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

A general RNA-templated RNA extension activity of E. coli RNA polymerase. 大肠杆菌RNA聚合酶的一般RNA模板RNA延伸活性。

IF 4.2 3区生物学

RNA Pub Date : 2025-04-16 DOI: 10.1261/rna.080238.124

Drew Galls, Andreas U Mueller, Emily Greenwald, Andrew Z Fire

{"title":"A general RNA-templated RNA extension activity of E. coli RNA polymerase.","authors":"Drew Galls, Andreas U Mueller, Emily Greenwald, Andrew Z Fire","doi":"10.1261/rna.080238.124","DOIUrl":"10.1261/rna.080238.124","url":null,"abstract":"Multisubunit \"DNA-dependent\" RNA polymerases (RNAPs) have noncanonical RNA-directed RNA synthesis activity; this allows the synthesis of complementary RNA from RNA templates. Such noncanonical RNAP activities are biologically significant, serving RNA pathogens such as hepatitis delta virus (HDV) and contributing to cellular gene regulation. Despite the broad biological implications of these processes, our understanding of the underlying RNAP mechanisms remains incomplete. Using Escherichia coli RNAP, a multisubunit RNAP, as a model, we describe here the general RNA-templated RNA extension activity of that enzyme. Our data argue that the 3' end of an added RNA template can fold back and pair with upstream bases in the template, creating an intramolecular primer:template duplex as short as 1-2 base pairs. The RNAP then extends this intramolecular duplex, incorporating nucleotides complementary to the template. RNA-templated RNA extension occurred in minutes and did not appear to be suppressed by the presence of a promoter-containing DNA template. Excepting oligonucleotides implicitly designed to prevent any possibility of 3' end self-priming, every RNA template we tested could be extended by the enzyme, highlighting the general nature of this reaction. These data define a general activity of a cellular RNAP. Unrestricted, this activity could contribute to the emergence and replication of RNA-based agents such as HDV and viroids; if highly regulated, the activity could limit these same elements.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"663-678"},"PeriodicalIF":4.2,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12001968/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143450111","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

Circuit logic: interdependent RNA modifications shape mRNA and noncoding RNA structure and function. 电路逻辑：相互依赖的RNA修饰形成mRNA和非编码RNA的结构和功能。

IF 4.2 3区生物学

RNA Pub Date : 2025-04-16 DOI: 10.1261/rna.080421.125

Jennifer Porat

{"title":"Circuit logic: interdependent RNA modifications shape mRNA and noncoding RNA structure and function.","authors":"Jennifer Porat","doi":"10.1261/rna.080421.125","DOIUrl":"10.1261/rna.080421.125","url":null,"abstract":"Continued advances in high-throughput detection of posttranscriptional RNA modifications have enabled large-scale, mechanistic studies into the importance of RNA modifications in regulating the structure, function, and stability of coding and noncoding RNAs. More recently, this has expanded beyond investigations of independent single modifications, revealing the breadth of modification complexities in single transcripts and the biogenesis pathways involved that lead to coordinately modified RNA species. This has resulted in the concept of modification circuits, where one modification can promote or inhibit the subsequent installation of other modifications, or when modifications are coordinated across different RNA species. These circuits play important roles in the biogenesis of multistepped posttranscriptional modifications, modulate ribonucleoprotein complex formation and conformational switches, and mediate codon-biased translation through the coordination of mRNA and tRNA modifications. Here, I review evidence of complex modification circuits in mRNA and noncoding RNA and highlight open questions concerning the molecular mechanisms giving rise to modification circuits and their importance in the context of RNA processing and maturation.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"613-622"},"PeriodicalIF":4.2,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12001972/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143568082","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

DIS3L, cytoplasmic exosome catalytic subunit, is essential for development but not cell viability in mice. 细胞质外泌体催化亚基DIS3L是小鼠发育所必需的，但不是细胞活力。

IF 4.2 3区生物学

RNA Pub Date : 2025-04-16 DOI: 10.1261/rna.080350.124

Michał Brouze, Marcin Szpila, Areta Czerwińska, Wiktor Antczak, Seweryn Mroczek, Tomasz M Kuliński, Anna Hojka-Osińska, Dominik Cysewski, Olga Gewartowska, Dorota Adamska, Jakub Gruchota, Ewa Borsuk, Andrzej Dziembowski

{"title":"DIS3L, cytoplasmic exosome catalytic subunit, is essential for development but not cell viability in mice.","authors":"Michał Brouze, Marcin Szpila, Areta Czerwińska, Wiktor Antczak, Seweryn Mroczek, Tomasz M Kuliński, Anna Hojka-Osińska, Dominik Cysewski, Olga Gewartowska, Dorota Adamska, Jakub Gruchota, Ewa Borsuk, Andrzej Dziembowski","doi":"10.1261/rna.080350.124","DOIUrl":"10.1261/rna.080350.124","url":null,"abstract":"Among numerous enzymes involved in RNA decay, processive exoribonucleases are the most prominent group responsible for the degradation of entire RNA molecules. The role of mammalian cytoplasmic 3'-5' exonuclease DIS3L at the organismal level remained unknown. Herein, we established knock-in and knockout (KO) mouse models to study DIS3L functions in mice. DIS3L in mice is indeed a subunit of the cytoplasmic exosome complex, the disruption of which leads to severe embryo degeneration and death in mice soon after implantation. These changes could not be prevented by supplementing extraembryonic tissue with functional DIS3L through the construction of chimeric embryos. Preimplantation Dis3l -/- embryos were unaffected in their morphology and ability to produce functional embryonic stem (ES) cells, showing that DIS3L is not essential for cell viability. There were also no major changes at the transcriptome level for both ES cells and blastocysts, as revealed by RNA-seq experiments. Notably, however, Dis3l KO led to inhibition of global protein synthesis. These results point to the essential role of DIS3L in mRNA metabolism, which is crucial for proper protein synthesis during embryo development.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"646-662"},"PeriodicalIF":4.2,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12001971/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143371194","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

Different RNA recognition by ProQ and FinO depends on the sequence surrounding intrinsic terminator hairpins. ProQ和FinO识别RNA的不同取决于内在终止子发夹周围的序列。

IF 4.2 3区生物学

RNA Pub Date : 2025-04-16 DOI: 10.1261/rna.080206.124

Maria D Mamońska, Maciej M Basczok, Ewa M Stein, Julia Kurzawska, Mikołaj Olejniczak

引用次数: 0

Prevention of ribozyme catalysis through cDNA synthesis enables accurate RT-qPCR measurements of context-dependent ribozyme activity. 通过cDNA合成防止核酶催化使RT-qPCR准确测量上下文依赖的核酶活性。

IF 4.2 3区生物学

RNA Pub Date : 2025-04-16 DOI: 10.1261/rna.080243.124

Nina Y Alperovich, Olga B Vasilyeva, Samuel W Schaffter

{"title":"Prevention of ribozyme catalysis through cDNA synthesis enables accurate RT-qPCR measurements of context-dependent ribozyme activity.","authors":"Nina Y Alperovich, Olga B Vasilyeva, Samuel W Schaffter","doi":"10.1261/rna.080243.124","DOIUrl":"10.1261/rna.080243.124","url":null,"abstract":"Self-cleaving ribozymes are important tools in synthetic biology, biomanufacturing, and nucleic acid therapeutics. These broad applications deploy ribozymes in many genetic and environmental contexts, which can influence activity. Thus, accurate measurements of ribozyme activity across diverse contexts are crucial for validating new ribozyme sequences and ribozyme-based biotechnologies. Ribozyme activity measurements that rely on RNA extraction, such as RNA sequencing or reverse transcription-quantitative polymerase chain reaction (RT-qPCR), are generalizable to most applications and have high sensitivity. However, the activity measurement is indirect, taking place after RNA is isolated from the environment of interest and copied to DNA. Thus, these measurements may not accurately reflect the activity in the original context. Here, we develop and validate an RT-qPCR method for measuring context-dependent ribozyme activity using a set of self-cleaving RNAs for which context-dependent ribozyme cleavage is known in vitro. We find that RNA extraction and reverse transcription conditions can induce substantial ribozyme cleavage, resulting in incorrect activity measurements with RT-qPCR. To restore the accuracy of the RT-qPCR measurements, we introduce an oligonucleotide into the sample preparation workflow that inhibits ribozyme activity. We then apply our method to measure ribozyme cleavage of RNAs produced in Escherichia coli These results have broad implications for many ribozyme measurements and technologies.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"633-645"},"PeriodicalIF":4.2,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12001966/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143573933","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

The PUF RNA-binding protein, FBF-2, maintains stem cells without binding to RNA. PUF RNA结合蛋白FBF-2在不与RNA结合的情况下维持干细胞。

IF 4.2 3区生物学

RNA Pub Date : 2025-04-16 DOI: 10.1261/rna.080307.124

Brian H Carrick, Sarah L Crittenden, MaryGrace Linsley, Stephany J Costa Dos Santos, Marvin Wickens, Judith Kimble

引用次数: 0

Positioning of sperm tail longitudinal columns depends on NSUN7, an RNA-binding protein destabilizing elongated spermatid transcripts. 精子尾部纵向柱的定位依赖于Nsun7，一种破坏长形精子转录本稳定的RNA结合蛋白。

IF 4.2 3区生物学

RNA Pub Date : 2025-04-16 DOI: 10.1261/rna.080320.124

Ekaterina A Guseva, Olga A Averina, Sergey V Isaev, Philipp I Pletnev, Elizaveta E Bragina, Oleg A Permyakov, Vitaly S Buev, Anastasia V Priymak, Mariia A Emelianova, Lizaveta Pshanichnaya, Evgeny A Romanov, Svetlana E Novikova, Kirill S Petriukov, Anna Ya Golovina, Olga O Grigorieva, Vasily N Manskikh, Diana S Korshunova, Yuliya Yu Silaeva, Alexey V Deykin, Maria P Rubtsova, Victor G Zgoda, Alexander M Mazur, Egor B Prokhortchouk, Olga A Dontsova, Petr V Sergiev

{"title":"Positioning of sperm tail longitudinal columns depends on NSUN7, an RNA-binding protein destabilizing elongated spermatid transcripts.","authors":"Ekaterina A Guseva, Olga A Averina, Sergey V Isaev, Philipp I Pletnev, Elizaveta E Bragina, Oleg A Permyakov, Vitaly S Buev, Anastasia V Priymak, Mariia A Emelianova, Lizaveta Pshanichnaya, Evgeny A Romanov, Svetlana E Novikova, Kirill S Petriukov, Anna Ya Golovina, Olga O Grigorieva, Vasily N Manskikh, Diana S Korshunova, Yuliya Yu Silaeva, Alexey V Deykin, Maria P Rubtsova, Victor G Zgoda, Alexander M Mazur, Egor B Prokhortchouk, Olga A Dontsova, Petr V Sergiev","doi":"10.1261/rna.080320.124","DOIUrl":"10.1261/rna.080320.124","url":null,"abstract":"Spermatozoid's flagella assemble in transcriptionally silent spermatids and thus depend on posttranscriptional regulation of gene expression. Mutations in Nsun7 gene are known to cause male infertility in human and mice. We identified m5C-specific NSUN7 RNA methyltransferase as a protein present in elongated spermatids and interacting with RNAs specific for this type of spermatozoid's precursor cells. Inactivation of the Nsun7 gene in mice leads to upregulation of its RNA interactors, thus indicating that NSUN7 downregulates a set of RNAs in the elongated spermatids. A physiologic consequence of Nsun7 gene knockout is male infertility, which is mechanistically explained by the observed mispositioning of longitudinal columns relative to the axonemal microtubular doublets leading to a motility defect.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"709-723"},"PeriodicalIF":4.2,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12001970/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143543373","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

The PAZ domain of Aedes aegypti Dicer 2 is critical for accurate and high-fidelity size determination of virus-derived small interfering RNAs. 埃及伊蚊Dicer 2的PAZ结构域对于准确和高保真地确定病毒衍生的小干扰rna的大小至关重要。

IF 4.2 3区生物学

RNA Pub Date : 2025-04-16 DOI: 10.1261/rna.080149.124

Melinda Reuter, Rhys H Parry, Melanie McFarlane, Rommel J Gestuveo, Rozeena Arif, Alexander A Khromykh, Benjamin Brennan, Margus Varjak, Alfredo Castello, Lars Redecke, Esther Schnettler, Alain Kohl

{"title":"The PAZ domain of Aedes aegypti Dicer 2 is critical for accurate and high-fidelity size determination of virus-derived small interfering RNAs.","authors":"Melinda Reuter, Rhys H Parry, Melanie McFarlane, Rommel J Gestuveo, Rozeena Arif, Alexander A Khromykh, Benjamin Brennan, Margus Varjak, Alfredo Castello, Lars Redecke, Esther Schnettler, Alain Kohl","doi":"10.1261/rna.080149.124","DOIUrl":"10.1261/rna.080149.124","url":null,"abstract":"The exogenous siRNA (exo-siRNA) pathway is a critical RNA interference response involved in controlling arbovirus replication in mosquito cells. It is initiated by the detection of viral long double-stranded RNA (dsRNA) by the RNase III enzyme Dicer 2 (Dcr2), which is processed into predominantly 21 nt virus-derived small interfering RNAs (vsiRNAs) that are taken up by the Argonaute 2 (Ago2) protein to target viral single-stranded RNAs. The detailed understanding of Dicer structure, function and domains owes much to studies outside the context of viral infection and studies in model organisms, and as such how Dcr2 domains contribute to detecting viral dsRNA to mount antiviral responses in infected mosquito cells remains less well understood. Here, we used a Dcr2 reconstitution system in Aedes aegypti derived Dcr2 knockout (KO) cells to assess the contribution of the PIWI-Argonaute-Zwille (PAZ) domain to induction of the exo-siRNA pathway following infection with Semliki Forest virus (SFV; Togaviridae, Alphavirus). Amino acids critical for PAZ activity were identified, and loss of PAZ function affected the production of 21 nt vsiRNAs-with enrichment of 22 nt SFV-derived small RNAs observed-and silencing activity. This study establishes PAZ domain's functional contribution to Dcr2 processing of viral dsRNA to 21 nt vsiRNAs.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"679-691"},"PeriodicalIF":4.2,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12001973/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143415090","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

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 : 2025-04-15 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":"https://doi.org/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 non-canonical 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":""},"PeriodicalIF":4.2,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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