RNA最新文献_第2页

New reporters for monitoring cellular NMD.

IF 4.2 3区生物学

RNA Pub Date : 2025-03-18 DOI: 10.1261/rna.080272.124

Hanna Alalam, Monika Šafhauzer, Per Sunnerhagen

{"title":"New reporters for monitoring cellular NMD.","authors":"Hanna Alalam, Monika Šafhauzer, Per Sunnerhagen","doi":"10.1261/rna.080272.124","DOIUrl":"10.1261/rna.080272.124","url":null,"abstract":"Nonsense-mediated decay (NMD) is a eukaryotic surveillance pathway that controls degradation of cytoplasmic transcripts with aberrant features. NMD-controlled RNA degradation acts to regulate a large fraction of the mRNA population. It has been implicated in cellular responses to infections and environmental stress, as well as in deregulation of tumor-promoting genes. NMD is executed by a set of three core factors conserved in evolution, UPF1-3, as well as additional influencing proteins such as kinases. Monitoring NMD activity is challenging due to the difficulties in quantitating RNA decay rates in vivo, and consequently, it has also been problematic to identify new factors influencing NMD. Here, we developed a genetic selection system in yeast to capture new components affecting NMD status. The reporter constructs link NMD target sequences with nutrient-selectable genetic markers. By crossing these reporters into a genome-wide library of deletion mutants and quantitating colony growth on a selective medium, we robustly detect previously known NMD components in a high-throughput fashion. In addition, we identify novel mutations influencing NMD status and implicate ribosome recycling as important for NMD. By using our constructed combinations of promoters, NMD target sequences, and selectable markers, the system can also efficiently detect mutations with a minor effect, or in special environments. Furthermore, it can be used to explore how NMD acts on targets of different structures.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"600-611"},"PeriodicalIF":4.2,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912909/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143067906","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

Terminal nucleotidyltransferase Tent2 microRNA A-tailing enzyme regulates excitatory/inhibitory balance in the hippocampus. 末端核苷酸转移酶Tent2 microRNA A尾酶调节海马的兴奋/抑制平衡

IF 4.2 3区生物学

RNA Pub Date : 2025-03-18 DOI: 10.1261/rna.080240.124

Patrycja Wardaszka-Pianka, Bozena Kuzniewska, Natalia Guminska, Anna Hojka-Osinska, Monika Puchalska, Jacek Milek, Aleksandra Stawikowska, Pawel Krawczyk, Francois Philippe Pauzin, Tomasz Wojtowicz, Kasia Radwanska, Clive Raymond Bramham, Andrzej Dziembowski, Magdalena Dziembowska

{"title":"Terminal nucleotidyltransferase Tent2 microRNA A-tailing enzyme regulates excitatory/inhibitory balance in the hippocampus.","authors":"Patrycja Wardaszka-Pianka, Bozena Kuzniewska, Natalia Guminska, Anna Hojka-Osinska, Monika Puchalska, Jacek Milek, Aleksandra Stawikowska, Pawel Krawczyk, Francois Philippe Pauzin, Tomasz Wojtowicz, Kasia Radwanska, Clive Raymond Bramham, Andrzej Dziembowski, Magdalena Dziembowska","doi":"10.1261/rna.080240.124","DOIUrl":"https://doi.org/10.1261/rna.080240.124","url":null,"abstract":"One of the post-transcriptional mechanisms regulating the stability of RNA molecules involves the addition of non-templated nucleotides to their 3' ends, a process known as RNA tailing. To systematically investigate the physiological consequences of terminal nucleotidyltransferase TENT2 absence on RNA 3' end modifications in the mouse hippocampus, we developed a new Tent2 knockout mouse. Electrophysiological measurements revealed increased excitability in Tent2 KO hippocampal neurons, and behavioral analyses showed decreased anxiety and improved fear extinction in these mice. At the molecular level, we observed changes in miRNAs monoadenylation in Tent2 KO mouse hippocampus, but found no effect of the TENT2 loss on the mRNAs total poly(A) tail length, as measured by Direct Nanopore RNA sequencing. Moreover, differential expression analysis revealed transcripts related to synaptic transmission to be downregulated in the hippocampus of Tent2 knockout mice. These changes may explain the observed behavioral and electrophysiological alterations. Our data thus establishes a link between TENT2-dependent miRNA tailing and the balance of inhibitory and excitatory neurotransmission.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143658549","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

Pervasive formation of double-stranded RNAs by overlapping sense/antisense transcripts in budding yeast mitosis and meiosis.

IF 4.2 3区生物学

RNA Pub Date : 2025-03-18 DOI: 10.1261/rna.080290.124

Ugo Szachnowski, Emmanuelle Becker, Igor Stuparević, Maxime Wery, Olivier Sallou, Mateo Boudet, Anthony Bretaudeau, Antonin Morillon, Michael Primig

{"title":"Pervasive formation of double-stranded RNAs by overlapping sense/antisense transcripts in budding yeast mitosis and meiosis.","authors":"Ugo Szachnowski, Emmanuelle Becker, Igor Stuparević, Maxime Wery, Olivier Sallou, Mateo Boudet, Anthony Bretaudeau, Antonin Morillon, Michael Primig","doi":"10.1261/rna.080290.124","DOIUrl":"10.1261/rna.080290.124","url":null,"abstract":"Previous RNA profiling studies revealed coexpression of overlapping sense/antisense (s/a) transcripts in pro- and eukaryotic organisms. Functional analyses in yeast have shown that certain s/a mRNA/mRNA and mRNA/lncRNA pairs form stable double-stranded RNAs (dsRNAs) that affect transcript stability. Little is known, however, about the genome-wide prevalence of dsRNA formation and its potential functional implications during growth and development in diploid budding yeast. To address this question, we monitored dsRNAs in a Saccharomyces cerevisiae strain expressing the ribonuclease DCR1 and the RNA-binding protein AGO1 from Naumovozyma castellii We identify dsRNAs at 347 s/a loci that express partially or completely overlapping transcripts during mitosis, meiosis, or both stages of the diploid life cycle. We associate dsRNAs with s/a loci previously thought to be exclusively regulated by antisense interference, and others that encode antisense RNAs, which down-regulate sense mRNA-encoded protein levels. To facilitate hypothesis building, we developed the sense/antisense double-stranded RNA (SensR) expression viewer. Users are able to retrieve different graphical displays of dsRNA and RNA expression data using genome coordinates and systematic or standard names for mRNAs and different types of stable or cryptic long noncoding RNAs (lncRNAs). Our data are a useful resource for improving yeast genome annotation and for work on RNA-based regulatory mechanisms controlling transcript and protein levels. The data are also interesting from an evolutionary perspective, since natural antisense transcripts that form stable dsRNAs have been detected in many species from bacteria to humans. The SensR viewer is freely accessible at https://sensr.genouest.org.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"497-513"},"PeriodicalIF":4.2,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912912/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143029577","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 recognition by minimal ProQ from Neisseria meningitidis.

IF 4.2 3区生物学

RNA Pub Date : 2025-03-18 DOI: 10.1261/rna.080207.124

Maciej Basczok, Mikołaj Olejniczak

{"title":"RNA recognition by minimal ProQ from Neisseria meningitidis.","authors":"Maciej Basczok, Mikołaj Olejniczak","doi":"10.1261/rna.080207.124","DOIUrl":"10.1261/rna.080207.124","url":null,"abstract":"Neisseria meningitidis minimal ProQ is a global RNA-binding protein belonging to the family of FinO-domain proteins. The N. meningitidis ProQ consists only of the FinO domain accompanied by short N- and C-terminal extensions. To better understand how this minimal FinO-domain protein recognizes RNAs, we compared its binding to seven different natural RNA ligands of this protein. Next, two of these RNAs, rpmG-3' and AniS, were subject to further mutational studies. The data showed that N. meningitidis ProQ binds the lower part of the intrinsic transcription terminator hairpin, and that the single-stranded sequences on the 5' and 3' side of the terminator stem are required for tight binding. However, the specific lengths of 5' and 3' RNA sequences required for optimal binding differed between the two RNAs. Additionally, our data show that the 2'-OH and 3'-OH groups of the 3' terminal ribose contribute to RNA binding by N. meningitidis ProQ. In summary, the minimal ProQ protein from N. meningitidis has generally similar requirements for RNA binding as the isolated FinO domains of other proteins of this family, but differs from them in detailed RNA features that are optimal for specific RNA recognition.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"549-565"},"PeriodicalIF":4.2,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143060480","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.

IF 4.2 3区生物学

RNA Pub Date : 2025-03-14 DOI: 10.1261/rna.080409.125

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

引用次数: 0

Prevention of ribozyme catalysis through cDNA synthesis enables accurate RT-qPCR measurements of context-dependent ribozyme activity.

IF 4.2 3区生物学

RNA Pub Date : 2025-03-06 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":"https://doi.org/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. So 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 (E. coli). These results have broad implications for many ribozyme measurements and technologies.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Inconsistencies in the published rabbit ribosomal rRNAs: a proposal for uniformity in sequence and site numbering.

IF 4.2 3区生物学

RNA Pub Date : 2025-03-06 DOI: 10.1261/rna.080294.124

Swastik De, Michelle Zhou, Zuben P Brown, Raymond N Burton-Smith, Yaser Hashem, Tatyana Pestova, Christopher U T Hellen, Joachim Frank

引用次数: 0

Circuit logic: interdependent RNA modifications shape mRNA and noncoding RNA structure and function.

IF 4.2 3区生物学

RNA Pub Date : 2025-03-05 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":"https://doi.org/10.1261/rna.080421.125","url":null,"abstract":"Continued advances in high throughput detection of post-transcriptional 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 multi-stepped post-transcriptional 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":""},"PeriodicalIF":4.2,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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.

IF 4.2 3区生物学

RNA Pub Date : 2025-03-05 DOI: 10.1261/rna.080206.124

Maria D Mamonska, Maciej M Basczok, Ewa M Stein, Julia Kurzawska, Mikolaj Olejniczak

引用次数: 0

Positioning of sperm tail longitudinal columns depend on Nsun7, an RNA binding protein destabilizing elongated spermatid transcripts.

IF 4.2 3区生物学

RNA Pub Date : 2025-03-03 DOI: 10.1261/rna.080320.124

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

{"title":"Positioning of sperm tail longitudinal columns depend on Nsun7, an RNA binding protein destabilizing elongated spermatid transcripts.","authors":"Ekaterina Guseva, Olga Averina, Sergey Isaev, Philipp Pletnev, Elizaveta Bragina, Oleg Permyakov, Vitaly Buev, Anastasia Priymak, Mariia Emelianova, Lizaveta Pshanichnaya, Evgeny Romanov, Svetlana E Novikova, Kirill Petriukov, Anna Golovina, Olga Grigorieva, Vasily Manskikh, Diana Korshunova, Yuliya Silaeva, Alexey Deykin, Maria Rubtsova, Victor Zgoda, Alexander Mazur, Egor Prokhortchouk, Olga Dontsova, Petr V Sergiev","doi":"10.1261/rna.080320.124","DOIUrl":"https://doi.org/10.1261/rna.080320.124","url":null,"abstract":"Spermatozoid's flagella assemble in transcriptionally silent spermatids and thus depends on post-transcriptional 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 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 motility defect.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0