RNA最新文献_第8页

Neuronal subtype-specific ribosomal protein mRNA expression. 神经元亚型特异性核糖体蛋白mRNA表达。

IF 4.3 3区生物学

RNA Pub Date : 2026-06-16 DOI: 10.1261/rna.080954.126

Joaquín Garat, Sofía Niño-Rivero, Patricia Lagos, Andrés Di Paolo, Pablo Smircich, José Sotelo-Silveira

{"title":"Neuronal subtype-specific ribosomal protein mRNA expression.","authors":"Joaquín Garat, Sofía Niño-Rivero, Patricia Lagos, Andrés Di Paolo, Pablo Smircich, José Sotelo-Silveira","doi":"10.1261/rna.080954.126","DOIUrl":"10.1261/rna.080954.126","url":null,"abstract":"Current understanding recognizes that ribosomal proteins (RPs) have regulatory roles beyond their canonical structural functions in translation, raising the question of how their expression is organized across cell types. Given the diversity of neuronal cell types, understanding RP gene expression at the neuronal subtype level is an important and previously inaccessible question. Here, leveraging advances in single-cell transcriptomics, we analyzed single-cell RNA-seq data sets from the mouse cerebral cortex and hippocampus to examine RP mRNA expression across neuronal subtypes. We observed distinct RP mRNA expression profiles between excitatory and inhibitory neurons and found that higher Rps27 transcript levels in inhibitory neurons corresponded to increased RPS27 protein abundance. Beyond excitatory-inhibitory differences, RP mRNA expression further segregated across well-defined neuronal subclasses, with 59 of 84 RP genes differentially expressed, including enrichment of Rpl21 in Lamp5 and Rps27 in Vip interneurons. These patterns were consistent across cortical regions and reproducible across two independent single-cell technologies (Smart-seq2 and 10x Genomics). Analysis of aging- and stress-associated data sets revealed stable RP expression signatures, with limited phenotype-linked changes. Together, we present a comprehensive atlas of ribosomal protein gene expression at neuronal subclass resolution, revealing robust subclass-specific transcriptional signatures, suggesting an underestimated regulatory layer.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1077-1100"},"PeriodicalIF":4.3,"publicationDate":"2026-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13271003/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147646351","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

ADARs mediate distinct RNA editing activity and gene regulation in the Caenorhabditis elegans germline. ADARs介导秀丽隐杆线虫种系中不同的RNA编辑活性和基因调控。

IF 4.3 3区生物学

RNA Pub Date : 2026-06-16 DOI: 10.1261/rna.080820.125

Emily A Erdmann, Leanne H Kelley, Heather A Hundley

{"title":"ADARs mediate distinct RNA editing activity and gene regulation in the Caenorhabditis elegans germline.","authors":"Emily A Erdmann, Leanne H Kelley, Heather A Hundley","doi":"10.1261/rna.080820.125","DOIUrl":"10.1261/rna.080820.125","url":null,"abstract":"Tissues rely on unique landscapes of gene regulation to allow the organism to correctly develop, function, and respond to changes. One component of these gene regulatory networks is RNA binding proteins (RBPs), which bind and modify RNA molecules leading to changes in the cellular fate of transcripts. The adenosine deaminase acting on RNA (ADAR) family of RBPs modify RNAs by catalyzing the deamination of adenosine (A) to inosine (I), known as A-to-I RNA editing. Prompted by recent evidence that ADARs play important roles in germline biology, we profiled editing activity of the A-to-I editing enzyme ADR-2 on transcripts in the Caenorhabditis elegans germline. These analyses revealed that many germline editing events are distinct from editing events in other tissues; however, the previously described role of the inactive deaminase ADR-1 in regulating editing activity by ADR-2 is conserved in the germline. We find that complete loss or misregulation of editing has little effect on the expression of edited transcripts within the germline; however, loss of ADARs results in the misexpression of several unedited germline transcripts. Intriguingly, further investigation suggests that these expression changes are buffered at the translational level. In all, the results of this study suggest that ADARs show unique activity in the C. elegans germline and that compensatory mechanisms exist to lessen the immediate consequences of loss of ADAR function within the germline.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1020-1031"},"PeriodicalIF":4.3,"publicationDate":"2026-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13271001/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147594424","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

Synthesis and RNA transcription of colored 4-selenouridine triphosphate with atom mutagenesis. 带原子诱变的有色4-硒尿嘧啶三磷酸合成及RNA转录。

IF 4.3 3区生物学

RNA Pub Date : 2026-06-16 DOI: 10.1261/rna.080814.125

Dan Liu, Huiyan Sun, Sibo Jiang, Jin Pei, Zhen Huang

{"title":"Synthesis and RNA transcription of colored 4-selenouridine triphosphate with atom mutagenesis.","authors":"Dan Liu, Huiyan Sun, Sibo Jiang, Jin Pei, Zhen Huang","doi":"10.1261/rna.080814.125","DOIUrl":"10.1261/rna.080814.125","url":null,"abstract":"4-Selenouridine (4SeU) is one of the naturally occurring modifications of tRNAs, possibly maintaining the three-dimensional structural stability of tRNA and playing a critical role in stress responses. By using the 4-Se-atomic probe, previously we have revealed more insights into the RNA noncanonical interactions and uridine participation in diversified RNA functions and structures. To further explore the Se-atomic probe, herein we report the first synthesis of 4-selenouridine triphosphate (4SeUTP) and the enzymatic incorporation of 4SeUTP into RNAs. Interestingly, we found that 4SeUTP possessed unique properties, including red-shifted base absorption (365 nm), colored base (yellow), and higher base acidity (pKa = 7.85) reduced by an Se-atom. Further, 4SeUTP was recognized by T7 RNA polymerase as well as UTP counterpart, and its transcription of RNAs (such as 4SeU-hammerhead ribozyme RNA) was up to the native level. Furthermore, the transcribed 4SeU-hammerhead ribozyme had higher cleaving activity (∼1.8-fold) than the corresponding native ribozyme. In conclusion, 4SeUTP can be a fine substrate of RNA polymerase, and the 4SeU-RNAs can be enzymatically synthesized with better catalytic activity, opening a new avenue for investigating the biochemical functions and structures of RNAs, especially catalytic RNAs.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1032-1040"},"PeriodicalIF":4.3,"publicationDate":"2026-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147627001","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

Cancer-associated synonymous mutations reveal stress signal-dependent mRNA folding that selectively modulates protein function. 癌症相关的同义突变揭示了胁迫信号依赖性mRNA折叠选择性调节蛋白质功能。

IF 4.3 3区生物学

RNA Pub Date : 2026-06-16 DOI: 10.1261/rna.080976.126

Sivakumar Vadivel Gnanasundram, Lixiao Wang, Sa Chen, Ondrej Bonczek, Borivoj Vojtesek, Robin Fahraeus

{"title":"Cancer-associated synonymous mutations reveal stress signal-dependent mRNA folding that selectively modulates protein function.","authors":"Sivakumar Vadivel Gnanasundram, Lixiao Wang, Sa Chen, Ondrej Bonczek, Borivoj Vojtesek, Robin Fahraeus","doi":"10.1261/rna.080976.126","DOIUrl":"10.1261/rna.080976.126","url":null,"abstract":"Recent technical advances have facilitated studies on changes in mRNA structures in response to signaling pathways. However, whether mRNA structures can affect the function of the encoded protein remains poorly understood. In-cell RNA structural probing (SHAPE-MaP) demonstrates how two cancer-associated synonymous mutations (CASMs) at proline codon 34 (c.102 C > A and c.102 C > G) prevent DNA damage-induced TP53 mRNA folding, whereas the non-cancer-associated c.102 C > U mutation does not. Transcript and chromatin immunoprecipitation (ChIP) analysis reveal that p53 expressed from CASM34 has reduced promoter binding and reduced induction of p53 downstream target genes PUMA and 14-3-3-σ, but not p21 CDKN1A Transcriptome analysis reveals a CASM34-mediated global attenuation of DNA damage-responsive gene expression. Together, the results demonstrate that CASM34 interferes with signal-induced p53 mRNA folding during DNA damage, leading to selective modulation of p53 protein activity. More broadly, our findings highlight a general concept by which cancer-associated synonymous mutations target signal-induced mRNA structures that influence the encoded protein.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1147-1155"},"PeriodicalIF":4.3,"publicationDate":"2026-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147717897","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

A method of comprehensive sequencing analysis of the small RNA fragmentome (RiboMarker). 一种小RNA片段组（ribommarker）的综合测序分析方法。

IF 4.3 3区生物学

RNA Pub Date : 2026-06-16 DOI: 10.1261/rna.080861.125

Rachel C Clark, Aidan C Manning, Jonathan M Howard, Sergio Barberán-Soler, Sergei A Kazakov

{"title":"A method of comprehensive sequencing analysis of the small RNA fragmentome (RiboMarker).","authors":"Rachel C Clark, Aidan C Manning, Jonathan M Howard, Sergio Barberán-Soler, Sergei A Kazakov","doi":"10.1261/rna.080861.125","DOIUrl":"10.1261/rna.080861.125","url":null,"abstract":"Small RNAs and RNA fragments (sRNAs) found in blood and other biofluids have emerged as promising biomarkers for cancer and other pathologies. Sequencing analysis of sRNAs representing the entire RNA fragmentome could improve understanding of their roles in cancer development and be used for discovery of new biomarkers, cancer detection, and personalized treatment management. Conventional methods of sRNA-seq library preparation are limited to detection of sRNAs with 5'-P and 3'-OH ends (sRNA Type 1) that represent only ∼10% of the whole RNA fragmentome, whereas sRNA Types having other termini are hidden. Although recently developed sRNA-seq methods provide detection of some or all hidden sRNAs, these methods cannot both detect all and distinguish between sRNAs of different RNA Types. Here we describe the RiboMarker approach for preparation of sRNA sequencing libraries that addresses these shortcomings. It uses distinctive enzymatic pretreatment(s) providing conversion between the RNA termini that can enrich for or deplete specific sRNA type(s) upfront of the universal method of library preparation. To monitor the efficacy of these pretreatments, we leveraged a pool of synthetic RNAs of different RNA Types and lengths spiked in brain or plasma RNA samples. This allows identification and analysis of relative abundance, sequencing profiles, and RNA Types of naturally occurring sRNAs representing different RNA classes. Using the RiboMarker approach, we demonstrated its capability to enhance the capacity and sensitivity of distinguishing between plasma RNA samples from different donors (simulating healthy individuals and cancer patients) by selecting and using sRNAs of specific RNA Type(s).","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1156-1181"},"PeriodicalIF":4.3,"publicationDate":"2026-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13225065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147609769","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

Genetic and genomic approaches to explore roles for the conserved 3'-5' exoribonuclease EXOSC10 in normal and malignant cells. 遗传学和基因组学方法探索保守的3‘-5’外核糖核酸酶EXOSC10在正常和恶性细胞中的作用。

IF 4.3 3区生物学

RNA Pub Date : 2026-05-18 DOI: 10.1261/rna.080981.126

Radhika Sain, Julian Primig, Michael Primig

引用次数: 0

Bioinformatic and experimental analyses revealed pathogen-derived pathoPEP candidates predicted to control plant miRNA expression and infection. 生物信息学和实验分析表明，病原菌衍生的pathoPEPs候选物有望控制植物miRNAs的表达和感染。

IF 4.3 3区生物学

RNA Pub Date : 2026-05-18 DOI: 10.1261/rna.080819.125

Emmanuel Clostres, Christophe Penno, Abdelhak El-Amrani, Virginie Daburon, Kévin Gazengel, Cécile Monard, Stéphanie Daval

{"title":"Bioinformatic and experimental analyses revealed pathogen-derived pathoPEP candidates predicted to control plant miRNA expression and infection.","authors":"Emmanuel Clostres, Christophe Penno, Abdelhak El-Amrani, Virginie Daburon, Kévin Gazengel, Cécile Monard, Stéphanie Daval","doi":"10.1261/rna.080819.125","DOIUrl":"10.1261/rna.080819.125","url":null,"abstract":"The partners of an ecological association tend to copy the biological system of their hosts. We hypothesized that microorganisms, particularly pathogens, have acquired the ability to express short peptides (pathoPEPs) homologous to host miPEPs, thus modulating the expression of the corresponding host microRNA (miRNA) and the function of miRNA-targeted genes. The pathosystem involving interactions between Brassica napus and its pathogen Plasmodiophora brassicae was studied. The data set contains RNA-seq and ribosomal profiling from two plant genotypes inoculated with one pathogen isolate. Using in silico analysis, we identified three putative pathoPEPs produced by P. brassicae and their targeted plant miRNA genes. A link between the level of infection of B. napus by P. brassicae and the expression of pathoPEPs and their targeted miRNA genes was found, with the expression of the latter two being inversely related. Finally, we identified differential expression and translation of genes predicted to be targets of pathoPEP-regulated miRNAs. These genes, involved in auxin pathway, immune defense, root architecture, or carbohydrate metabolism, are thought to enable P. brassicae, through its pathoPEPs, to hijack plant's metabolic pathways (e.g., hormonal pathways, sugar synthesis, root morphology), thereby facilitating its invasion. Using in silico approaches, the involvement of miPEPs from this host-pathogen system as a host post-transcriptional regulatory pathway is described herein for the first time.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"915-929"},"PeriodicalIF":4.3,"publicationDate":"2026-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147487116","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

The PIN domain of SMG-5 functionally interacts with SMG-6 to stimulate NMD. SMG-5的PIN结构域在功能上与SMG-6相互作用以刺激NMD。

IF 4.3 3区生物学

RNA Pub Date : 2026-05-18 DOI: 10.1261/rna.080653.125

Matthew S Modena, Chloe M Wohlenberg, Marcus J Viscardi, Christian R Dunn, Benjamin L Haag, Joshua A Arribere

{"title":"The PIN domain of SMG-5 functionally interacts with SMG-6 to stimulate NMD.","authors":"Matthew S Modena, Chloe M Wohlenberg, Marcus J Viscardi, Christian R Dunn, Benjamin L Haag, Joshua A Arribere","doi":"10.1261/rna.080653.125","DOIUrl":"10.1261/rna.080653.125","url":null,"abstract":"Nonsense-mediated mRNA decay (NMD) is a translational-dependent mRNA decay pathway that regulates mRNAs and protects cells from the deleterious, truncated protein products of mRNAs with early stop codons. Despite substantial effort, the central biochemical reactions that comprise mRNA decay during NMD remain elusive. Research by our laboratory and others centers around the observation that NMD target mRNA cleavage by the endonuclease SMG-6 requires the presence of another NMD factor, SMG-5, although the molecular basis of SMG-6's requirement for SMG-5 remained elusive. Here we present work to explain the requirement of SMG-5 in SMG-6-mediated mRNA cleavage. We revisit previous observations that SMG-5 contains a catalytically inactive PIN nuclease domain, and we show that although SMG-5 lacks conventional active site residues, the PIN domain of SMG-5 nevertheless contains highly conserved residues that are essential to NMD. We show that AlphaFold predicts an interaction between SMG-5 and SMG-6 PIN domains, an interaction that we substantiate via in vitro pulldowns. We use the in silico models to design point mutations that perturb-and restore-NMD function in Caenorhabditis elegans via a compensatory salt bridge flip. Altogether, our data support the idea that SMG-5 and SMG-6 interact to form a functional complex, and we suggest molecular roles for the overlooked SMG-5 PIN domain in SMG-6-mediated mRNA cleavage.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"858-869"},"PeriodicalIF":4.3,"publicationDate":"2026-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146119877","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

Regulation of mRNA decay and translation during the mammalian cell cycle. 哺乳动物细胞周期中mRNA衰变和翻译的调控。

IF 4.3 3区生物学

RNA Pub Date : 2026-05-18 DOI: 10.1261/rna.080910.125

Jimmy Ly, Ekaterina Khalizeva, Yi Fei Tao, Iain M Cheeseman

引用次数: 0

Ancestral intronic splicing regulatory elements in the SCNα gene family. SCNα基因家族中的祖先内含子剪接调控元件。

IF 4.3 3区生物学

RNA Pub Date : 2026-05-18 DOI: 10.1261/rna.080730.125

Ekaterina Chernyavskaya, Margarita Vorobeva, Sergei A Spirin, Dmitry A Skvortsov, Olga A Dontsova, Dmitri D Pervouchine

{"title":"Ancestral intronic splicing regulatory elements in the SCNα gene family.","authors":"Ekaterina Chernyavskaya, Margarita Vorobeva, Sergei A Spirin, Dmitry A Skvortsov, Olga A Dontsova, Dmitri D Pervouchine","doi":"10.1261/rna.080730.125","DOIUrl":"10.1261/rna.080730.125","url":null,"abstract":"SCNα genes encode components of voltage-gated sodium channels that are crucial for generating electrical signals. Humans have 10 paralogous SCNα genes, some of which contain duplicated mutually exclusive exons 5a and 5b. In reconstructing their evolutionary history, we found multiple unannotated copies of exon 5 in distant species and showed that exon 5 duplication goes back to a common ancestor of the SCNα gene family. We characterized splicing patterns of exons 5a and 5b across tissues, tumors, and developmental stages, and demonstrated that the nonsense-mediated decay (NMD) system is not the major factor contributing to their mutually exclusive choice. Comparison of SCN2A, SCN3A, SCN5A, and SCN9A intronic nucleotide sequences revealed multiple Rbfox2 binding sites and two highly conserved intronic splicing regulatory elements (ISRE) that are shared between paralogs. Minigene mutagenesis and blockage by antisense oligonucleotides showed that the formation of RNA structure between ISRE promotes exon 5b skipping in SCN9A The inclusion of exon 5b is also promoted by siRNA-mediated knockdown of Rbfox2, which makes the collective action of RNA structure and Rbfox2 compatible with the model of a structural RNA bridge. ISRE sequences are conserved from human to elephant shark and may represent an ancient, evolutionarily conserved regulatory mechanism. Our results demonstrate the power of comparative sequences analysis in application to paralogs for elucidating splicing regulatory programs.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"827-842"},"PeriodicalIF":4.3,"publicationDate":"2026-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146228451","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