IF 4.2 3区生物学

RNA Pub Date : 2025-05-08 DOI: 10.1261/rna.080342.124

Quinn H Abram, Lindsay A Matthews, Alba Guarné, Selena M Sagan

{"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":"https://doi.org/10.1261/rna.080342.124","url":null,"abstract":"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.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Assessing Microprocessor Complex Mutations with a Microsensor System. 用微传感器系统评估微处理器复杂突变。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-06 DOI: 10.1261/rna.080338.124

Sheng Bao, Thi Nhu-Y Le, Cong Truc Le, Nguyen Bao Tran Le, Tuan Anh Nguyen

引用次数: 0

Unraveling Unbreakable Hairpins: Characterizing RNA secondary structures that are persistent after dinucleotide shuffling. 解开牢不可破的发夹：表征二核苷酸洗牌后持续存在的RNA二级结构。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-06 DOI: 10.1261/rna.080176.124

Alyssa Pratt, David Anthony Hendrix

{"title":"Unraveling Unbreakable Hairpins: Characterizing RNA secondary structures that are persistent after dinucleotide shuffling.","authors":"Alyssa Pratt, David Anthony Hendrix","doi":"10.1261/rna.080176.124","DOIUrl":"https://doi.org/10.1261/rna.080176.124","url":null,"abstract":"The sequence of nucleotides that make up an RNA determines its structure, which determines its function. The RNA hairpin, also known as a stem-loop, is a ubiquitous and fundamental feature of RNA secondary structure. A common method of randomizing an RNA sequence is dinucleotide shuffling with the Altschul-Erickson algorithm, which preserves the dinucleotide content of the sequence. This algorithm generates randomized sequences by sampling Eulerian paths through the de Bruijn graph representation of the original sequence. We identified a subset of RNA hairpins in the bpRNA-1m meta-database that always form hairpins after repeated application of dinucleotide shuffling. We investigated these \"unbreakable hairpins\" and found several common properties. First, we found that unbreakable hairpins had on average similar folding energies compared to other hairpins of similar lengths, although they frequently contained ultra-stable hairpin loops. We found that they tend to be split by purines and pyrimidines on opposite sides of the stem. Furthermore, we found that this specific sequence feature restricts the number of distinct Eulerian paths through their de Bruijn graph representation, resulting in a small number of distinguishable dinucleotide-shuffled sequences. Beyond this algorithmic means of identification, these distinct sequences may have biological significance because we found that a significant percentage occur in a specific location of 16S ribosomal RNAs. Finally, we present a formula to calculate the number of possible unique dinucleotide shuffled sequences for an input RNA sequence, which has utility for the general application of the Altschul-Erickson algorithm.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144034645","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}

引用次数: 0

Structures of RNA phosphotransferase Tpt1 reveal distinct binding modes for an RNA 2'-PO4 splice junction versus a 5'-PO4 mononucleotide. RNA磷酸转移酶Tpt1的结构揭示了RNA 2'-PO4剪接与5'-PO4单核苷酸的不同结合模式。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-05 DOI: 10.1261/rna.080444.125

Agata Jacewicz, Masad J Damha, Stewart Shuman

引用次数: 0

Regulation of Cardiac Hypertrophy by RNA Readers. RNA阅读器对心肌肥厚的调控。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-02 DOI: 10.1261/rna.080557.125

Francesco Paneni, Sarah Costantino

引用次数: 0

Comprehensive analysis of m6A-seq data reveals distinct features of conserved and unique m6A sites in mammals. 对m6A-seq数据的综合分析揭示了哺乳动物中保守和独特的m6A位点的明显特征。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-02 DOI: 10.1261/rna.080222.124

Guo-Shi Chai, Hong-Xuan Chen, Dong-Zhao Ma, Ze-Hui Ren, Xue-Hong Liu, Zhang Zhang, Guan-Zheng Luo

{"title":"Comprehensive analysis of m6A-seq data reveals distinct features of conserved and unique m6A sites in mammals.","authors":"Guo-Shi Chai, Hong-Xuan Chen, Dong-Zhao Ma, Ze-Hui Ren, Xue-Hong Liu, Zhang Zhang, Guan-Zheng Luo","doi":"10.1261/rna.080222.124","DOIUrl":"https://doi.org/10.1261/rna.080222.124","url":null,"abstract":"N6-methyladenine (m6A) stands out as the most prevalent internal chemical modification on mammalian mRNA, playing a vital role in diverse biological processes. However, the characteristics of m6A across different cell lines and tissues remain poorly understood. In this study, we systematically evaluated 193 published m6A-seq datasets using newly established quality metrics, identifying ~1.5 million high-confidence m6A sites in human and mouse. By categorizing m6A sites into different consistency levels, we observed that those with high consistency levels were enriched near mRNA stop codons and the 5' end of lncRNA, interacted more frequently with known m6A-binding proteins, and influenced mRNA/lncRNA expression homeostasis. Furthermore, the promoters of genes marked by these consistent sites exhibited higher CpG density, with METTL3 preferentially binding to these regions. Conversely, low-consistency or unique m6A sites were enriched near mRNA start codons and distributed evenly across lncRNA, interacting with newly discovered m6A-binding proteins. These findings enhanced our understanding of the diverse characteristics and potential functional roles of m6A in mammals.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144046327","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}

引用次数: 0

The influence of downstream structured elements within mRNA on the dynamics of intersubunit rotation in ribosomes. mRNA下游结构元件对核糖体亚基间旋转动力学的影响。

IF 4.2 3区生物学

RNA Pub Date : 2025-04-17 DOI: 10.1261/rna.080291.124

Bassem Shebl, Anna Pavlova, Preston Kellenberger, Dongmei Yu, Drew Menke, James C Gumbart, Peter V Cornish

{"title":"The influence of downstream structured elements within mRNA on the dynamics of intersubunit rotation in ribosomes.","authors":"Bassem Shebl, Anna Pavlova, Preston Kellenberger, Dongmei Yu, Drew Menke, James C Gumbart, Peter V Cornish","doi":"10.1261/rna.080291.124","DOIUrl":"https://doi.org/10.1261/rna.080291.124","url":null,"abstract":"Proper codon/anti-codon pairing within the ribosome necessitates linearity of the transcript. Any structures formed within a messenger RNA (mRNA) must be unwound before the respective codon is interpreted. Linearity, however, is not always the norm; some intricate structures within mRNA are able to exert unique ribosome/mRNA interactions to regulate translation. Intrinsic kinetic and thermal stability in many of these structures are efficient in slowing translation causing pausing of the ribosome. Altered translation kinetics arising from atypical interactions have been shown to affect intersubunit rotation. Here, we employ single-molecule Förster Resonance Energy Transfer (smFRET), to observe changes in intersubunit rotation of the ribosome as it approaches downstream structured nucleic acid. The emergence of the hyper-rotated state is critically dependent on the distance between downstream structure and the ribosome suggesting interactions with the helicase center are allosterically coupled to intersubunit rotation. Further, molecular dynamics (MD) simulations were performed to determine ribosomal protein/mRNA interactions that may play a pivotal role in helicase activity and ultimately unwinding of downstream structure.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144028309","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}

引用次数: 0

Dynamic RNA binding and unfolding by nonsense-mediated mRNA decay factor UPF2. 无义介导的mRNA衰变因子UPF2的动态RNA结合和展开。

IF 4.2 3区生物学

RNA Pub Date : 2025-04-17 DOI: 10.1261/rna.080300.124

Jenn-Yeu Alvin Szeto, Mirella Vivoli Vega, Justine Mailliot, George Orriss, Lingling Sun, Joshua C Bufton, Kyle T Powers, Sathish K N Yadav, Imre Berger, Christiane Schaffitzel

{"title":"Dynamic RNA binding and unfolding by nonsense-mediated mRNA decay factor UPF2.","authors":"Jenn-Yeu Alvin Szeto, Mirella Vivoli Vega, Justine Mailliot, George Orriss, Lingling Sun, Joshua C Bufton, Kyle T Powers, Sathish K N Yadav, Imre Berger, Christiane Schaffitzel","doi":"10.1261/rna.080300.124","DOIUrl":"https://doi.org/10.1261/rna.080300.124","url":null,"abstract":"Nonsense-mediated mRNA decay (NMD) is an mRNA surveillance pathway involved in translational control and gene expression regulation. Core NMD factors UPF1, UPF2 and UPF3B are conserved from yeast to humans and essential to target mRNAs with a premature stop codon for decay. UPF2 binding to UPF1 activates UPF1's ATPase and helicase activities, and UPF2 binding to UPF3B is important for its association with the exon-junction complex and efficient NMD. However, UPF2's association with RNA remains largely uncharacterized. Here, we analyze nucleic acid binding, identifying the first and third MIF4G domains of UPF2 as main RNA-/DNA-binding modules. We find that UPF2's MIF4G domain-3 has RNA annealing activity while full-length UPF2 unfolds our reporter hairpin-RNA structure. We show that UPF2 preferentially binds and stabilizes single-stranded RNA (ss-RNA) in a sequence-independent manner. Concomitant to ss-RNA binding, UPF2 undergoes a distinct conformational change in its otherwise highly dynamic structure. UPF2's RNA binding and unfolding activity may support UPF1's helicase and mRNP remodeling activity and, in combination with UPF3B, stabilize UPF1's association with nonsense mRNA.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144029402","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}

引用次数: 0

Comparative analyses of disease-linked missense mutations in the RNA exosome modeled in budding yeast reveal distinct functional consequences in translation. 在出芽酵母中建模的RNA外泌体中与疾病相关的错义突变的比较分析揭示了翻译中不同的功能后果。

IF 4.2 3区生物学

RNA Pub Date : 2025-04-17 DOI: 10.1261/rna.080447.125

Maria C Sterrett, Lauryn A Cureton, Lauren N Cohen, Ambro van Hoof, Sohail Khoshnevis, Milo B Fasken, Anita H Corbett, Homa Ghalei

{"title":"Comparative analyses of disease-linked missense mutations in the RNA exosome modeled in budding yeast reveal distinct functional consequences in translation.","authors":"Maria C Sterrett, Lauryn A Cureton, Lauren N Cohen, Ambro van Hoof, Sohail Khoshnevis, Milo B Fasken, Anita H Corbett, Homa Ghalei","doi":"10.1261/rna.080447.125","DOIUrl":"https://doi.org/10.1261/rna.080447.125","url":null,"abstract":"The RNA exosome is a multi-subunit, evolutionarily conserved ribonuclease complex that is essential for processing, decay and surveillance of many cellular RNAs. Missense mutations in genes encoding the structural subunits of the RNA exosome complex cause a diverse range of diseases, collectively known as RNA exosomopathies, often involving neurological and developmental defects. The varied symptoms suggest that different mutations lead to distinct in vivo consequences. To investigate these functional consequences and distinguish whether they are unique to each RNA exosomopathy mutation, we generated a collection of in vivo models by introducing pathogenic missense mutations in orthologous S. cerevisiae genes. Comparative RNA-seq analysis assessing broad transcriptomic changes in each mutant model revealed that three yeast mutant models, rrp4-G226D, rrp40-W195R and rrp46-L191H, which model mutations in the genes encoding EXOSC2, EXOSC3 and EXOSC5, respectively, had the largest transcriptomic differences. While some transcriptomic changes, particularly in transcripts related to ribosome biogenesis, were shared among mutant models, each mutation also induced unique transcriptomic changes. Thus, our data suggests that while there are some shared consequences, there are also distinct differences in RNA exosome function by each variant. Assessment of ribosome biogenesis and translation defects in the three models revealed distinct differences in polysome profiles. Collectively, our results provide the first comparative analyses of RNA exosomopathy mutant models and suggest that different RNA exosome gene mutations result in in vivo consequences that are both unique and shared across each variant, providing further insight into the biology underlying each distinct pathology.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144009809","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}

引用次数: 0

Conformational heterogeneity in the dGsw purine riboswitch: role of Mg²⁺ and 2'-dG in aptamer folding. dGsw 嘌呤核糖开关的构象异质性：Mg²⁺和 2'-dG 在适配体折叠中的作用。

IF 4.2 3区生物学

RNA Pub Date : 2025-04-16 DOI: 10.1261/rna.080274.124

Susmit Narayan Chaudhury, Erdong Ding, Nathan E Jespersen, José N Onuchic, Karissa Y Sanbonmatsu

{"title":"Conformational heterogeneity in the dGsw purine riboswitch: role of Mg2+ and 2'-dG in aptamer folding.","authors":"Susmit Narayan Chaudhury, Erdong Ding, Nathan E Jespersen, José N Onuchic, Karissa Y Sanbonmatsu","doi":"10.1261/rna.080274.124","DOIUrl":"10.1261/rna.080274.124","url":null,"abstract":"Recent advancements in RNA structural biology have focused on unraveling the complexities of noncoding mRNA like riboswitches. These cis-acting regulatory regions undergo structural changes in response to specific cellular metabolites, leading to up- or downregulation of downstream genes. The purine riboswitch family regulates prokaryotic genes involved in purine degradation and biosynthesis. They feature an aptamer domain organized around a three-way helical junction, where ligand encapsulation occurs at the junctional core. We chemically probed the aptamer domain of the 2'-dG-sensing purine riboswitch from Mesoplasma florum (dGsw) under various solution conditions to understand how Mg2+ and 2'-dG influence riboswitch folding. We find that 2'-dG binding strongly depends on Mg2+, indicating that Mg2+ is essential for priming dGsw for ligand interactions. We identified a previously undescribed sequence in the 5' tail of dGsw that is complementary to a conserved helix. The inclusion of this region led to intramolecular competition between the alternate helix, Palt, and P1. Mutational analysis confirmed that the 5' flanking end of the aptamer domain forms an alternate helix in the absence of ligand. Molecular dynamics simulations revealed that this alternative conformation is stable. This helix may facilitate the formation of an antiterminator helix by opening the three-way junction surrounding the 2'-dG binding site. Our study establishes the importance of a closed terminal P1 helix conformation for metabolite binding and suggests that the delicate interplay between P1 and Palt fine-tunes downstream gene regulation. These insights offer a new perspective on riboswitch structure and enhance our understanding of the role that a conformational ensemble plays in riboswitch activity and regulation.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"724-733"},"PeriodicalIF":4.2,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12001964/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143531459","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}

引用次数: 0

RNA最新文献