IF 4.2 3区生物学

RNA Pub Date : 2025-05-28 DOI: 10.1261/rna.080566.125

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 Sontheimer, Ildar Gainetdinov

{"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 Sontheimer, Ildar Gainetdinov","doi":"10.1261/rna.080566.125","DOIUrl":"https://doi.org/10.1261/rna.080566.125","url":null,"abstract":"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.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Tissue-specific SEC31A alternative splicing is regulated by RBM47 and controls lipid transport. 组织特异性SEC31A选择性剪接受RBM47调控并控制脂质转运。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-28 DOI: 10.1261/rna.080572.125

Felix Ostwaldt, Sarah Ploessner, Benjamin Dimos-Roehl, Marco Preussner, Florian Heyd

{"title":"Tissue-specific SEC31A alternative splicing is regulated by RBM47 and controls lipid transport.","authors":"Felix Ostwaldt, Sarah Ploessner, Benjamin Dimos-Roehl, Marco Preussner, Florian Heyd","doi":"10.1261/rna.080572.125","DOIUrl":"https://doi.org/10.1261/rna.080572.125","url":null,"abstract":"The importance of coat protein complex II (COPII) for protein secretion has been known for decades. However, how large cargo like pro-collagens 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 tissues-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 trans-acting factors controlling tissue-specific alternative splicing.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Copy Number Determination of Sperm-Borne Small RNAs Implied in the Intergenerational Inheritance of Metabolic Syndromes. 代谢综合征代际遗传中精子携带小rna的拷贝数测定。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-28 DOI: 10.1261/rna.080480.125

Lisa Koenig, Victoria Guggenberger, Kristeli Eleftheriou, Zsuzsanna Pinter, Alessandro Marotto, Christoph R Kreutz, Mark Wossidlo, Virginie Marchand, Yuri Motorin, Matthias R Schaefer

{"title":"Copy Number Determination of Sperm-Borne Small RNAs Implied in the Intergenerational Inheritance of Metabolic Syndromes.","authors":"Lisa Koenig, Victoria Guggenberger, Kristeli Eleftheriou, Zsuzsanna Pinter, Alessandro Marotto, Christoph R Kreutz, Mark Wossidlo, Virginie Marchand, Yuri Motorin, Matthias R Schaefer","doi":"10.1261/rna.080480.125","DOIUrl":"https://doi.org/10.1261/rna.080480.125","url":null,"abstract":"Mammalian spermatocytes harbour small RNAs that are mostly degradation products of abundant non-coding RNAs, including ribosomal RNA-derived small RNAs (rsRNAs) and tRNA-derived RNAs (tDRs). Notably, tDRs have been implicated in inheriting paternally acquired traits in rodents. Direct experimental proof for this notion comes from manipulating fertilized murine oocytes through microinjection of small RNA preparations, resulting in metabolic changes measurable in the offspring. How these paternally transmitted small RNAs could function mechanistically in the developing zygote remains to be understood. Since nothing is known about how many small RNAs are required for functional impact, we aimed to determine the copy numbers of specific small RNAs contained in a single spermatocyte. Using hybridization-based methods that avoid amplification-induced biases, we estimated average copy numbers for specific tDRs and rsRNAs per murine spermatocyte. While the measured numbers allow an approximation of how many rRNA- and tRNA-derived RNAs enter a murine oocyte during fertilization, the magnitude of these numbers underscores the need for remaining cautious when interpreting the effects of non-physiological copy numbers of small RNAs that were used to manipulate a biological system.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144174767","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

OpenASO: RNA Rescue - designing splice-modulating antisense oligonucleotides through community science. RNA救援——通过社区科学设计剪接调节的反义寡核苷酸。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-27 DOI: 10.1261/rna.080288.124

Victor Tse, Martin Guiterrez, Jill Townley, Jonathan Romano, Jennifer Pearl, Guillermo Chacaltana, Eterna Players, Rhiju Das, Jeremy Sanford, Michael Stone

{"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 Sanford, Michael Stone","doi":"10.1261/rna.080288.124","DOIUrl":"10.1261/rna.080288.124","url":null,"abstract":"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 F8 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 F8 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 suggests 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.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data. 评估从结构数据中识别rna结合蛋白足迹的新型计算方法。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-21 DOI: 10.1261/rna.080215.124

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 Yeo

{"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 Yeo","doi":"10.1261/rna.080215.124","DOIUrl":"https://doi.org/10.1261/rna.080215.124","url":null,"abstract":"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 datasets that map distinct, yet intertwined post-transcriptional 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 datasets, 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 datasets 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 towards closing other critical data-analysis gaps.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Implications for OLE RNA as a natural integral membrane RNA. OLE RNA作为天然完整膜RNA的意义。

IF 4.2 3区生物学

RNA Pub Date : 2025-05-20 DOI: 10.1261/rna.080489.125

Seth Eugene Lyon, Ronald R Breaker

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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