RNA最新文献

{"title":"SERIPH: a two-step extraction protocol for selective enrichment of semi-extractable RNAs.","authors":"Naoko Fujiwara, Junichi Iwakiri, Chao Zeng, Daiki Kohsho, Kiyoshi Asai, Michiaki Hamada, Tetsuro Hirose","doi":"10.1261/rna.081061.126","DOIUrl":"10.1261/rna.081061.126","url":null,"abstract":"<p><p>Conventional RNA extraction with acid guanidinium thiocyanate-phenol-chloroform (AGPC) reagents incompletely recovers a subset of transcripts, termed semi-extractable RNAs (seRNAs). This underrepresented RNA population includes architectural RNAs (arcRNAs), which scaffold membraneless organelles, as well as stress-induced downstream-of-gene readthrough transcripts (DoGs). Although our previously developed AGPC extraction method incorporating physical disruption, such as heating or needle shearing, enhances seRNA recovery, it also co-extracts abundant, readily extractable RNAs, resulting in mixed populations that hinder precise characterization. Here, we present SERIPH (<u>s</u>emi-<u>e</u>xtractable <u>R</u>NA isolation from the <u>i</u>nter<u>ph</u>ase), a simple two-step protocol that selectively enriches seRNAs by separating them from readily extractable RNA species. In SERIPH, the aqueous phase containing extractable RNAs is first removed following conventional AGPC extraction. The remaining interphase is subsequently subjected to the extraction procedure incorporating physical disruption, yielding a fraction selectively enriched for semi-extractable transcripts. Transcriptome-wide RNA sequencing demonstrates that SERIPH robustly enriches established seRNAs, including arcRNAs and stress-induced DoGs, while efficiently depleting abundant mRNAs. Compared with the previous extraction method alone, SERIPH increases both the number and genomic extent of detectable DoG loci and enhances sensitivity for weakly semi-extractable transcripts that fall below conventional threshold-based classifications. SERIPH further reveals enrichment of intron-retaining transcript subsets within the semi-extractable RNA fraction. By expanding the detectable seRNA repertoire and enabling selective enrichment, SERIPH establishes a practical framework for focused, high-resolution analysis of seRNA populations. This methodological advance facilitates comprehensive characterization of seRNAs and supports studies of RNA processing, transcriptional regulation, and RNA-mediated nuclear organization in stress responses and disease.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1514-1528"},"PeriodicalIF":4.3,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13492121/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148332571","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}

{"title":"Quantitative comparison of methodologies for translation site imaging in living cells.","authors":"Agata D Misiaszek, Esther Griesbach, Egle Jaugaite, Aurelio Ortale, Jan Eglinger, Tobias Hochstoeger, Jeffrey A Chao","doi":"10.1261/rna.080881.125","DOIUrl":"10.1261/rna.080881.125","url":null,"abstract":"<p><p>Single-molecule imaging of translation sites in living cells has enabled the dynamics of protein synthesis to be investigated with high spatial and temporal resolution. These methodologies utilize the interaction between a multimerized epitope tag and its cognate fluorescent single-chain variable fragment or nanobody to detect nascent polypeptides as they emerge from the ribosome. Here, we present a systematic comparison of current methodologies and determine that the ALFA-tag reduces perturbations of mRNA expression and increases the fluorescent signal of translation sites.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1355-1364"},"PeriodicalIF":4.3,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13492120/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148265869","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}

{"title":"Trailer Hitch tunes condensate phase behavior and mRNA partitioning to regulate P-body homeostasis during <i>Drosophila melanogaster</i> oogenesis.","authors":"Samantha N Milano, Livia V Bayer, Julie J Ko, Gwendolyn S Posner, Caroline E Casella, Diana P Bratu","doi":"10.1261/rna.081011.126","DOIUrl":"10.1261/rna.081011.126","url":null,"abstract":"<p><p>Processing bodies (P-bodies) are cytoplasmic granules that regulate mRNA storage, repression, and decay, yet how their internal organization supports selective mRNA regulation remains poorly understood. Here, we show that the conserved LSm protein Trailer Hitch (Tral) is a key organizer of P-body architecture and function in the <i>Drosophila melanogaster</i> female germline. Using quantitative confocal imaging, super-resolution microscopy, and chemical perturbation of intermolecular interactions, we demonstrate that Tral coordinates the incorporation and spatial organization of the core P-body proteins Me31B and Cup. Loss of Tral alters their partitioning into P-bodies, promotes demixing into distinct subdomains, and shifts condensates toward a less dynamic, structurally heterogeneous state. These organizational changes have functional consequences for mRNA storage: Tral depletion selectively releases maternal mRNA <i>bicoid</i>, while <i>nanos</i> mRNA remains P-body associated and stable. We further identify <i>twinstar</i> mRNA, encoding the homolog of the actin regulator Cofilin, as a Tral-dependent P-body client whose localization and organization within P-bodies requires Tral:RNA interactions and electrostatic forces. Reduced <i>twinstar</i> mRNA levels in the absence of Tral are associated with decreased nuclear G-actin and altered transcription of <i>me31B</i> and <i>cup</i>, revealing a potential feedback mechanism that links cytoplasmic P-body organization to nuclear gene expression. Together, these findings establish Tral as a central regulator of P-body architecture that couples condensate organization to selective mRNA regulation and transcriptional homeostasis.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1388-1410"},"PeriodicalIF":4.3,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148258644","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}

{"title":"Cleavage specificity of <i>E. coli</i> YicC endoribonuclease.","authors":"Sarah A Barnes, Michael B Lazarus, David H Bechhofer","doi":"10.1261/rna.081057.126","DOIUrl":"10.1261/rna.081057.126","url":null,"abstract":"<p><p><i>Escherichia coli</i> YicC enzyme is the founding member of a family of endoribonucleases that is encoded in most bacterial species. Previous structural studies revealed that this ribonuclease binds RNA by a novel mechanism in which the hexameric apoprotein presents an open channel that undergoes a large rotation upon RNA binding and clamps down on the RNA. The current study follows up on these findings by examining the cleavage of various oligonucleotide substrates designed to probe recognition elements required for YicC binding and cleavage. A 26 nucleotide RNA oligomer (oligo), with a <i>K</i> _D in the low micromolar range, was the standard to which numerous oligos with altered sequence were compared. In vitro RNase assays and fluorescence anisotropy binding measurements indicated that the preferred substrates for YicC were relatively small RNAs that contain some secondary structure. Larger RNAs or highly structured RNAs were less-than-optimal substrates. Similarly, RyhB RNA, an ∼90 nucleotide, iron-responsive RNA of <i>E. coli</i>, which has been described as a target of YicC binding and/or cleavage, was a poor YicC substrate in our assays. These results suggest that the native substrates for YicC-family members are very small RNAs or RNA fragments derived from larger RNAs.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1411-1421"},"PeriodicalIF":4.3,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148258610","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}

{"title":"A mutation in the nuclear speckle and splicing factor SRRM2 is associated with multisystem proteinopathy and causes dysregulation of synapse-associated genes.","authors":"Qingyu Shi, Chloe Lauder, Jolie M Miller, Yong-Dong Wang, Noha Elsakrmy, Sofija Volkanoska, Brian D Freibaum, Joanne Wuu, Michael Benatar, Hui Peng, Hong Joo Kim, J Paul Taylor, Haissi Cui","doi":"10.1261/rna.080836.125","DOIUrl":"10.1261/rna.080836.125","url":null,"abstract":"<p><p>Multisystem proteinopathy (MSP) is a pleiotropic degenerative disorder which affects the nervous system, muscles, and bones. The identification of risk factors and their molecular contribution to MSP expands our understanding of disease mechanisms. Here, we describe a family with dominantly inherited MSP, in which a mutation in the serine/arginine repetitive matrix protein 2 gene (<i>SRRM2)</i> that co-segregates with disease, is identified. SRRM2 is essential for nuclear speckle formation and a constitutive member of the RNA splicing machinery. To investigate how the mutation in SRRM2 might contribute to MSP pathogenesis, we examined its effect on a model cell line, where the point mutation was introduced in the endogenous gene. Surprisingly, we found that the resulting single amino acid exchange led to the loss of protein-protein interaction between SRRM2 and the splicing factor ACIN1. Transcriptome studies further revealed widespread differential gene expression, which converged on the dysregulation of synapse-associated pathways. Together, our findings identify SRRM2 as a novel MSP risk factor and provide mechanistic insights into how its mutation can be linked to MSP pathology.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1436-1452"},"PeriodicalIF":4.3,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13492126/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148272650","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}

{"title":"Targeting <i>HORMAD1</i> splicing enhances MEK inhibitor sensitivity in breast cancers.","authors":"Chenyan Sun, Huacheng Luo, Jing Zhang","doi":"10.1261/rna.081080.126","DOIUrl":"10.1261/rna.081080.126","url":null,"abstract":"<p><p>Mutations in BRCA1 are key drivers of breast cancer by impairing homologous recombination. While these tumors are often sensitive to PARP inhibitors, resistance frequently emerges, highlighting the need to identify additional molecular vulnerabilities. HORMAD1 is frequently overexpressed in triple-negative breast cancer and associated with genomic instability, yet its role in therapy response in BRCA1-deficient tumors remains unclear. Here, transcriptomic profiling of BRCA1-mutant breast cancer identified <i>HORMAD1</i> as one of the most upregulated and alternatively spliced genes. The splicing inhibitor isoginkgetin globally altered alternative splicing patterns in BRCA1-mutant cells, promoting <i>HORMAD1</i> exon 4 inclusion. We found that RNA-binding protein RBM38 is correlated with exon 4 inclusion, and RBM38 knockdown further sensitized BRCA1-mutant cells to <i>MEK1</i> inhibition. Together, these findings define an RBM38-HORMAD1 signaling as a potential therapeutic vulnerability in BRCA1-mutant breast cancer and suggest that targeting splicing regulation may represent a promising strategy to enhance treatment efficacy.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1345-1354"},"PeriodicalIF":4.3,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148272674","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}

{"title":"EF-P inhibits ribosomal α-hydroxy acid incorporation: strategic tRNA body selection for co-incorporating α-hydroxy acids and nonproteinogenic amino acids into depsipeptides.","authors":"Takayuki Katoh","doi":"10.1261/rna.081083.126","DOIUrl":"10.1261/rna.081083.126","url":null,"abstract":"<p><p>Genetic code reprogramming has enabled the ribosomal incorporation of diverse nonproteinogenic amino acids (npAAs) into nascent peptide chains. While backbone-altering npAAs-such as β-amino, γ-amino, d-amino, and <i>N</i>-methylamino acids-are typically poor substrates, the development of engineered tRNAs, notably tRNA^Pro1E2, has facilitated their efficient incorporation. tRNA^Pro1E2 possesses a distinct D-arm motif recognized by the translation factor EF-P, which enhances peptide bond formation with these npAAs. α-Hydroxy acids can also be ribosomally incorporated to form ester bonds, serving as valuable building blocks for novel bioactive depsipeptides. In this study, α-hydroxy acid incorporation was unexpectedly found to be significantly inhibited by EF-P when charged onto EF-P-responsive tRNAs, such as tRNA^Pro1 and tRNA^Pro1E2 This inhibition was effectively disrupted by a single mutation in the D-arm motif. To enable the efficient co-incorporation of α-hydroxy acids and other backbone-altering npAAs (e.g., β- and d-amino acids) in a single translation, a dual-tRNA strategy was employed: α-hydroxy acids were charged onto an EF-P-insensitive tRNA (tRNA^AsnE2), while β-/d-amino acids were charged onto tRNA^Pro1E2 Using this approach, a model depsipeptide containing two α-hydroxy acids, one β-amino acid, and one d-amino acid was successfully synthesized in an EF-P-dependent manner.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1365-1372"},"PeriodicalIF":4.3,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13492118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148272679","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}

{"title":"The Tor pathway, ribosome concentration, and wobble decoding mediate inhibitory effects of the Leu-Pro CUC-CCG codon pair in <i>Saccharomyces cerevisiae</i>.","authors":"Brandon S Bruno, Evan M Platten, Lisa Houston, Christina E Brule, Elizabeth J Grayhack","doi":"10.1261/rna.081015.126","DOIUrl":"10.1261/rna.081015.126","url":null,"abstract":"<p><p>Translation elongation and efficiency are modulated by the genetic code, with reduced translation efficiency and slow translation caused by 17 inhibitory codon pairs in the yeast <i>Saccharomyces cerevisiae</i> Nine of these inhibitory pairs are functionally important as they are disproportionately strongly conserved within orthologous genes in <i>Saccharomyces sensu stricto</i> For three pairs, including CGA-CGA, inhibition is triggered by ribosome collisions followed by known quality control responses, but the mechanisms by which nine other pairs cause inhibition are unknown. Here, our examination of the molecular basis of inhibition by one such pair, the highly conserved Leu-Pro CUC-CCG codon pair, yielded four findings. First, inhibition is mediated by tRNA^Leu(UAG), which decodes CUC by a U•C wobble interaction and effectively competes with the nonessential Watson-Crick base-pairing tRNA^Leu(GAG) Second, despite nearly universal conservation of U33 in tRNAs, the C33 alteration in tRNA^Leu(GAG) does not significantly impair its function. Third, inhibition likely is mediated by ribosome collisions, as many suppressors bear mutations known or predicted to reduce ribosome concentration, and as local reduction in ribosome concentration suppresses inhibition. Thus, differences between CUC-CCG and CGA-CGA inhibition likely occur downstream from ribosome collisions. Fourth, we find a link between the metabolic state and CUC-CCG inhibition, as we find six suppressor mutations in <i>SCH9</i>, a downstream effector of TORC1 that mediates ribosome production. As Sch9 is inactive during starvation, causing reduced ribosome concentration, one biological function of inhibitory pairs may be to mediate a change in relative expression during starvation conditions.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1453-1472"},"PeriodicalIF":4.3,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13492127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148265898","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}

{"title":"RNA•DNA:DNA triplex formation by <i>HIF1α-AS1</i> modulates individual base pair stabilities in the <i>adrenomedullin</i> DNA target duplex.","authors":"Nina M Krause, Julia Wirmer-Bartoschek, Christian Richter, Matthias S Leisegang, Ralf P Brandes, Harald Schwalbe","doi":"10.1261/rna.080909.125","DOIUrl":"10.1261/rna.080909.125","url":null,"abstract":"<p><p>Long noncoding RNAs (lncRNAs) play key roles in gene regulation. One potential regulation mechanism involves the formation of RNA•DNA:DNA triplexes. In these triplexes, the lncRNA binds in the major groove of a target DNA via Hoogsteen base pair formation. Here, we investigated the impact of the underlying RNA binding on the stability of the DNA duplex target to gain insights into the triplex stability at base pair resolution with an isolated triplex system. Quantification of the temperature-dependent exchange of imino hydrogen atoms with solvent of the target DNA duplex allows determination of the changes in the stability of individual DNA duplex base pairs upon triplex formation. The data shown here investigates an antiparallel triplex, formed between the lncRNA hypoxia-inducible factor 1-α antisense RNA 1 (<i>HIF1α-AS1</i>) and the DNA target adrenomedullin (<i>ADM</i>), important in cardiovascular diseases. Triplex formation alters DNA structure and stability by affecting both hydrogen bonding strength and nucleobase-stacking interactions. These thermodynamic insights support bioinformatic methods to predict triplex stability and enhance our understanding of RNA•DNA:DNA triplex formation.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1320-1327"},"PeriodicalIF":4.3,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13374514/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147842257","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}

{"title":"Past studies suggest potential therapies for newly discovered retinitis pigmentosa mutations in U6 and U4 snRNAs.","authors":"David A Brow","doi":"10.1261/rna.081086.126","DOIUrl":"10.1261/rna.081086.126","url":null,"abstract":"","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"1195-1198"},"PeriodicalIF":4.3,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13374513/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147875585","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}