RNA Biology最新文献_第4页

Germ granule-mediated mRNA storage and translational control. 胚芽颗粒介导的mRNA储存和翻译控制。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-02-06 DOI: 10.1080/15476286.2025.2462276

Hoang-Anh Pham-Bui, Mihye Lee

引用次数: 0

Release and degradation of dissolved environmental RNAs from zebrafish cells. 斑马鱼细胞中溶解的环境 RNA 的释放和降解。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-04-24 DOI: 10.1080/15476286.2025.2486281

Zhongneng Xu, Shuichi Asakawa

{"title":"Release and degradation of dissolved environmental RNAs from zebrafish cells.","authors":"Zhongneng Xu, Shuichi Asakawa","doi":"10.1080/15476286.2025.2486281","DOIUrl":"10.1080/15476286.2025.2486281","url":null,"abstract":"The sources and degradation profiles of dissolved environmental RNAs from fish in water remain unknown. In this study, laboratory experiments and mathematical modelling were conducted to investigate the permeability of RNA extracted from zebrafish cells through filters, the release of dissolved environmental RNAs from live and dying zebrafish cells, and the degradation of RNA extracted from zebrafish cells in a non-sterile aqueous environment. This research aimed to provide biological and ecological insights into fish RNAs dissolved in water. The results showed that most of the RNA extracted from zebrafish cells was detected in the filtrates after passage through 0.45 µm filters. Over the course of the 6-day experiment, dynamic levels of the RNAs in the liquid environment containing live or dying zebrafish cells were determined. The release and degradation rates of dissolved environmental RNA from zebrafish cells were calculated using mathematical modelling. RNA extracted from zebrafish cells degraded in non-sterile water in the tubes, and after 2 months, more than 15% of the RNAs in the water remained detectable. The half-life of the RNA in the tubes was approximately 20 ~ 43 days. The modelling results suggest that the levels of the dissolved environmental fish RNAs in natural waters or aquariums could be so low that it would be difficult to detect them using current techniques. The results obtained in this study will help develop new methods for measuring the dynamics of dissolved environmental fish RNAs in water and determining their significance.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-12"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12026185/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143754369","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

Evolution of the RNA alternative decay cis element into a high-affinity target for the immunomodulatory protein Roquin. RNA替代衰变顺式元件成为免疫调节蛋白Roquin的高亲和力靶标的进化。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-01-13 DOI: 10.1080/15476286.2024.2448391

Jan-Niklas Tants, Katharina Friedrich, Jasmina Neumann, Andreas Schlundt

{"title":"Evolution of the RNA alternative decay cis element into a high-affinity target for the immunomodulatory protein Roquin.","authors":"Jan-Niklas Tants, Katharina Friedrich, Jasmina Neumann, Andreas Schlundt","doi":"10.1080/15476286.2024.2448391","DOIUrl":"10.1080/15476286.2024.2448391","url":null,"abstract":"RNA cis elements play pivotal roles in regulatory processes, e.g. in transcriptional and translational regulation. Two stem-looped cis elements, the constitutive and alternative decay elements (CDE and ADE, respectively) are shape-specifically recognized in mRNA 3' untranslated regions (UTRs) by the immune-regulatory protein Roquin. Roquin initiates mRNA decay and contributes to balanced transcript levels required for immune homoeostasis. While the interaction of Roquin with several CDEs is described, our knowledge about ADE complex formation is limited to the mRNA of Ox40, a gene encoding a T-cell costimulatory receptor. The Ox40 3'UTR comprises both a CDE and ADE, each sufficient for Roquin-mediated control. Opposed to highly conserved and abundant CDE structures, ADEs are rarer, but predicted to exhibit a greater structural heterogeneity. This raises the question of how and when two structurally distinct cis elements evolved as equal target motifs for Roquin. Using an interdisciplinary approach, we here monitor the evolution of sequence and structure features of the Ox40 ADE across species. We designed RNA variants to probe en-detail determinants steering Roquin-RNA complex formation. Specifically, those reveal the contribution of a second RNA-binding interface of Roquin for recognition of the ADE basal stem region. In sum, our study sheds light on how the conserved Roquin protein selected ADE-specific structural features to evolve a second high-affinity mRNA target cis element relevant for adaptive immune regulation. As our findings also allow expanding the RNA target spectrum of Roquin, the approach can serve a paradigm for understanding RNA-protein specificity through back-tracing the evolution of the RNA element.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"22 1","pages":"1-12"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11730611/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143056062","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

Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 gene. 革兰氏阴性土壤细菌对四环素暴露的早期转录后反应揭示了DUF1127基因的意外衰减机制。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-07-01 DOI: 10.1080/15476286.2025.2521887

Jennifer A F Kothe, Till Sauerwein, Theresa Dietz, Robina Scheuer, Muhammad Elhossary, Susanne Barth-Weber, Jan Wähling, Konrad U Förstner, Elena Evguenieva-Hackenberg

{"title":"Early posttranscriptional response to tetracycline exposure in a gram-negative soil bacterium reveals unexpected attenuation mechanism of a DUF1127 gene.","authors":"Jennifer A F Kothe, Till Sauerwein, Theresa Dietz, Robina Scheuer, Muhammad Elhossary, Susanne Barth-Weber, Jan Wähling, Konrad U Förstner, Elena Evguenieva-Hackenberg","doi":"10.1080/15476286.2025.2521887","DOIUrl":"10.1080/15476286.2025.2521887","url":null,"abstract":"The gram-negative, soil-dwelling plant symbiont Sinorhizobium meliloti shares its free-living habitat with antibiotic producers. To learn about early steps of its adaptation to antibiotics, we analysed transcriptome changes after 10 min exposure to subinhibitory amount of tetracycline (Tc). RNA-seq revealed 297 differentially expressed genes. Besides ten upregulated ribosomal genes, there was no recognizable functional pattern in the observed changes. However, polar differential expression pattern was observed: Mostly, upregulated genes were first and downregulated genes downstream in operons. Furthermore, we detected mRNA stabilization upon Tc exposure for several up- and down-regulated genes. Thus, mRNA stabilization contributed to increased mRNA levels, but for downstream genes its effect was probably counteracted by premature transcriptional termination caused by disrupted coupling between transcription and translation. Using reporter constructs, we found that a DUF1127 gene, showing highest mRNA increase, is controlled by transcription attenuation depending on the translation of an upstream ORF (uORF). Our data suggest the following model: The attenuation strongly depends on the accessibility of C-rich codons at the beginning of the uORF. The accessibility is guaranteed by translation of the uORF, and is possible in a time window after a ribosome moves downstream and before a next ribosome occupies the ribosomal binding site (RBS). The accessibility is blocked either by impaired translation initiation or, in the absence of ribosome binding, by base-pairing between the RBS and the C-rich codons. We propose that this is used by bacteria to monitor ribosome availability and translation efficiency, and to ensure reciprocal expression of the DUF1127 gene.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-16"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12218461/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144326795","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

Profile of tRNA-derived short non-coding RNAs during monocyte differentiation and their role in macrophage survival. 单核细胞分化过程中trna衍生的短非编码rna及其在巨噬细胞存活中的作用

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-07-04 DOI: 10.1080/15476286.2025.2525886

Anahita Jayaram, Sanjeev Galande, Soroush Sharbati, Deepak Deshpande, Kamlesh Pawar

引用次数: 0

SARS-CoV-2 RNA-binding protein suppresses extracellular miRNA release. SARS-CoV-2 rna结合蛋白抑制细胞外miRNA释放。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-07-07 DOI: 10.1080/15476286.2025.2527494

Hyejin Mun, Chang Hoon Shin, Qingxuan Fei, Andrea Estefania Lopez Giraldo, Kyoung-Min Choi, Ji Won Lee, Kyungmin Kim, Kyung-Won Min, Leilei Shi, Mark T Bedford, Dong-Chan Kim, Yoo Lim Chun, Seonghyun Ryu, Dongin Kim, Jeong Ho Chang, Ryan T Westrope, Michelle Shay, Edward Nguyen, Junho K Hur, Abigail Agyenda, Nam Chul Kim, Sung-Ung Kang, Woonghee Lee, Je-Hyun Yoon

{"title":"SARS-CoV-2 RNA-binding protein suppresses extracellular miRNA release.","authors":"Hyejin Mun, Chang Hoon Shin, Qingxuan Fei, Andrea Estefania Lopez Giraldo, Kyoung-Min Choi, Ji Won Lee, Kyungmin Kim, Kyung-Won Min, Leilei Shi, Mark T Bedford, Dong-Chan Kim, Yoo Lim Chun, Seonghyun Ryu, Dongin Kim, Jeong Ho Chang, Ryan T Westrope, Michelle Shay, Edward Nguyen, Junho K Hur, Abigail Agyenda, Nam Chul Kim, Sung-Ung Kang, Woonghee Lee, Je-Hyun Yoon","doi":"10.1080/15476286.2025.2527494","DOIUrl":"10.1080/15476286.2025.2527494","url":null,"abstract":"SARS-CoV-2 is the betacoronavirus causing the COVID-19 pandemic. Although the SARS-CoV-2 genome and transcriptome were reported previously, the function of individual viral proteins is largely unknown. Utilizing biochemical and molecular biology methods, we identified that four SARS-CoV-2 RNA-binding proteins (RBPs) regulate the host RNA metabolism by direct interaction with mature miRNA let-7b revealed by Nuclear Magnetic Resonance spectroscopy (NMR). SARS-CoV-2 RBP Nsp9 primarily binds mature miRNA let-7b, a direct ligand of the Toll-like Receptor 7 (TLR7), one of the potential SARS-CoV-2 therapeutics. Nsp9 suppresses host gene expression possibly by promoting let-7b-mediated silencing of a cellular RNA polymerase, POLR2D. In addition, Nsp9 inhibits extracellular release of let-7b and subsequent antiviral activity via TLR7. These results demonstrate that SARS-CoV-2 hijacks the host RNA metabolism to suppress antiviral responses and to shut down cellular transcription. Our findings of how a natural ligand of TLR7, miRNA let-7b, is suppressed by SARS-CoV-2 RBPs will advance our understanding of COVID-19 and SARS-CoV-2 therapeutics.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-17"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12239786/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144542085","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

Novel non-coding FOXP3 transcript isoform associated to potential transcriptional interference in human regulatory T cells. 新的非编码FOXP3转录异构体与人类调节性T细胞中潜在的转录干扰相关。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-07-02 DOI: 10.1080/15476286.2025.2502719

Marcos Cases, Niclas Ritter, Hector Rincon-Arevalo, Sandy Kroh, Aysegül Adam, Marieluise Kirchner, Hanieh Moradian, Manfred Gossen, Maria Dzamukova, Artür Manukyan, Markus Landthaler, Christopher Kressler, Anja E Hauser, Daniel P Depledge, Julia K Polansky, Hyun-Dong Chang

{"title":"Novel non-coding FOXP3 transcript isoform associated to potential transcriptional interference in human regulatory T cells.","authors":"Marcos Cases, Niclas Ritter, Hector Rincon-Arevalo, Sandy Kroh, Aysegül Adam, Marieluise Kirchner, Hanieh Moradian, Manfred Gossen, Maria Dzamukova, Artür Manukyan, Markus Landthaler, Christopher Kressler, Anja E Hauser, Daniel P Depledge, Julia K Polansky, Hyun-Dong Chang","doi":"10.1080/15476286.2025.2502719","DOIUrl":"10.1080/15476286.2025.2502719","url":null,"abstract":"CD4+ regulatory T cells (TREGS) are critical for immune tolerance and the transcription factor Forkhead Box P3 (FOXP3) plays a crucial role in their differentiation and function. Recently, an alternative promoter has been reported for FOXP3, which is active only in TREGS and could have profound implications for the output of the locus, and therefore, for the functionality of these cells. By direct RNA sequencing we identified multiple novel FOXP3 transcriptional products, including one relatively abundant isoform with an extended 5' UTR that we named 'longFOXP3'. Western blotting, analysis of public mass spectrometry data, and transfection of in vitro transcribed RNA suggested that longFOXP3 is not coding. Furthermore, we show using two distinct RNA single-molecule fluorescence in situ hybridization technologies that transcription from the upstream promoter correlates with decreased levels of FOXP3 at the mRNA and protein levels. Together, we provide compelling evidence that the transcriptional output of the human FOXP3 locus is far more complex than that of the current annotation and warrants a more detailed analysis to identify coding and non-coding transcript isoforms. Furthermore, the alternative promoter may interfere with the activity of the canonical promoter, evoking intragenic transcriptional interference, and in this way, fine-tune the levels of FOXP3 in human TREGS.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"22 1","pages":"1-20"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12233831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144554358","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

Impact of Gemin5 in protein synthesis: phosphoresidues of the dimerization domain regulate ribosome binding. Gemin5在蛋白质合成中的影响：二聚化结构域的磷残基调节核糖体结合。

IF 3.4 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-08-03 DOI: 10.1080/15476286.2025.2540654

Salvador Abellan, Alejandra Escos, Rosario Francisco-Velilla, Encarnacion Martinez-Salas

{"title":"Impact of Gemin5 in protein synthesis: phosphoresidues of the dimerization domain regulate ribosome binding.","authors":"Salvador Abellan, Alejandra Escos, Rosario Francisco-Velilla, Encarnacion Martinez-Salas","doi":"10.1080/15476286.2025.2540654","DOIUrl":"10.1080/15476286.2025.2540654","url":null,"abstract":"RNA-binding proteins are involved in all steps of gene expression. Their malfunction has important consequences for cell growth through dysregulation of protein synthesis events leading to cancer. Gemin5 is a predominantly cytoplasmic protein involved in spliceosome assembly and gene expression reprogramming. The protein is phosphorylated at multiple sites, although the role of the individual phosphorylated residues remains poorly understood. With the aim to understand the impact of Gemin5 post-translation modifications for RNA-binding, protein synthesis, and therefore cell growth, we have analysed the role of conserved P-residues located in the dimerization domain of the protein in subcellular localization, protein stability, interactome, ribosome binding and translation regulation. We show that the activation of signalling pathways in response to a dsRNA mimic, which leads to phosphorylation of eIF2α, enhanced the intensity of Gemin5 binding to a cognate RNA ligand. In addition, ribosome binding decreased when Ser/Thr 847 and 852-854 are substituted by a non-phosphorylatable residue, consistent with decreased protein stability, and reduced number of associated factors. Similar analyses of phosphomimetic mutants (S847D and STS852-854DDD) suggested conformational changes of the protein structure as the responsible factor for the defective proteins. Moreover, cap-dependent protein synthesis was significantly altered by the triple substitution STS/DDD, pointing towards a role of these residues in protein synthesis regulation.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-15"},"PeriodicalIF":3.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12323416/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144744570","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

Precursor RNA structural patterns at SF3B1 mutation sensitive cryptic 3' splice sites. SF3B1突变敏感的隐式3'剪接位点的前体RNA结构模式。

IF 3.4 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-10-08 DOI: 10.1080/15476286.2025.2570043

Austin Herbert, Abigail Hatfield, Alexandra Randazza, Valeria Miyamoto, Katie Palmer, Lela Lackey

{"title":"Precursor RNA structural patterns at SF3B1 mutation sensitive cryptic 3' splice sites.","authors":"Austin Herbert, Abigail Hatfield, Alexandra Randazza, Valeria Miyamoto, Katie Palmer, Lela Lackey","doi":"10.1080/15476286.2025.2570043","DOIUrl":"10.1080/15476286.2025.2570043","url":null,"abstract":"SF3B1 is a core component of the spliceosome involved in branch point recognition and 3' splice site selection. The SF3B1 K700E mutation (lysine to glutamic acid) is common in myelodysplastic syndrome and other blood disorders. SF3B1 K700E mutants utilize novel cryptic 3' splice sites; however, the properties distinguishing SF3B1-sensitive splice junctions from other alternatively spliced junctions are unknown. We identify a subset of 192 cryptic 3' splice junctions with significantly altered use in SF3B1 K700E cells, termed SF3B1-sensitive cryptic 3' splice sites, and 2800 cryptic 3' splice sites used in SF3B1 wild-type, termed SF3B1-resistant. We find that SF3B1-sensitive cryptic 3' splice sites are embedded in extended polypyrimidine tracts. Furthermore, canonical splice sites paired to SF3B1-sensitive cryptic 3' splice sites are significantly weaker than canonical 3' splice sites paired to SF3B1-resistant cryptic 3' splice sites. We test whether SF3B1-sensitive splice sites are structurally different from SF3B1-resistant 3' splice sites using chemical probing. We develop experimental RNA structure data for 83 SF3B1-sensitive junctions and 39 SF3B1-resistant junctions. We find that the pattern of structural accessibility at the NAG splicing motif in cryptic and canonical 3' splice sites is similar. However, the magnitude of accessibility differences is less in paired SF3B1-sensitive splice sites than in paired SF3B1-mutant splice sites. Additionally, SF3B1-sensitive splice junctions are more flexible than SF3B1-resistant junctions. Our results suggest that SF3B1-sensitive splice junctions have unique structure and sequence properties, containing poorly differentiated, weak splice sites that lead to altered 3' splice site recognition in the presence of SF3B1 mutation.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-15"},"PeriodicalIF":3.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145244958","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

Correction. 修正。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-01-07 DOI: 10.1080/15476286.2025.2449742

引用次数: 0