions with proteins encoded by neighboring genes are predicted. Complete information on the predicted microprotein families, including evidence of transcription and translation, and structure predictions are available as an easily searchable resource for investigation of microprotein functions.
{"title":"The hidden bacterial microproteome","authors":"Igor Fesenko, Harutyun Sahakyan, Rajat Dhyani, Svetlana A. Shabalina, Gisela Storz, Eugene V. Koonin","doi":"10.1016/j.molcel.2025.01.025","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.01.025","url":null,"abstract":"Microproteins encoded by small open reading frames comprise the “dark matter” of proteomes. Although microproteins have been detected in diverse organisms from all three domains of life, many more remain to be identified, and only a few have been functionally characterized. In this comprehensive study of intergenic small open reading frames (ismORFs, 15–70 codons) in 5,668 bacterial genomes of the family <em>Enterobacteriaceae</em>, we identify 67,297 clusters of ismORFs subject to purifying selection. Expression of tagged <em>Escherichia coli</em> microproteins is detected for 11 of the 16 tested, validating the predictions. Although the ismORFs mainly code for hydrophobic, potentially transmembrane, unstructured, or minimally structured microproteins, some globular folds, oligomeric structures, and possible interactions with proteins encoded by neighboring genes are predicted. Complete information on the predicted microprotein families, including evidence of transcription and translation, and structure predictions are available as an easily searchable resource for investigation of microprotein functions.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"1 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143451887","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}
Features of circular RNAs (circRNAs) produced by back-splicing of eukaryotic exon(s) make them resistant to degradation by linear RNA decay machineries. Thus, a general circRNA degradation pathway under normal conditions has remained largely elusive. Here, we report that the endonucleolytic enzyme DIS3 is responsible for the degradation of circRNAs. Depletion of DIS3 leads to the upregulation of more than 60% of circRNAs with little effect on their linear cognates. Such DIS3-mediated circRNA degradation is conserved, occurs in the cytoplasm, and relies on DIS3’s endonucleolytic activity but is independent of the RNA exosome complex. Sequence enrichment analyses suggest that DIS3 prefers to degrade circRNAs containing U-rich motifs. Correspondingly, synthesized RNA circles with or without U-rich motifs exhibit decreased or increased stabilities, respectively. Together, these findings suggest a general regulation of circRNA turnover by DIS3.
{"title":"Degradation of circular RNA by the ribonuclease DIS3","authors":"Xiao Tao, Si-Nan Zhai, Chu-Xiao Liu, Youkui Huang, Jia Wei, Yi-Lin Guo, Xiao-Qi Liu, Xiang Li, Li Yang, Ling-Ling Chen","doi":"10.1016/j.molcel.2025.01.012","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.01.012","url":null,"abstract":"Features of circular RNAs (circRNAs) produced by back-splicing of eukaryotic exon(s) make them resistant to degradation by linear RNA decay machineries. Thus, a general circRNA degradation pathway under normal conditions has remained largely elusive. Here, we report that the endonucleolytic enzyme DIS3 is responsible for the degradation of circRNAs. Depletion of DIS3 leads to the upregulation of more than 60% of circRNAs with little effect on their linear cognates. Such DIS3-mediated circRNA degradation is conserved, occurs in the cytoplasm, and relies on DIS3’s endonucleolytic activity but is independent of the RNA exosome complex. Sequence enrichment analyses suggest that DIS3 prefers to degrade circRNAs containing U-rich motifs. Correspondingly, synthesized RNA circles with or without U-rich motifs exhibit decreased or increased stabilities, respectively. Together, these findings suggest a general regulation of circRNA turnover by DIS3.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"13 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143427466","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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