RNA最新文献 - Book学术

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

The m⁶A-binding protein YTHDF3 modulates the cardiac response to stress. m6A结合蛋白YTHDF3调节心脏对应激的反应。

IF 4.2 3区生物学

RNA Pub Date : 2025-06-16 DOI: 10.1261/rna.080442.125

Charles P Rabolli, Anindhya S Das, Volha A Golubeva, Jop H van Berlo, Federica Accornero

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

SMDesigner: a program to design sequence mutations to assess RNA structure. SMDesigner：设计序列突变以评估RNA结构的程序。

IF 4.2 3区生物学

RNA Pub Date : 2025-06-16 DOI: 10.1261/rna.080267.124

Lijuan Hou, Meryem Raies, Kadidia Dite Selly N'Diaye, Jonathan Perreault

{"title":"SMDesigner: a program to design sequence mutations to assess RNA structure.","authors":"Lijuan Hou, Meryem Raies, Kadidia Dite Selly N'Diaye, Jonathan Perreault","doi":"10.1261/rna.080267.124","DOIUrl":"10.1261/rna.080267.124","url":null,"abstract":"The structure of RNA is critical to its function. The advancement of structure prediction algorithms and deep sequencing technology has led to the discovery of numerous conserved RNA structures. However, functional analysis of these sequences is lagging behind the rate of novel RNAs' predictions. Traditionally, mutations are designed to alter the structure of RNA and tested individually to assess function. We developed a program for the large-scale characterization of the structure/function relationship in multiple RNAs. Structure Mutation Designer (SMDesigner) automatically selects both disruptive and compensatory mutations according to inputted structural information. As proof of concept, we designed mutations for riboswitches with SMDesigner and experimentally assessed six of these riboswitches and their mutant sequences using an in-line probing assay to verify the effects on their structure and function. The in-line probing results show expected changes in five of six sequence structure patterns, confirming that SMDesigner can be useful to explore RNA structure and subsequent function. SMDesigner can be download at: https://github.com/lilihou/SMDesigner_0.1/tree/main/dist.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"874-884"},"PeriodicalIF":4.2,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170191/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144024136","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

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 : 2025-06-16 DOI: 10.1261/rna.080444.125

Agata Jacewicz, Masad J Damha, Stewart Shuman

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 : 2025-06-16 DOI: 10.1261/rna.080176.124

Alyssa A Pratt, David A Hendrix

{"title":"Unraveling unbreakable hairpins: characterizing RNA secondary structures that are persistent after dinucleotide shuffling.","authors":"Alyssa A Pratt, David A Hendrix","doi":"10.1261/rna.080176.124","DOIUrl":"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.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"885-895"},"PeriodicalIF":4.2,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170181/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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 : 2025-06-16 DOI: 10.1261/rna.080557.125

Sarah Costantino, Francesco Paneni

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 : 2025-06-16 DOI: 10.1261/rna.080291.124

Bassem Shebl, Anna Pavlova, Preston Kellenberger, Dongmei Yu, Drew E 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 E Menke, James C Gumbart, Peter V Cornish","doi":"10.1261/rna.080291.124","DOIUrl":"10.1261/rna.080291.124","url":null,"abstract":"Proper codon/anticodon 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 hyperrotated 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":"973-987"},"PeriodicalIF":4.2,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170187/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Crystallographic and cryoEM analyses reveal SARS-CoV-2 SL5 is a mobile T-shaped four-way junction with deep pockets. 晶体学和低温电镜分析显示，SARS-CoV-2 SL5是一个具有深口袋的移动t形四向结。

IF 4.2 3区生物学

RNA Pub Date : 2025-06-16 DOI: 10.1261/rna.080413.125

Christopher P Jones, Adrian R Ferré-D'Amaré

{"title":"Crystallographic and cryoEM analyses reveal SARS-CoV-2 SL5 is a mobile T-shaped four-way junction with deep pockets.","authors":"Christopher P Jones, Adrian R Ferré-D'Amaré","doi":"10.1261/rna.080413.125","DOIUrl":"10.1261/rna.080413.125","url":null,"abstract":"Stem-loop 5 (SL5) is a structural element that is conserved across coronavirus genomic RNAs. It spans the start codon from which the long ORF1 is translated in full-length viral RNA. Phylogenetic conservation indicates that it is comprised of four paired elements, but the specific 3D arrangement of these helices has remained unknown. Now, we have solved the crystal structure of SL5 from SARS-CoV-2 at 3.3 Å resolution, finding that the RNA adopts a T-shaped four-way junction fold in which two coaxial stacks of two helices each pack orthogonally. This arrangement results in deep pockets at the helical junction, where cations bind. Except for limited interactions in this region, the structure is remarkable for the paucity of tertiary contacts. We confirmed the stability of this fold in solution by FRET and carried out single-particle cryogenic-sample electron microscopy (cryoEM). The resulting ∼5 Å resolution cryoEM map, and 3D variability analysis, suggest conformational flexibility at the junction. In vitro translation of structure-guided mutants demonstrated that SL5 inhibits protein synthesis. Thus, it is likely that SL5 recruits additional factors in vivo. This, and its characteristic clefts at the four-way junction, make SL5 an attractive target for the discovery of RNA-targeted antiviral small molecules.","PeriodicalId":21401,"journal":{"name":"RNA","volume":"31 7","pages":"949-960"},"PeriodicalIF":4.2,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12170182/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144317846","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