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}
Pub Date : 2025-02-17DOI: 10.1016/j.molcel.2025.01.020
Katharina G. Wandera, Stefan Schmelz, Angela Migur, Anuja Kibe, Peer Lukat, Tatjana Achmedov, Neva Caliskan, Wulf Blankenfeldt, Chase L. Beisel
Anti-CRISPR proteins (Acrs) inhibit CRISPR-Cas immune defenses, with almost all known Acrs acting on the Cas nuclease-CRISPR (cr)RNA ribonucleoprotein (RNP) complex. Here, we show that AcrVIB1 from Riemerella anatipestifer, the only known Acr against Cas13b, principally acts upstream of RNP complex formation by promoting unproductive crRNA binding followed by crRNA degradation. AcrVIB1 tightly binds to Cas13b but not to the Cas13b-crRNA complex, resulting in enhanced rather than blocked crRNA binding. However, the more tightly bound crRNA does not undergo processing and fails to activate collateral RNA cleavage even with target RNA. The bound crRNA is also accessible to RNases, leading to crRNA turnover in vivo even in the presence of Cas13b. Finally, cryoelectron microscopy (cryo-EM) structures reveal that AcrVIB1 binds a helical domain of Cas13b responsible for securing the crRNA, keeping the domain untethered. These findings reveal an Acr that converts an effector nuclease into a crRNA sink to suppress CRISPR-Cas defense.
{"title":"AcrVIB1 inhibits CRISPR-Cas13b immunity by promoting unproductive crRNA binding accessible to RNase attack","authors":"Katharina G. Wandera, Stefan Schmelz, Angela Migur, Anuja Kibe, Peer Lukat, Tatjana Achmedov, Neva Caliskan, Wulf Blankenfeldt, Chase L. Beisel","doi":"10.1016/j.molcel.2025.01.020","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.01.020","url":null,"abstract":"Anti-CRISPR proteins (Acrs) inhibit CRISPR-Cas immune defenses, with almost all known Acrs acting on the Cas nuclease-CRISPR (cr)RNA ribonucleoprotein (RNP) complex. Here, we show that AcrVIB1 from <em>Riemerella anatipestifer</em>, the only known Acr against Cas13b, principally acts upstream of RNP complex formation by promoting unproductive crRNA binding followed by crRNA degradation. AcrVIB1 tightly binds to Cas13b but not to the Cas13b-crRNA complex, resulting in enhanced rather than blocked crRNA binding. However, the more tightly bound crRNA does not undergo processing and fails to activate collateral RNA cleavage even with target RNA. The bound crRNA is also accessible to RNases, leading to crRNA turnover <em>in vivo</em> even in the presence of Cas13b. Finally, cryoelectron microscopy (cryo-EM) structures reveal that AcrVIB1 binds a helical domain of Cas13b responsible for securing the crRNA, keeping the domain untethered. These findings reveal an Acr that converts an effector nuclease into a crRNA sink to suppress CRISPR-Cas defense.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"80 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143427469","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 : 2025-02-12DOI: 10.1016/j.molcel.2025.01.017
Aaztli R. Coria, Akruti Shah, Mohammad Shafieinouri, Sarah J. Taylor, Emilien Orgebin, Wilfried Guiblet, Jennifer T. Miller, Indra Mani Sharma, Colin Chih-Chien Wu
18S nonfunctional rRNA decay (NRD) detects and eliminates translationally nonfunctional 18S rRNA. Although this process is critical for ribosome quality control, the mechanisms underlying nonfunctional 18S rRNA turnover remain elusive, particularly in mammals. Here, we show that mammalian 18S NRD initiates through the integrated stress response (ISR) via GCN2. Nonfunctional 18S rRNA induces translational arrest at start sites. Biochemical analyses demonstrate that ISR activation limits translation initiation and attenuates collisions between scanning 43S preinitiation complexes and stalled nonfunctional ribosomes. The ISR promotes 18S NRD and 40S ribosomal protein turnover by RNF10-mediated ubiquitination. Ultimately, RIOK3 binds the resulting ubiquitinated 40S subunits and facilitates 18S rRNA decay. Overall, mammalian 18S NRD acts through GCN2, followed by ubiquitin-dependent 18S rRNA degradation involving the ubiquitin E3 ligase RNF10 and the atypical protein kinase RIOK3. These findings establish a dynamic feedback mechanism by which the GCN2-RNF10-RIOK3 axis surveils ribosome functionality at the translation initiation step.
{"title":"The integrated stress response regulates 18S nonfunctional rRNA decay in mammals","authors":"Aaztli R. Coria, Akruti Shah, Mohammad Shafieinouri, Sarah J. Taylor, Emilien Orgebin, Wilfried Guiblet, Jennifer T. Miller, Indra Mani Sharma, Colin Chih-Chien Wu","doi":"10.1016/j.molcel.2025.01.017","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.01.017","url":null,"abstract":"18S nonfunctional rRNA decay (NRD) detects and eliminates translationally nonfunctional 18S rRNA. Although this process is critical for ribosome quality control, the mechanisms underlying nonfunctional 18S rRNA turnover remain elusive, particularly in mammals. Here, we show that mammalian 18S NRD initiates through the integrated stress response (ISR) via GCN2. Nonfunctional 18S rRNA induces translational arrest at start sites. Biochemical analyses demonstrate that ISR activation limits translation initiation and attenuates collisions between scanning 43S preinitiation complexes and stalled nonfunctional ribosomes. The ISR promotes 18S NRD and 40S ribosomal protein turnover by RNF10-mediated ubiquitination. Ultimately, RIOK3 binds the resulting ubiquitinated 40S subunits and facilitates 18S rRNA decay. Overall, mammalian 18S NRD acts through GCN2, followed by ubiquitin-dependent 18S rRNA degradation involving the ubiquitin E3 ligase RNF10 and the atypical protein kinase RIOK3. These findings establish a dynamic feedback mechanism by which the GCN2-RNF10-RIOK3 axis surveils ribosome functionality at the translation initiation step.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"86 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143393298","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 : 2025-02-12DOI: 10.1016/j.molcel.2025.01.013
Zixuan Huang, Frances F. Diehl, Mengjiao Wang, Yi Li, Aixia Song, Fei Xavier Chen, Nicolle A. Rosa-Mercado, Roland Beckmann, Rachel Green, Jingdong Cheng
Cells tightly regulate ribosome homeostasis to adapt to changing environments. Ribosomes are degraded during stress, but the mechanisms responsible remain unclear. Here, we show that starvation induces the selective depletion of 40S ribosomes following their ubiquitylation by the E3 ligase RNF10. The atypical kinase RIOK3 specifically recognizes these ubiquitylated 40S ribosomes through a unique ubiquitin-interacting motif, visualized by cryoelectron microscopy (cryo-EM). RIOK3 binding and ubiquitin recognition are essential for 40S ribosome degradation during starvation. RIOK3 induces the degradation of ubiquitylated 40S ribosomes through progressive decay of their 18S rRNA beginning at the 3′ end, as revealed by cryo-EM structures of degradation intermediates. Together, these data define a pathway and mechanism for stress-induced degradation of 40S ribosomes, directly connecting ubiquitylation to regulation of ribosome homeostasis.
{"title":"RIOK3 mediates the degradation of 40S ribosomes","authors":"Zixuan Huang, Frances F. Diehl, Mengjiao Wang, Yi Li, Aixia Song, Fei Xavier Chen, Nicolle A. Rosa-Mercado, Roland Beckmann, Rachel Green, Jingdong Cheng","doi":"10.1016/j.molcel.2025.01.013","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.01.013","url":null,"abstract":"Cells tightly regulate ribosome homeostasis to adapt to changing environments. Ribosomes are degraded during stress, but the mechanisms responsible remain unclear. Here, we show that starvation induces the selective depletion of 40S ribosomes following their ubiquitylation by the E3 ligase RNF10. The atypical kinase RIOK3 specifically recognizes these ubiquitylated 40S ribosomes through a unique ubiquitin-interacting motif, visualized by cryoelectron microscopy (cryo-EM). RIOK3 binding and ubiquitin recognition are essential for 40S ribosome degradation during starvation. RIOK3 induces the degradation of ubiquitylated 40S ribosomes through progressive decay of their 18S rRNA beginning at the 3′ end, as revealed by cryo-EM structures of degradation intermediates. Together, these data define a pathway and mechanism for stress-induced degradation of 40S ribosomes, directly connecting ubiquitylation to regulation of ribosome homeostasis.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"6 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143393296","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 : 2025-02-11DOI: 10.1016/j.molcel.2025.01.019
Regina T. Nostramo, Paolo L. Sinopoli, Alicia Bao, Sara Metcalf, Lauren M. Peltier, Anita K. Hopper
From archaea to humans, a subset of transfer RNA (tRNA) genes possesses an intron that must be removed from transcribed pre-tRNAs to generate mature, functional tRNAs. Evolutionary conservation of tRNA intron sequences suggests that tRNA introns perform sequence-dependent cellular functions, which are presently unknown. Here, we demonstrate that free introns of tRNAs (fitRNAs) in Saccharomyces cerevisiae serve as small regulatory RNAs that inhibit mRNA levels via long (13–15 nt) statistically improbable stretches of (near) perfect complementarity to mRNA coding regions. The functions of fitRNAs are both constitutive and inducible because genomic deletion or inducible overexpression of tRNAIle introns led to corresponding increases or decreases in levels of complementary mRNAs. Remarkably, although tRNA introns are usually rapidly degraded, fitRNATrp selectively accumulates following oxidative stress, and target mRNA levels decrease. Thus, fitRNAs serve as gene regulators that fine-tune basal mRNA expression and alter the network of mRNAs that respond to oxidative stress.
{"title":"Free introns of tRNAs as complementarity-dependent regulators of gene expression","authors":"Regina T. Nostramo, Paolo L. Sinopoli, Alicia Bao, Sara Metcalf, Lauren M. Peltier, Anita K. Hopper","doi":"10.1016/j.molcel.2025.01.019","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.01.019","url":null,"abstract":"From archaea to humans, a subset of transfer RNA (tRNA) genes possesses an intron that must be removed from transcribed pre-tRNAs to generate mature, functional tRNAs. Evolutionary conservation of tRNA intron sequences suggests that tRNA introns perform sequence-dependent cellular functions, which are presently unknown. Here, we demonstrate that free introns of tRNAs (fitRNAs) in <em>Saccharomyces cerevisiae</em> serve as small regulatory RNAs that inhibit mRNA levels via long (13–15 nt) statistically improbable stretches of (near) perfect complementarity to mRNA coding regions. The functions of fitRNAs are both constitutive and inducible because genomic deletion or inducible overexpression of tRNA<sup>Ile</sup> introns led to corresponding increases or decreases in levels of complementary mRNAs. Remarkably, although tRNA introns are usually rapidly degraded, fitRNA<sup>Trp</sup> selectively accumulates following oxidative stress, and target mRNA levels decrease. Thus, fitRNAs serve as gene regulators that fine-tune basal mRNA expression and alter the network of mRNAs that respond to oxidative stress.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"13 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143385070","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 : 2025-02-07DOI: 10.1016/j.molcel.2025.01.018
Annabelle Campbell, Hanna F. Esser, A. Maxwell Burroughs, Otto Berninghausen, L. Aravind, Thomas Becker, Rachel Green, Roland Beckmann, Allen R. Buskirk
Although many antibiotics inhibit bacterial ribosomes, the loss of known factors that rescue stalled ribosomes does not lead to robust antibiotic sensitivity in E. coli, suggesting the existence of additional mechanisms. Here, we show that the RNA helicase HrpA rescues stalled ribosomes in E. coli. Acting selectively on ribosomes that have collided, HrpA uses ATP hydrolysis to split stalled ribosomes into subunits. Cryoelectron microscopy (cryo-EM) structures reveal how HrpA simultaneously binds to two collided ribosomes, explaining its selectivity, and how its helicase module engages downstream mRNA such that, by exerting a pulling force on the mRNA, it would destabilize the stalled ribosome. These studies show that ribosome splitting is a conserved mechanism that allows proteobacteria to tolerate ribosome-targeting antibiotics.
{"title":"The RNA helicase HrpA rescues collided ribosomes in E. coli","authors":"Annabelle Campbell, Hanna F. Esser, A. Maxwell Burroughs, Otto Berninghausen, L. Aravind, Thomas Becker, Rachel Green, Roland Beckmann, Allen R. Buskirk","doi":"10.1016/j.molcel.2025.01.018","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.01.018","url":null,"abstract":"Although many antibiotics inhibit bacterial ribosomes, the loss of known factors that rescue stalled ribosomes does not lead to robust antibiotic sensitivity in <em>E. coli</em>, suggesting the existence of additional mechanisms. Here, we show that the RNA helicase HrpA rescues stalled ribosomes in <em>E. coli</em>. Acting selectively on ribosomes that have collided, HrpA uses ATP hydrolysis to split stalled ribosomes into subunits. Cryoelectron microscopy (cryo-EM) structures reveal how HrpA simultaneously binds to two collided ribosomes, explaining its selectivity, and how its helicase module engages downstream mRNA such that, by exerting a pulling force on the mRNA, it would destabilize the stalled ribosome. These studies show that ribosome splitting is a conserved mechanism that allows proteobacteria to tolerate ribosome-targeting antibiotics.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"1 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143258313","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}
The landscape of N6-methyadenosine (m6A) on different RNA isoforms is still incompletely understood. Here, in HEK293T cells, we endogenously label the methylated m6A sites on single Oxford Nanopore Technology (ONT) direct RNA sequencing (DRS) reads by APOBEC1-YTH-induced C-to-U mutations 10–100 nt away, obtaining 1,020,237 5-mer single-read m6A signals. We then trained m6Aiso, a deep residual neural network model that accurately identifies and quantifies m6A at single-read resolution. Analyzing m6Aiso-determined m6A on single reads and isoforms uncovers distance-dependent linkages of m6A sites along single molecules. It also uncovers specific methylation of identical m6A sites on intron-retained isoforms, partly due to their differential distances to exon junctions and isoform-specific binding of TARBP2. Moreover, we find that transcription factor SMAD3 promotes m6A deposition on its transcribed RNA isoforms during epithelial-mesenchymal transition, resulting in isoform-specific regulation of m6A on isoforms with alternative promoters. Our study underscores the effectiveness of m6Aiso in elucidating the intricate dynamics and complexities of m6A across RNA isoforms.
{"title":"Single-molecule m6A detection empowered by endogenous labeling unveils complexities across RNA isoforms","authors":"Wenbing Guo, Zhijun Ren, Xiang Huang, Jiayin Liu, Jingwen Shao, Xiaojun Ma, Chuanchuan Wei, Yixian Cun, Jialiang He, Jie Zhang, Zehong Wu, Yang Guo, Zijun Zhang, Zhengming Feng, Jianbo He, Jinkai Wang","doi":"10.1016/j.molcel.2025.01.014","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.01.014","url":null,"abstract":"The landscape of <em>N</em><sup><em>6</em></sup>-methyadenosine (m<sup>6</sup>A) on different RNA isoforms is still incompletely understood. Here, in HEK293T cells, we endogenously label the methylated m<sup>6</sup>A sites on single Oxford Nanopore Technology (ONT) direct RNA sequencing (DRS) reads by APOBEC1-YTH-induced C-to-U mutations 10–100 nt away, obtaining 1,020,237 5-mer single-read m<sup>6</sup>A signals. We then trained m6Aiso, a deep residual neural network model that accurately identifies and quantifies m<sup>6</sup>A at single-read resolution. Analyzing m6Aiso-determined m<sup>6</sup>A on single reads and isoforms uncovers distance-dependent linkages of m<sup>6</sup>A sites along single molecules. It also uncovers specific methylation of identical m<sup>6</sup>A sites on intron-retained isoforms, partly due to their differential distances to exon junctions and isoform-specific binding of TARBP2. Moreover, we find that transcription factor SMAD3 promotes m<sup>6</sup>A deposition on its transcribed RNA isoforms during epithelial-mesenchymal transition, resulting in isoform-specific regulation of m<sup>6</sup>A on isoforms with alternative promoters. Our study underscores the effectiveness of m6Aiso in elucidating the intricate dynamics and complexities of m<sup>6</sup>A across RNA isoforms.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"40 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143258312","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 : 2025-02-07DOI: 10.1016/j.molcel.2024.12.026
Jeong Hyun Ahn, Yiran Guo, Heankel Lyons, Samuel G. Mackintosh, Benjamin K. Lau, Ricky D. Edmondson, Stephanie D. Byrum, Aaron J. Storey, Alan J. Tackett, Ling Cai, Benjamin R. Sabari, Gang Greg Wang
Recurrent cancer-causing fusions of NUP98 produce higher-order assemblies known as condensates. How NUP98 oncofusion-driven condensates activate oncogenes remains poorly understood. Here, we investigate NUP98-PHF23, a leukemogenic chimera of the disordered phenylalanine-and-glycine (FG)-repeat-rich region of NUP98 and the H3K4me3/2-binding plant homeodomain (PHD) finger domain of PHF23. Our integrated analyses using mutagenesis, proteomics, genomics, and condensate reconstitution demonstrate that the PHD domain targets condensate to the H3K4me3/2-demarcated developmental genes, while FG repeats determine the condensate composition and gene activation. FG repeats are necessary to form condensates that partition a specific set of transcriptional regulators, notably the KMT2/MLL H3K4 methyltransferases, histone acetyltransferases, and BRD4. FG repeats are sufficient to partition transcriptional regulators and activate a reporter when tethered to a genomic locus. NUP98-PHF23 assembles the chromatin-bound condensates that partition multiple positive regulators, initiating a feedforward loop of reading-and-writing the active histone modifications. This network of interactions enforces an open chromatin landscape at proto-oncogenes, thereby driving cancerous transcriptional programs.
{"title":"The phenylalanine-and-glycine repeats of NUP98 oncofusions form condensates that selectively partition transcriptional coactivators","authors":"Jeong Hyun Ahn, Yiran Guo, Heankel Lyons, Samuel G. Mackintosh, Benjamin K. Lau, Ricky D. Edmondson, Stephanie D. Byrum, Aaron J. Storey, Alan J. Tackett, Ling Cai, Benjamin R. Sabari, Gang Greg Wang","doi":"10.1016/j.molcel.2024.12.026","DOIUrl":"https://doi.org/10.1016/j.molcel.2024.12.026","url":null,"abstract":"Recurrent cancer-causing fusions of NUP98 produce higher-order assemblies known as condensates. How NUP98 oncofusion-driven condensates activate oncogenes remains poorly understood. Here, we investigate NUP98-PHF23, a leukemogenic chimera of the disordered phenylalanine-and-glycine (FG)-repeat-rich region of NUP98 and the H3K4me3/2-binding plant homeodomain (PHD) finger domain of PHF23. Our integrated analyses using mutagenesis, proteomics, genomics, and condensate reconstitution demonstrate that the PHD domain targets condensate to the H3K4me3/2-demarcated developmental genes, while FG repeats determine the condensate composition and gene activation. FG repeats are necessary to form condensates that partition a specific set of transcriptional regulators, notably the KMT2/MLL H3K4 methyltransferases, histone acetyltransferases, and BRD4. FG repeats are sufficient to partition transcriptional regulators and activate a reporter when tethered to a genomic locus. NUP98-PHF23 assembles the chromatin-bound condensates that partition multiple positive regulators, initiating a feedforward loop of reading-and-writing the active histone modifications. This network of interactions enforces an open chromatin landscape at proto-oncogenes, thereby driving cancerous transcriptional programs.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"16 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143258314","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 : 2025-02-06DOI: 10.1016/j.molcel.2025.01.011
Leonardo Luís Artico, Ana Paula Arruda
Cytosolic Ca2+ transients are critical signals for autophagy regulation; however, how they translate into functional autophagic events remains unclear. In this issue of Molecular Cell, Zheng et al.1 identify CaMKIIβ as a key player decoding Ca2+ transients at the ER surface to initiate autophagosome formation through the FIP200 complex.
{"title":"CaMKIIβ Ca2+ptures ER signals to initiate autophagosome biogenesis","authors":"Leonardo Luís Artico, Ana Paula Arruda","doi":"10.1016/j.molcel.2025.01.011","DOIUrl":"https://doi.org/10.1016/j.molcel.2025.01.011","url":null,"abstract":"Cytosolic Ca<sup>2+</sup> transients are critical signals for autophagy regulation; however, how they translate into functional autophagic events remains unclear. In this issue of <em>Molecular Cell</em>, Zheng et al.<span><span><sup>1</sup></span></span> identify CaMKIIβ as a key player decoding Ca<sup>2+</sup> transients at the ER surface to initiate autophagosome formation through the FIP200 complex.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"13 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143192668","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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