IF 4.2 3区生物学

RNA Pub Date : 2025-07-16 DOI: 10.1261/rna.080480.125

Lisa König, 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 König, 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":"10.1261/rna.080480.125","url":null,"abstract":"Mammalian spermatocytes harbor small RNAs that are mostly degradation products of abundant noncoding 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 nonphysiological copy numbers of small RNAs that were used to manipulate a biological system.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1041-1052"},"PeriodicalIF":4.2,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12265938/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

RNA G-quadruplex structure targeting and imaging: recent advances and future directions. RNA g -四重体结构靶向与成像：最新进展及未来发展方向。

IF 4.2 3区生物学

RNA Pub Date : 2025-07-16 DOI: 10.1261/rna.080587.125

Tian-Ying Wu, Hill Lam Lau, Rachelle J Santoso, Chun Kit Kwok

{"title":"RNA G-quadruplex structure targeting and imaging: recent advances and future directions.","authors":"Tian-Ying Wu, Hill Lam Lau, Rachelle J Santoso, Chun Kit Kwok","doi":"10.1261/rna.080587.125","DOIUrl":"10.1261/rna.080587.125","url":null,"abstract":"RNA guanine (G)-quadruplexes (rG4s) are noncanonical structures formed by G-rich RNA sequences and have been demonstrated to play critical roles in various biological events, including translation, transcription, RNA processing, and other cellular functions. In contrast to DNA G-quadruplexes (dG4s), research on rG4s has been relatively limited until recently. Recent advances in targeting and imaging of rG4s have opened new avenues for understanding their functional significance and therapeutic potential. In this review, we summarize the innovative platforms and tools being developed to target rG4s, highlight the novel and important imaging probes that have been generated and applied for rG4 structure visualization in different biological contexts, and discuss the challenges and perspectives for further advancing these technologies and toolsets to facilitate rG4 targeting and imaging with greater precision and resolution across the Tree of Life. These scientific developments and breakthroughs will enable the discovery of new biological insights regarding rG4s and help decipher their molecular mechanisms and implications for health and disease.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1053-1080"},"PeriodicalIF":4.2,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12265945/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144235031","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

Comparative analysis of convergent and divergent T7 RNA polymerase promoters for the synthesis of dsRNA in vivo and in vitro. 趋同型和发散型T7 RNA聚合酶启动子在体内和体外合成dsRNA的比较分析

IF 4.2 3区生物学

RNA Pub Date : 2025-07-11 DOI: 10.1261/rna.080556.125

Sebastian J Ross, John Ray, Peter M Kilby, Mark J Dickman

{"title":"Comparative analysis of convergent and divergent T7 RNA polymerase promoters for the synthesis of dsRNA in vivo and in vitro.","authors":"Sebastian J Ross, John Ray, Peter M Kilby, Mark J Dickman","doi":"10.1261/rna.080556.125","DOIUrl":"https://doi.org/10.1261/rna.080556.125","url":null,"abstract":"Double-stranded RNA plays a key role in various biological processes. The discovery of RNA interference, a gene-silencing mechanism, revolutionised the study of gene function. dsRNA has since been used in novel therapeutics and as an agricultural biocontrol alternative to chemical pesticides. Microbial production typically involves expression systems with convergent T7 promoters. However, convergent transcription from DNA-dependent RNA polymerases can lead to transcriptional interference. In this study, we designed multiple plasmid DNA constructs to investigate the effect of convergent and divergent T7 RNA polymerase production of dsRNA via in vitro transcription and in vivo in E. coli, prior to dsRNA yield quantification and analysis of product quality. We demonstrate that higher yields of larger dsRNA are typically obtained using convergent promoters during in vivo production. A typical fold increase of 2.1 was obtained for dsRNA > 400 bp. However, production of smaller dsRNA (< 250 bp) by divergent promoters resulted in increased yields (2.2 fold). Furthermore, our data demonstrates that in vitro transcription production of dsRNA using divergent T7 promoters results in significantly higher yields of dsRNA, with a maximum fold increase of 6.46. Finally, independent of size, we demonstrate that dsRNA synthesised from DNA templates with multiple transcriptional terminators, compared to run-off transcription, improved the quality and purity of dsRNA due to decreased formation of dsRNA multimers or aggregates. This study highlights alternative optimal strategies for the production of a wide range of different sized dsRNA both in vitro and in microbial systems.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144619952","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

Pseudouridine reprogramming in the human T cell epitranscriptome: from primary to immortalized states. 假尿嘧啶重编程在人T细胞上转录组：从初级到永生化状态。

IF 4.2 3区生物学

RNA Pub Date : 2025-07-09 DOI: 10.1261/rna.080633.125

Oleksandra Fanari, Dylan Bloch, Yuchen Qiu, Michele Meseonznik, Dinara Boyko, Amr Makhamreh, Meni Wanunu, Sara H Rouhanifard

{"title":"Pseudouridine reprogramming in the human T cell epitranscriptome: from primary to immortalized states.","authors":"Oleksandra Fanari, Dylan Bloch, Yuchen Qiu, Michele Meseonznik, Dinara Boyko, Amr Makhamreh, Meni Wanunu, Sara H Rouhanifard","doi":"10.1261/rna.080633.125","DOIUrl":"https://doi.org/10.1261/rna.080633.125","url":null,"abstract":"Immortalized cell lines are commonly used as proxies for primary cells in human biology research. For example, Jurkat leukemic T cells fundamentally contributed to uncovering T cell signaling, activation, and immune responses. However, the immortalization process can alter key cellular properties, and researchers widely believe this process could significantly change RNA modification machinery and modification sites. In this study, we focus on pseudouridine (ψ), one of the most abundant mRNA modifications, and compare ψ profiles in mRNA from primary and immortalized T cells using direct RNA sequencing (DRS). Surprisingly, 87% of ψ-sites were shared between the two cell types, primarily in transcripts encoding proteins involved in essential cellular processes, including RNA-modification regulation. Furthermore, the analysis of the 13% of sites unique to each cell type reveals that Jurkat cells contained transcripts linked to immune activation and oncogenesis, while primary T cells contained transcripts associated with calcium signaling and intracellular trafficking. We provide a list of these genes, which should be considered when using immortalized cells to study RNA modifications in immunology contexts. Most differences were driven by whether the mRNA was present or absent in the immortalized or primary cell type. Interestingly, RNA-modification enzyme expression levels were highly conserved in both cell types. This suggests that site-specific differences in ψ levels arise from regulatory processes acting in trans rather than differences in modification enzyme levels.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144601385","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

M⁶A methylation inhibits recruitment of the Dand5 3'UTR to the left-right determinant Bicc1. M6A甲基化抑制Dand5 3'UTR向左右行列式Bicc1的募集。

IF 4.2 3区生物学

RNA Pub Date : 2025-07-09 DOI: 10.1261/rna.080526.125

Benjamin Rothé, Mateusz Mendel, Simon Fortier, Daniel B Constam

引用次数: 0

Proteins that recognize unique features of U7 snRNA and may substitute for Gemin5 in the assembly of U7-specific Sm ring. 识别U7 snRNA独特特征并可能替代Gemin5组装U7特异性Sm环的蛋白质。

IF 4.2 3区生物学

RNA Pub Date : 2025-07-01 DOI: 10.1261/rna.080491.125

Xiao-Cui Yang, Zbigniew Dominski

{"title":"Proteins that recognize unique features of U7 snRNA and may substitute for Gemin5 in the assembly of U7-specific Sm ring.","authors":"Xiao-Cui Yang, Zbigniew Dominski","doi":"10.1261/rna.080491.125","DOIUrl":"https://doi.org/10.1261/rna.080491.125","url":null,"abstract":"U7 snRNA is a 60-nucleotide component of U7 snRNP, a multi-subunit endonuclease that cleaves precursors of metazoan replication-dependent histone mRNAs at the 3' end, hence generating mature histone mRNAs. The Sm site in U7 snRNA differs from the Sm site in spliceosomal snRNAs and promotes the assembly of a unique Sm ring of the U7 snRNP containing Lsm10 and Lsm11 instead of the spliceosomal SmD1 and SmD2 proteins. The assembly of the spliceosomal Sm ring depends on the SMN complex, with one of its nine subunits, Gemin5, recognizing the spliceosomal-type Sm site. While the assembly of the U7-specific Sm ring also requires the SMN complex, the identity of the protein that recognizes the unusual Sm site of U7 snRNA resulting in the incorporation of Lsm10 and Lsm11 has not been determined. Here, we looked for proteins that interact with U7 snRNA. Among U7 snRNA binders, mass spectrometry identified Polypyrimidine Tract-Binding Protein 1 (PTBP1) and Insulin-Like Growth Factor 2 mRNA-Binding Protein 3 (IGF2BP3). The binding of these two proteins to U7 snRNA depends on its unique Sm site and on the upstream CUCUUU motif that base pairs with histone pre-mRNAs and defines substrate specificity of U7 snRNP. Among proteins bound to U7 snRNA, we also identified hnRNP A1. We show that hnRNP A1 interacts with the SMN protein of the SMN complex, a likely prerequisite for the protein that substitutes for Gemin5 in the assembly of U7-specific Sm ring. Finally, our studies also suggest a mechanism that explains why Gemin5 does not bind the Sm site of U7 snRNA.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144542100","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

Crystal structures of free-state tRNALeu reveal conformational flexibility of Type-II tRNAs. 自由态tRNALeu的晶体结构揭示了ii型trna的构象灵活性。

IF 4.2 3区生物学

RNA Pub Date : 2025-06-25 DOI: 10.1261/rna.080596.125

Gyuhyeok Cho, Jaehun Yoo, Kiroo Shin, Jangmin Lee, Jihyo Lim, Jungwook Kim

引用次数: 0

RNA aptamers as tools for the purification and analysis of in vivo assembled Ribonucleoproteins. RNA适体作为纯化和分析体内组装核糖核蛋白的工具。

IF 4.2 3区生物学

RNA Pub Date : 2025-06-20 DOI: 10.1261/rna.080460.125

Daniel G Rocca, Ute Kothe

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 : 2025-06-16 DOI: 10.1261/rna.080338.124

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

引用次数: 0

RNase L produces tRNA-derived RNAs that contribute to translation inhibition. RNase L产生trna来源的rna，有助于翻译抑制。

IF 4.2 3区生物学

RNA Pub Date : 2025-06-16 DOI: 10.1261/rna.080419.125

Yoshika Takenaka, Asuka Yamada, Yoshihisa Tomioka, Yasutoshi Akiyama, Pavel Ivanov

{"title":"RNase L produces tRNA-derived RNAs that contribute to translation inhibition.","authors":"Yoshika Takenaka, Asuka Yamada, Yoshihisa Tomioka, Yasutoshi Akiyama, Pavel Ivanov","doi":"10.1261/rna.080419.125","DOIUrl":"10.1261/rna.080419.125","url":null,"abstract":"Ribonuclease L (RNase L) is an RNase which is activated by viral double-stranded RNAs (dsRNAs). RNase L cleaves not only viral RNAs but also host RNAs, including mRNAs and tRNAs, which contributes to innate immune defense against viruses. While it has been reported that RNase L-mediated bulk mRNA cleavage induces rapid translation repression independently of the integrated stress response, the significance of RNase L-mediated tRNA cleavage remains largely unknown. Here we show that RNase L cleaves various tRNA species in the anticodon loops, generating transfer RNA-derived RNAs (tDRs) similar to tRNA-derived stress-induced RNAs (tiRNAs) that are generated by a stress-responsive RNase angiogenin (ANG). Three tRNA species (tRNALeu, tRNASeC , and tRNASer) were cleaved within the variable loops as well as in the anticodon loops by RNase L, generating noncanonical tDRs. As RNase L-induced 5'-tDRAla/Cys were similar in length to 5'-tiRNAAla/Cys that possess a translation inhibitory effect, we examined whether RNase L-induced 5'-tDRAla also inhibited translation. In vitro translation analysis showed that RNase L-induced 5'-tDRAla significantly inhibits mRNA translation like 5'-tiRNAAla, suggesting that the production of 5'-tDRAla may be involved in the mechanism of RNase L-mediated stress response during viral infection. Our data shed new light on the potential roles of tDRs in innate immunity against viral infection.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"961-972"},"PeriodicalIF":4.2,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170186/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144054291","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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