RNA最新文献

{"title":"Structural and functional characterization of the SLA' structure at the 3' terminus of the Zika virus negative-strand intermediate.","authors":"Quinn H Abram, Lindsay A Matthews, Alba Guarné, Selena M Sagan","doi":"10.1261/rna.080342.124","DOIUrl":"10.1261/rna.080342.124","url":null,"abstract":"<p><p>Flavivirus infections, including those of Dengue virus (DENV) and Zika virus (ZIKV), result in a high disease burden globally, yet many aspects of their viral life cycle remain poorly understood. For example, while some features of the mechanism of negative-strand RNA synthesis are known, relatively little is known about the initiation of positive-strand RNA synthesis in the flavivirus life cycle. Viral RNA replication is initiated via the recruitment of the viral NS5 RNA-dependent RNA polymerase (RdRp) to stem-loop A (SLA) at the 5' terminus of positive-strand genomic RNA. Subsequent genome cyclization is thought to facilitate loading of NS5 onto the 3' terminus of the genomic RNA to initiate negative-strand RNA synthesis. Conversely, it is not clear whether RNA structures in the negative-strand replicative intermediate similarly recruit NS5 to promote positive-strand RNA synthesis, providing specificity to this process. Herein, we characterized the secondary structure of the 3' terminus of the negative-strand replicative intermediate in ZIKV and DENV1-4 in silico and in vitro. We observed that the 3' terminus of the negative strand is capable of forming a secondary structure which mirrors SLA, which we term SLA'. While we demonstrate that SLA' forms in vitro and is capable of interacting with NS5, introduction of G·U wobble base pairs that disrupt SLA', while keeping SLA largely intact, suggest that SLA' is not necessary for viral RNA replication. As such, this work suggests that in contrast to related viruses, the positive-strand promoter is unlikely to be provided by specific structure(s) at the 3' terminus of the negative-strand replicative intermediate.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1139-1153"},"PeriodicalIF":4.2,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12265937/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144022016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Implications for OLE RNA as a natural integral membrane RNA.","authors":"Seth E Lyon, Ronald R Breaker","doi":"10.1261/rna.080489.125","DOIUrl":"10.1261/rna.080489.125","url":null,"abstract":"<p><p>Ornate, large, extremophilic (OLE) RNAs, found in many Gram-positive bacterial species, represent an unusual class of noncoding RNAs, which form a large ribonucleoprotein complex that localizes to cell membranes. Although the precise biochemical functions of OLE RNAs remain to be discovered, several lines of evidence suggest that they participate in forming particles that function as the master regulators of their bacterial hosts. Thus, OLE RNA might be a molecular relic of RNA World organisms that contributed to cellular stress responses long before the evolutionary emergence of proteins. Recent reports of partial 3D structures strongly suggest that OLE RNAs form a molecular dimer whose complex structure spans the phospholipid bilayer of membranes. The implications of these findings on the functions of OLE RNA and on the capabilities of RNA polymers more broadly are discussed.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1031-1040"},"PeriodicalIF":4.2,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12265935/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144111605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Absolute quantification of mammalian microRNAs for therapeutic RNA cleavage and detargeting.","authors":"Carolyn Kraus, Jiayi Wang, Haiying Zheng, Jennifer Broderick, Nandagopal Ajaykumar, Mina Zamani, Mengqi Yang, Katharine Cecchini, Shun-Qing Liang, Olena Kolumba, Kathryn Chase, Jooyoung Lee, Wen Xue, Erik J Sontheimer, Ildar Gainetdinov","doi":"10.1261/rna.080566.125","DOIUrl":"10.1261/rna.080566.125","url":null,"abstract":"<p><p>MicroRNAs (miRNAs) are small regulatory RNAs that destabilize partially complementary transcripts and cleave perfectly paired targets. miRNAs are often expressed in a specific tissue, allowing miRNA-directed cleavage to be used to prevent genome editing or gene replacement therapy in unintended cell types, a strategy called detargeting. miRNA intracellular concentration influences the potency of gene silencing, yet the absolute steady-state levels of just a few miRNAs have been determined in mammalian tissues. Here, we report the absolute abundance of miRNAs in 14 human and mouse cell lines and 17 mouse tissues, including eight brain regions. Our experiments in human cultured cells demonstrate that both miRNA and target levels influence efficacy of cleavage of fully complementary transcripts. We report the miRNA concentration required for productive cleavage of highly expressed transcripts and identify mouse miRNAs that reach this threshold in vivo.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1081-1090"},"PeriodicalIF":4.2,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12265943/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144174760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"OpenASO: RNA Rescue-designing splice-modulating antisense oligonucleotides through community science.","authors":"Victor Tse, Martin Guiterrez, Jill Townley, Jonathan Romano, Jennifer Pearl, Guillermo Chacaltana, Eterna Players, Rhiju Das, Jeremy R Sanford, Michael D Stone","doi":"10.1261/rna.080288.124","DOIUrl":"10.1261/rna.080288.124","url":null,"abstract":"<p><p>Splice-modulating antisense oligonucleotides (ASOs) are precision RNA-based drugs that are becoming an established modality to treat human disease. Previously, we reported the discovery of ASOs that target a novel, putative intronic RNA structure to rescue splicing of multiple pathogenic variants of <i>F8</i> exon 16 that cause hemophilia A. However, the conventional approach to discovering splice-modulating ASOs is both laborious and expensive. Here, we describe a novel approach that integrates data-driven RNA structure prediction and community science to discover splice-modulating ASOs. Using a splicing-deficient pathogenic variant of <i>F8</i> exon 16 as a model, we show that 25% of the top-scoring molecules designed in the Eterna OpenASO challenge have a statistically significant impact on enhancing exon 16 splicing. Additionally, we show that a distinct combination of ASOs designed by Eterna players can additively enhance the inclusion of the splicing-deficient exon 16 variant. Together, our data suggest that crowdsourcing designs from a community of citizen scientists may accelerate and complement traditional avenues for the discovery of splice-modulating ASOs with potential to treat human disease.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1091-1102"},"PeriodicalIF":4.2,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12265936/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144161828","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Human CCR4 deadenylase homolog Angel1 is a non-stop mRNA decay factor.","authors":"Tim Nicholson-Shaw, Megan E Dowdle, Yasmeen Ajaj, Mark Perelis, Amit Fulzele, Gene W Yeo, Eric J Bennett, Jens Lykke-Andersen","doi":"10.1261/rna.080399.125","DOIUrl":"10.1261/rna.080399.125","url":null,"abstract":"<p><p>Translation elongation stalls trigger mRNA decay and degradation of the nascent polypeptide via translation-dependent quality control pathways. One such pathway, non-stop mRNA decay (NSD), targets aberrant mRNAs that lack stop codons, for example, due to premature polyadenylation. Here we identify Angel1, a CCR4 deadenylase homolog whose biochemical activity remains poorly defined, as a rate-limiting factor for NSD in human cells. Angel1 associates with mRNA coding regions and proteins involved in ribosome-associated quality control and mRNA decay, consistent with a factor that monitors translation elongation stalls. Depletion of Angel1 causes stabilization of reporter mRNAs that are targeted for NSD by the absence of stop codons, but not an mRNA targeted for nonsense-mediated decay. A conserved catalytic residue of Angel1 is critical for its function in NSD. Our findings identify Angel1 as a human NSD factor and suggest that Angel1 catalytic activity plays a critical role in the NSD pathway.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1195-1205"},"PeriodicalIF":4.2,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12265940/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144182731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tissue-specific SEC31A alternative splicing is regulated by RBM47 and controls lipid transport.","authors":"Felix Ostwaldt, Sarah Plößner, Benjamin Dimos-Röhl, Marco Preussner, Florian Heyd","doi":"10.1261/rna.080572.125","DOIUrl":"10.1261/rna.080572.125","url":null,"abstract":"<p><p>The importance of coat protein complex II (COPII) for protein secretion has been known for decades. However, how large cargo like procollagens or chylomicrons are secreted remains incompletely understood, as COPII vesicles are usually too small to accommodate such bulky cargo. Here we introduce alternative splicing as another regulatory layer in controlling secretion of large cargo. We use RNA-seq data from various human tissues to identify tissue-specific alternative splicing in secretion-associated genes. This identifies an uncharacterized exon in SEC31A, a component of the COPII machinery, whose inclusion is highly tissue-specific, with high inclusion, for example, in digestive tissues. We show that inclusion of this exon increases lipid transport, thereby connecting SEC31A alternative splicing with the secretion of large cargo. Furthermore, by correlating SEC31A alternative splicing with the expression of RNA-binding proteins across multiple tissues, we identify and then validate RBM47 as the regulator of SEC31A alternative splicing. This serves as proof-of-principle for a broadly applicable in silico approach to facilitate the identification of <i>trans</i>-acting factors controlling tissue-specific alternative splicing.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1125-1138"},"PeriodicalIF":4.2,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12265942/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144174770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular basis for the interactions of eIF2β with eIF5, eIF2B, and 5MP1 and their regulation by CK2.","authors":"Paul A Wagner, Meimei Song, Paul Doran, Aysenur Seker, Ralf Ficner, Bernhard Kuhle, Assen Marintchev","doi":"10.1261/rna.080652.125","DOIUrl":"10.1261/rna.080652.125","url":null,"abstract":"<p><p>The heterotrimeric GTPase eukaryotic translation initiation factor 2 (eIF2) delivers the initiator Met-tRNAi to the ribosomal translation preinitiation complex (PIC). eIF2β has three lysine-rich repeats (K-boxes), important for binding to the GTPase-activating protein eIF5, the guanine nucleotide exchange factor eIF2B, and the regulator eIF5-mimic protein (5MP). Here, we combine X-ray crystallography with NMR to understand the molecular basis and dynamics of these interactions. The crystal structure of yeast eIF5-CTD in complex with eIF2β K-box 3 reveals an extended binding site on eIF2β, far beyond the K-box. We show that eIF2β contains three distinct binding sites, centered on each of the K-boxes, and that human eIF5, eIF2Bε, and 5MP1 can bind to all three sites. Our results reveal how eIF2B speeds up the dissociation of eIF5 from eIF2-GDP to promote nucleotide exchange; and how 5MP1 can destabilize eIF5 binding to eIF2 and the PIC, to promote stringent start codon selection. All these affinities are increased by CK2 phosphomimetic mutations, highlighting the role of CK2 in both remodeling and stabilizing the translation apparatus.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144650290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data.","authors":"Orel Mizrahi, Meredith Corley, Ori Feldman, Thorben Fröhlking, Lei Sun, Alison Ziesel, Maciej Antczak, Mattia Bernetti, Shaimae I Elhajjajy, Wenze Huang, Grady G Nguyen, Samuel S Park, Raul I Perez Martell, Luke Trinity, Kui Xu, Tomasz Zok, Giovanni Bussi, Hosna Jabbari, Yaron Orenstein, Sharon Aviran, Michelle M Meyer, Gene W Yeo","doi":"10.1261/rna.080215.124","DOIUrl":"10.1261/rna.080215.124","url":null,"abstract":"<p><p>RNA-binding proteins (RBP) play diverse roles in mRNA processing and function. However, from thousands of RBPs encoded in the human genome, a detailed molecular understanding of their interactions with RNA is available only for a small fraction. In most cases, our knowledge of the combination of RNA sequence and structure required for specific RBP binding is insufficient for accurately predicting binding sites transcriptome-wide. In this context, the rapidly expanding collection of transcriptomic data sets that map distinct, yet intertwined posttranscriptional marks, such as RNA structure and RBP binding, presents an opportunity for integrative analysis to better characterize RBP binding. A grand challenge faced by our community is that relatively little information on the secondary structure context within and near RBP-binding sites has been gleaned from integrating such data sets, partially due to lack of suitable computational methods. To engage scientists from diverse backgrounds in addressing this gap, the RNA Society organized the RBP Footprint Grand Challenge in 2021, an international community effort to develop new methods or leverage existing ones for predicting RBP-binding sites through analysis of a growing volume of sequence, structure, and binding data and to experimentally validate select predictions. Here, we report the initiative, analyses, and methods developed by the participants, validation results, and five new in vivo binding data sets generated for validation. We hope our work will inspire additional innovation in computational methods, further utilization of available data resources, and future endeavors to engage the community in collaborating toward closing other critical data-analysis gaps.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1103-1124"},"PeriodicalIF":4.2,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12265944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144120775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"EDC4 C-terminal domain scaffolds P-body assembly and links P-body dynamics to p53-mediated tumor suppression.","authors":"Yu-Hsuan Cheng, Ting-Wen Chen, Wei-Chung Chiang, Jean-Cheng Kuo, Yi-Sheng Ho, Michelle Noble, Chung-Te Chang","doi":"10.1261/rna.080561.125","DOIUrl":"10.1261/rna.080561.125","url":null,"abstract":"<p><p>Processing bodies (P-bodies) are membraneless organelles in eukaryotic cells that play a central role in mRNA metabolism, including mRNA decay, storage, and translational repression. However, the molecular mechanisms governing their assembly remain incompletely understood. Here, we identify the C-terminal domain of EDC4 as the minimal region required for P-body formation, with residues 1266-1401 driving phase separation and EDC4 condensation. To investigate the functional relevance of P-body integrity, we used the microprotein Nobody (NBDY) as a selective perturbation tool. Our results revealed that the NBDY 22-41 peptide directly binds the EDC4 C-terminal domain and inhibits its self-association, thereby selectively dissolving P-bodies without affecting the canonical mRNA decay pathway. Using this tool, we further examined the impact of P-body disruption on gene expression. Transcriptome profiling combined with quantitative validation revealed that P-body loss activates the p53 pathway and enhances the stability of associated transcripts. Consistent with these findings, clinical data show that NBDY overexpression is associated with p53 pathway activation in various cancers, and the NBDY 22-41 fragment reduces tumor cell proliferation and invasion, suggesting a potentially complex role of P-body dynamics in cancer biology. Together, our study defines the EDC4 C-terminal domain as a core scaffold for P-body assembly and uncovers a regulatory role of P-body dynamics in p53-mediated gene expression, with potential implications for cancer biology.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1176-1194"},"PeriodicalIF":4.2,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12265941/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144034478","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Alu RNA pseudoknot alterations influence SRP9/SRP14 association.","authors":"Daniel Gussakovsky, Mira J F Brown, Higor Sette Pereira, Markus Meier, G Pauline Padilla-Meier, Nicole A Black, Evan P Booy, Jörg Stetefeld, Trushar R Patel, Sean A McKenna","doi":"10.1261/rna.080359.124","DOIUrl":"10.1261/rna.080359.124","url":null,"abstract":"<p><p>There are over 1 million Alu elements in the human genome which can be transcribed into discrete, RNA polymerase III transcribed noncoding Alu RNAs. These Alu RNAs often interact with and are regulated by the protein heterodimer SRP9/SRP14. This interaction is dependent on a 5' pseudoknot domain in the Alu RNA that is thought to be held together by a canonical nucleotide triad within a U-turn motif. Herein, we discover a significant reduction in BC200 expression after mutation of a critical guanosine in the U-turn motif within its pseudoknot domain. We studied a recently discovered short human Alu RNA, EB120, which lacks the canonical Alu RNA U-turn nucleotide triad. We tested the expression of EB120 in 18 different human cell lines and tissues. EB120 was found to lack association with SRP9/SRP14 in a cellular context. Small-angle X-ray scattering followed by atomistic computation structure prediction suggests the BC200 Alu domain and its U-turn mutant both possess a canonical Alu RNA fold, while EB120 lacks one. Our results highlight the structural diversity of Alu RNA, and the impact mutations may have on Alu RNA function.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1154-1175"},"PeriodicalIF":4.2,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12265939/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144036975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}