IF 4.2 3区生物学

RNA Pub Date : 2025-06-16 DOI: 10.1261/rna.080521.125

Mary McMahon, Lynne E Maquat

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 : 2025-06-16 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":"10.1261/rna.080447.125","url":null,"abstract":"The RNA exosome is a multisubunit, 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 Saccharomyces 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 suggest 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":"988-1012"},"PeriodicalIF":4.2,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170193/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evaluating computational tools for protein-coding sequence detection: Are they up to the task? 评估蛋白质编码序列检测的计算工具：它们能胜任任务吗？

IF 4.2 3区生物学

RNA Pub Date : 2025-06-11 DOI: 10.1261/rna.080416.125

D J Champion, Ting-Hsuan Chen, Susan Thomson, Michael A Black, Paul P Gardner

{"title":"Evaluating computational tools for protein-coding sequence detection: Are they up to the task?","authors":"D J Champion, Ting-Hsuan Chen, Susan Thomson, Michael A Black, Paul P Gardner","doi":"10.1261/rna.080416.125","DOIUrl":"https://doi.org/10.1261/rna.080416.125","url":null,"abstract":"Background: Detecting protein coding genes in nucleotide sequences is a significant challenge for understanding genome and transcriptome function, yet the reliability of bioinformatic tools for this task remains largely unverified. This is despite some tools being available for several decades, and widely used for genome and transcriptome annotation.Results: We perform an assessment of nucleotide sequence and alignment-based de novo protein-coding detection tools. The controls we use exclude any previous training dataset and include coding exons as a positive set and length-matched intergenic and shuffled sequences as negative sets. Our work demonstrates that several widely used tools are neither accurate nor computationally efficient for the protein-coding sequence detection problem. In fact, just three of nine tools significantly outperformed a naive scoring scheme. Furthermore, we note a high discrepancy between self-reported accuracies and the accuracy achieved in our study. Our results show that the extra dimension from conserved and variable nucleotides in alignments have a significant advantage over single sequence approaches.Conclusions: These results highlight significant limitations in existing protein-coding annotation tools that are widely used for lncRNA annotation. This shows a need for more robust and efficient approaches to training and assessing the performance of tools for identifying protein-coding sequences. Our study paves the way for future advancements in comparative genomic approaches and we hope will popularise more robust approaches to genome and transcriptome annotation.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144275864","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

Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion. lncRNA SChLAP1的结构分析揭示了蛋白质结合界面和构象异质逆转录病毒插入。

IF 4.2 3区生物学

RNA Pub Date : 2025-06-11 DOI: 10.1261/rna.080488.125

James P Falese, Emily J McFadden, Christopher A d'Inzeo, Amanda E Hargrove

{"title":"Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion.","authors":"James P Falese, Emily J McFadden, Christopher A d'Inzeo, Amanda E Hargrove","doi":"10.1261/rna.080488.125","DOIUrl":"https://doi.org/10.1261/rna.080488.125","url":null,"abstract":"The lncRNA Second Chromosome Locus Associated with Prostate 1 (SChLAP1) was previously identified as a predictive biomarker and potential driver of aggressive prostate cancer. Recent work suggested that SChLAP1 may bind the SWI/SNF chromatin remodeling complex to promote prostate cancer metastasis, though the exact role of SWI/SNF recognition is debated. To date, there are no detailed biochemical studies of apo SChLAP1 or SChLAP1:protein complexes. Herein, we report the first secondary structure model of SChLAP1 using SHAPE-MaP in vitro, in cellulo, and ex cellulo (protein-free). Comparison of the ex cellulo and in cellulo data via ΔSHAPE identified putative protein binding regions within SChLAP1. In addition, phylogenetic analysis revealed that SChLAP1 is a primate-conserved lncRNA, with two exons significantly derived from primate-specific retroviral insertions. In particular, we characterized a complex structural landscape in a protein binding region at the 3'end of SChLAP1 derived from a THE1B-type retroviral insertion, suggesting a role for an exapted RNA structure in SChLAP1:protein recognition and prostate cancer progression. Lastly, pulldowns of SChLAP1 substructures enabled identification of previously unestablished SChLAP1-interacting proteins. This work lays the foundation for future efforts to selectively target and disrupt SChLAP1 structures and/or protein interfaces and to develop new therapeutic avenues in prostate cancer treatment.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144275865","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

Novel ADAR2 variants in children with seizures, intellectual disability and motor delay have reduced RNA editing. 患有癫痫、智力残疾和运动迟缓儿童的新型ADAR2变异减少了RNA编辑。

IF 4.2 3区生物学

RNA Pub Date : 2025-06-06 DOI: 10.1261/rna.080600.125

Qiupei Du, Anna Cherian, Raymond J Louie, Giulia Barcia, Natasha Rudy, Rima Nabbout, Eugenie Sarda, Maelle Charpie, Wesley G Patterson, Liam Peter Keegan, Mary A O'Connell

{"title":"Novel ADAR2 variants in children with seizures, intellectual disability and motor delay have reduced RNA editing.","authors":"Qiupei Du, Anna Cherian, Raymond J Louie, Giulia Barcia, Natasha Rudy, Rima Nabbout, Eugenie Sarda, Maelle Charpie, Wesley G Patterson, Liam Peter Keegan, Mary A O'Connell","doi":"10.1261/rna.080600.125","DOIUrl":"https://doi.org/10.1261/rna.080600.125","url":null,"abstract":"The ADARB1 gene encodes the ADAR2 RNA editing enzyme, which edits the GRIA2 transcript Q/R editing site with almost 100% efficiency in the nervous system. The edited GRIA2R transcript encodes the GLUA2 R subunit isoform of tetrameric AMPA receptors, which is essential to prevent seizures associated with aberrantly elevated AMPA receptor cation permeability. Rare biallelic variants in ADARB1 cause severe infant and childhood seizures and developmental delays in seven cases we previously described. Here, we report two new homozygous ADARB1 variants and study ADAR2 variant editing activities at the GRIA2 Q/R site and other editing sites in cell cultures. One new variant in the second dsRNA binding domain (dsRBD II) retains up to 60% editing activity, whereas another, in the deaminase domain, eliminates RNA editing activity. Reduced GRIA2 Q/R site editing increases AMPA receptor permeability by upregulating the expression of the GLUA2 Q isoform and reducing overall GLUA2 subunit levels, resulting in AMPA receptors that lack GLUA2 and are calcium-permeable. Since failure to edit the GRIA2 Q/R site leads to failure of intron 11 splicing, we also examined the effects of ADAR2 variants on the splicing of a mouse Gria2-based reporter and concluded that ADAR2 variants affect splicing only through their effects on RNA editing activity. To expand the number of variants in ADARB1, some variants reported in ClinVar have also been analysed by in silico methods to predict which are likely to be most deleterious and associated with seizures in patients.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144249386","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

Rho-dependent transcription termination: mechanisms and roles in bacterial fitness and adaptation to environmental changes. rho依赖性转录终止：细菌适应度和适应环境变化的机制和作用。

IF 4.2 3区生物学

RNA Pub Date : 2025-06-03 DOI: 10.1261/rna.080486.125

Thuy Duong Do, Nara Figueroa-Bossi, Johnathan C Black, Eric Eveno, Mildred Delaleau, Lionello Bossi, Marc Boudvillain

{"title":"Rho-dependent transcription termination: mechanisms and roles in bacterial fitness and adaptation to environmental changes.","authors":"Thuy Duong Do, Nara Figueroa-Bossi, Johnathan C Black, Eric Eveno, Mildred Delaleau, Lionello Bossi, Marc Boudvillain","doi":"10.1261/rna.080486.125","DOIUrl":"https://doi.org/10.1261/rna.080486.125","url":null,"abstract":"The bacterial transcription termination factor Rho is a rare example of an RNA helicase that functions as a ring-shaped ATP-powered six-subunit motor. Recent studies have linked Rho's distinctive architecture to a variety of regulatory mechanisms that shape the bacterial transcriptome at the global scale and control the transcription of individual genes in a context-dependent manner. In this review, we provide a comprehensive overview of the molecular mechanisms by which Rho triggers transcription termination. We examine the two prevailing modes of Rho's action: the \"catch-up\" mode, where Rho actively translocates along RNA and collides with the RNA polymerase to terminate transcription, and the \"stand-by\" mode where Rho, recruited by transcription elongation factor NusG, remains poised to engage RNA polymerase at specific sites or under particular constraints. Additionally, we highlight Rho's interplay with nucleoid-structuring protein H-NS in the regulation of bacterial chromatin transcription, as well as the crucial role played by Rho in the conditional regulation of specific genomic loci. We discuss how these mechanisms contribute to the fine-tuning of gene activity and integrate into broader regulatory networks, supporting bacterial adaptation to environmental changes and resilience to external challenges.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216795","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

Constructing an active chimeric pRNA ring with a stoichiometry of six and identifying 12 domains of the pRNA ring binding to the 12-subunit channel of phi29 DNA-packaging motor. 构建了一个化学计量为6的活性嵌合pRNA环，并鉴定了与phi29 DNA包装马达的12个亚基通道结合的12个pRNA环结构域。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-16 DOI: 10.1261/rna.080383.125

Margaret Bohmer, Daniel W Binzel, Wen Zhang, Peixuan Guo

{"title":"Constructing an active chimeric pRNA ring with a stoichiometry of six and identifying 12 domains of the pRNA ring binding to the 12-subunit channel of phi29 DNA-packaging motor.","authors":"Margaret Bohmer, Daniel W Binzel, Wen Zhang, Peixuan Guo","doi":"10.1261/rna.080383.125","DOIUrl":"10.1261/rna.080383.125","url":null,"abstract":"During the last stage of replication of double-stranded RNA or DNA viruses, their genome is packaged into a preassembled protein capsid. The bacterial virus phi29 dsDNA-packaging motor uses a noncoding packaging RNA (pRNA) molecule to gear its genomic DNA translocation. In this study, we constructed chimeric pRNAs by fusing the pRNA of bacterial virus M2 and that of phi29. The chimeric pRNAs can form dimers or trimers. The dimeric or trimeric pRNAs were active in the packaging of the phi29 dsDNA genome into the purified procapsid, which was subsequently converted into the infectious viruses, as proven by counting plaque-forming units (PFUs). These data show that the stoichiometry of the chimeric pRNAs on the motor is six subunits, a multiple of 2 and 3. Furthermore, AFM studies on pRNA fused to an RNA-triangle revealed hexamer formation. But how do the six identical RNAs anchor on the 12-subunit connector with the double stoichiometry? Structural analysis in combination with enzymatic and chemical probing data revealed that each native pRNA contributes two domains to bind to the 12-subunit DNA-packaging channel at three positively charged residues RKR, proving the formation of the hexameric ring. Resolving the hexamer versus pentamer debate clarifies the mechanism of dsDNA translocation in living organisms.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"836-849"},"PeriodicalIF":4.2,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12084888/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764950","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

tRNA pseudouridine synthase D (TruD) from Thermus thermophilus modifies U13 in tRNA^Asp, tRNA^Glu, and tRNA^Gln and U35 in tRNA^Tyr. 来自嗜热热菌的tRNA假尿嘧啶合成酶D （TruD）修饰tRNA Asp中的U13， tRNA Glu中的U13， tRNA Tyr中的tRNA Gln和U35。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-16 DOI: 10.1261/rna.080405.125

Ryota Yamagami, Kojiro Takahashi, Shogo Shingu, Miyu Namba, Kohsuke Kamizaki, Hiroyuki Hori

{"title":"tRNA pseudouridine synthase D (TruD) from Thermus thermophilus modifies U13 in tRNAAsp, tRNAGlu, and tRNAGln and U35 in tRNATyr.","authors":"Ryota Yamagami, Kojiro Takahashi, Shogo Shingu, Miyu Namba, Kohsuke Kamizaki, Hiroyuki Hori","doi":"10.1261/rna.080405.125","DOIUrl":"10.1261/rna.080405.125","url":null,"abstract":"Pseudouridine is a modified nucleoside found in various RNA species, including tRNA, rRNA, mRNA, and other noncoding RNAs. Pseudouridine is synthesized from uridine by pseudouridine synthases. While the landscape of pseudouridines in RNA has been extensively studied, much less is known about substrate RNA recognition mechanisms of pseudouridine synthases. Herein, we investigate the tRNA pseudouridine synthase D (TruD), which catalyzes the formation of pseudouridine at position 13 in tRNAAsp in Thermus thermophilus, a thermophilic eubacterium. To identify the tRNA substrates of TruD, we compared results of next-generation sequencing experiments combined with bisulfite probing of pseudouridine in tRNAs from both wild-type and a truD gene disruption mutant. Our data reveal that TruD recognizes tRNAAsp, tRNAGlu, and tRNAGln as substrate tRNAs. In addition, we discover that TruD modifies U35 in tRNATyr, which has previously been reported as a substrate of RluF in Escherichia coli These findings were validated through in vitro assays with recombinant TruD, which further demonstrated that TruD can act on other RNAs, including a CDC8 mRNA fragment, a known substrate of Pus7, the eukaryotic counterpart of TruD. Systematic mutational analysis of CDC8 transcripts reveals that TruD preferentially pseudouridylates the UNUAR sequence in tRNA substrates (N = any nucleotide, R = purine, U = target site). Finally, we identify over 600 mRNA fragments containing this recognition sequence in T. thermophilus ORFs and demonstrate the ability of TruD to act on these potential mRNA substrates. Our findings suggest the possibility that many other RNAs are modified by TruD in vivo.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"850-867"},"PeriodicalIF":4.2,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12084886/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143731506","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

Dissecting the stress granule RNA world: dynamics, strategies, and data. 剖析应激颗粒RNA世界：动力学、策略和数据。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-16 DOI: 10.1261/rna.080409.125

Giulia Biancon, Emma Busarello, Matthew Cheng, Stephanie Halene, Toma Tebaldi

引用次数: 0

Deciphering the influence of the [4Fe-4S] cluster of tRNA thiolation enzymes on tRNA binding. 解读tRNA巯基化酶[Fe-S]簇对tRNA结合的影响。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-16 DOI: 10.1261/rna.080292.124

Sylvain Gervason, Sambuddha Sen, Jean-Luc Ravanat, Sylvain Caillat, Djemel Hamdane, Béatrice Golinelli-Pimpaneau

{"title":"Deciphering the influence of the [4Fe-4S] cluster of tRNA thiolation enzymes on tRNA binding.","authors":"Sylvain Gervason, Sambuddha Sen, Jean-Luc Ravanat, Sylvain Caillat, Djemel Hamdane, Béatrice Golinelli-Pimpaneau","doi":"10.1261/rna.080292.124","DOIUrl":"10.1261/rna.080292.124","url":null,"abstract":"Iron-sulfur clusters [Fe-S] play crucial roles in diverse biological reactions, often serving as prosthetic groups for enzymes. Specifically, certain tRNA-modifying enzymes utilize these clusters to catalyze the thiolation of specific nucleosides. While the participation of [4Fe-4S] clusters in such catalytic processes is known, their potential influence on tRNA binding remains unexplored. In this study, we examine the impact of the cluster on the affinity for tRNA of TtuI from the archeon Methanococcus maripaludis, an enzyme responsible for the formation of 4-thiouridine at position 8 in tRNAs of archaea and bacteria, as well as Escherichia coli TtcA that catalyzes the biosynthesis of 2-thiocytidine at position 32 in bacterial tRNAs. For this purpose, we compare the change of fluorescence properties of judiciously located tryptophans upon tRNA binding between the apo-enzyme (lacking the cluster) and the holo-enzyme (incorporating a reconstituted cluster). Our results indicate that the presence of the [4Fe-4S] cluster does not alter the affinity of the thiolases for tRNA, thus ruling out any direct involvement of the cluster in tRNA binding and emphasizing the purely catalytic role of the [4Fe-4S] cluster in tRNA thiolation.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"735-742"},"PeriodicalIF":4.2,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12084879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143664467","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

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