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A comparison of Dictyostelium discoideum 3'-5' RNA polymerases reveals a conserved tRNAHis guanylyltransferase residue that plays a dual role in catalysis. 比较盘状盘基钢菌的3'-5' RNA聚合酶,发现一个保守的tRNAHis guan酰转移酶残基在催化中起双重作用。
IF 4.3 3区 生物学
RNA Pub Date : 2026-05-18 DOI: 10.1261/rna.080815.125
Grace N Johnecheck, Korey J Kihm, Jane E Jackman
{"title":"A comparison of <i>Dictyostelium discoideum</i> 3'-5' RNA polymerases reveals a conserved tRNA<sup>His</sup> guanylyltransferase residue that plays a dual role in catalysis.","authors":"Grace N Johnecheck, Korey J Kihm, Jane E Jackman","doi":"10.1261/rna.080815.125","DOIUrl":"10.1261/rna.080815.125","url":null,"abstract":"<p><p>The 3'-5' RNA polymerase family consists of eukaryotic tRNA<sup>His</sup> guanylyltransferase (Thg1) and Thg1 homologs known as Thg1-like proteins (TLPs) that exist in all three domains of life. Thg1 catalyzes an essential reaction adding a G<sub>-1</sub> nucleotide to the 5' end of the tRNA<sup>His</sup>, forming an identity element for tRNA aminoacylation. All TLPs studied, except <i>Dictyostelium discoideum</i> (Ddi) TLP2, perform in vitro Watson-Crick (WC) dependent addition of multiple nucleotides to repair truncated tRNA. DdiTLP2 has similar activity to Thg1, adding G<sub>-1</sub> to mt-tRNA<sup>His</sup>, but shares other biochemical properties with other TLPs, including a restriction to making WC base pairs during this reaction. We identified two regions in DdiTLP2 that lacked residues that are conserved in other Thg1/TLP enzymes. DdiTLP2 variants in both regions abolish enzymatic activity of DdiTLP2, indicating these regions are important for DdiTLP2 catalysis. Changing DdiThg1 D150 to the corresponding arginine found in DdiTLP2 causes an unexpected reversal of this enzyme's specificity, with a loss of its ability to incorporate a non-WC base-paired G<sub>-1</sub> to its physiological substrate, while gaining the ability to add WC base-paired G<sub>-1</sub> to mt-tRNA<sup>His</sup> Biochemical study of other changes to D150, combined with structural models, suggests a previously unknown role for D150 in controlling substrate specificity at the adenylation step by providing a checkpoint for correct setup of a WC base pair in the active site. Thg1 also appears to have adapted the role of the ancestral D150 residue for a second function, promoting non-WC nucleotide addition to its eukaryotic tRNA<sup>His</sup> substrate.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"843-857"},"PeriodicalIF":4.3,"publicationDate":"2026-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146119888","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
mRNA COVID-19 vaccines: science versus misinformation. mRNA COVID-19疫苗:科学与错误信息。
IF 4.3 3区 生物学
RNA Pub Date : 2026-05-18 DOI: 10.1261/rna.080944.126
Jeff Coller, Andrew Geall, Roberta Duncan, Clay Alspach, Sean Ryder, Melissa J Moore, Fátima Gebauer
{"title":"mRNA COVID-19 vaccines: science versus misinformation.","authors":"Jeff Coller, Andrew Geall, Roberta Duncan, Clay Alspach, Sean Ryder, Melissa J Moore, Fátima Gebauer","doi":"10.1261/rna.080944.126","DOIUrl":"10.1261/rna.080944.126","url":null,"abstract":"<p><p>The rapid development of COVID-19 vaccines as a result of Operation Warp Speed represented an extraordinary triumph of scientific innovation, with multiple vaccine platforms demonstrating remarkable efficacy in preventing severe disease, hospitalization, and death-ultimately saving millions of lives. The U.S. government, pharmaceutical companies, research institutions, and health agencies collaborated at an unprecedented scale to develop, test, and distribute vaccines, showcasing what coordinated medical innovation can accomplish. Vaccination programs successfully prevented catastrophic outcomes and enabled people to return to normal life during the crisis. COVID-19 vaccines continue to provide critical protection for vulnerable populations today, and the mRNA platforms developed have opened new possibilities for treating cancers and other diseases. Yet despite rigorous regulatory oversight and extensive clinical trial data, these vaccines have faced substantial misinformation campaigns that spread false claims about their safety and design. To address these misrepresentations and resultant public concerns, this document draws on rigorous scientific evidence to comprehensively examine the misconceptions surrounding mRNA technology, explaining how these vaccines work, their proven safety record, and their demonstrated benefits.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"759-771"},"PeriodicalIF":4.3,"publicationDate":"2026-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13182613/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147481684","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
Tuning tRNA synthetase inhibition reveals parabolic induction of stress granules limited in size and RNA content. 调节tRNA合成酶抑制显示抛物线诱导应激颗粒的大小和RNA含量有限。
IF 4.3 3区 生物学
RNA Pub Date : 2026-05-18 DOI: 10.1261/rna.080883.125
Max Baymiller, Noah S Helton, Benjamin Dodd, Stephanie L Moon
{"title":"Tuning tRNA synthetase inhibition reveals parabolic induction of stress granules limited in size and RNA content.","authors":"Max Baymiller, Noah S Helton, Benjamin Dodd, Stephanie L Moon","doi":"10.1261/rna.080883.125","DOIUrl":"10.1261/rna.080883.125","url":null,"abstract":"<p><p>Translation elongation defects cause ribosome stalling and activate the integrated stress response (ISR). During the ISR, translation initiation suppression and ribosome runoff drive mRNA condensation into stress granules. However, the effects of partial translation elongation inhibition on stress granules are poorly defined. We demonstrate that intermediate levels of tRNA synthetase inhibitors activate the ISR and cause assembly of stress granules in a parabolic dose-response pattern. These stress granules are limited in size and number due to ribosome association with mRNAs. Assembly of stress granules by intermediate levels of the prolyl-tRNA synthetase inhibitor halofuginone requires the canonical stress granule scaffolding proteins G3BP1/2 and GCN2-mediated ISR activation. We performed a candidate-based comparative analysis of the composition of stress granules induced by intermediate levels of halofuginone or canonical stressors arsenite or thapsigargin. The stress granules induced by halofuginone, arsenite, or thapsigargin harbor polyadenylated RNA and the canonical stress granule proteins PABPC1, G3BP1, and UBAP2L. We observe stress- and transcript-specific differences in the localization of candidate RNA molecules to stress granules. These results demonstrate that partial translation elongation inhibition permits stress granule assembly through the balance of ISR activation and mRNA association with ribosomes, with implications for the stress response associated with amino acid or tRNA deficiency, therapeutic tRNA synthetase inhibition, or diseases associated with tRNA synthetase mutations.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"870-884"},"PeriodicalIF":4.3,"publicationDate":"2026-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13182609/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146143406","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
Editing-independent effects of Drosophila Adar on heterochromatin silencing. 果蝇Adar在异染色质沉默中的编辑非依赖性作用。
IF 4.3 3区 生物学
RNA Pub Date : 2026-05-18 DOI: 10.1261/rna.080873.125
Khadija Hajji, Damiano Amoruso, Barbora Nováková, Nagraj Sambrani, Deying Yang, Anzer Khan, Vojtech Bystry, Alejandro Medaglia-Mata, Domenico Alessandro Silvestris, Ernesto Picardi, Mary A O'Connell, Liam P Keegan
{"title":"Editing-independent effects of <i>Drosophila</i> Adar on heterochromatin silencing.","authors":"Khadija Hajji, Damiano Amoruso, Barbora Nováková, Nagraj Sambrani, Deying Yang, Anzer Khan, Vojtech Bystry, Alejandro Medaglia-Mata, Domenico Alessandro Silvestris, Ernesto Picardi, Mary A O'Connell, Liam P Keegan","doi":"10.1261/rna.080873.125","DOIUrl":"10.1261/rna.080873.125","url":null,"abstract":"<p><p>ADAR RNA editing enzymes deaminate selected adenosines to inosines in dsRNA. In <i>Drosophila</i>, inosine in dsRNA inhibits cleavage by Dcr2, and some ADAR proteins contribute an additional, editing-independent inhibition. The <i>Drosophila</i> AdarG isoform, in particular, has been proposed to inhibit HP1-mediated heterochromatin silencing of repetitive sequences initiated by specific dsRNAs. To address the functions of AdarG, we overexpressed it from new <i>UAS-Adar</i> lines, under the control of a temperature-regulated <i>Act5C<sup>ts</sup>-GAL4</i> driver. Overexpression of the adult AdarG isoform or catalytically inactive AdarE374A led to larval lethality with some escaper pupae that show an ecdysone-related, head eversion defect. This indicates an editing-independent effect of high Adar expression. Pupae show aberrantly elevated innate immune and early ecdysone gene transcript expression, and no flies eclose. RNAi knockdown of <i>ecdysone receptor A</i> (<i>EcRA</i>) or increased expression of the histone H3K9me2,3-associated HP1 protein partially rescues AdarG overexpression defects and normalizes gene expression in rescued progeny flies. In other reports, <i>Drosophila</i> mutants with reduced HP1, or <i>egg</i> (SetDB1), <i>Su(var)3-9</i> double mutants with reduced histone H3K9me2,3 also produce larvae with ecdysone-related and innate immune defects. We show that overexpressed AdarG inhibits histone H3K9me-mediated epigenetic silencing through an editing-independent effect, most likely at the dsRNA/Dcr2/Ago2 initiation stage.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"962-981"},"PeriodicalIF":4.3,"publicationDate":"2026-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147435098","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 novel NLP-based method and algorithm to discover RNA-binding protein (RBP) motifs, contexts, binding preferences, and interactions. 一种新的基于nlp的方法和算法来发现rna结合蛋白(RBP)基序、背景、结合偏好和相互作用。
IF 4.3 3区 生物学
RNA Pub Date : 2026-05-18 DOI: 10.1261/rna.080892.125
Shaimae I Elhajjajy, Zhiping Weng
{"title":"A novel NLP-based method and algorithm to discover RNA-binding protein (RBP) motifs, contexts, binding preferences, and interactions.","authors":"Shaimae I Elhajjajy, Zhiping Weng","doi":"10.1261/rna.080892.125","DOIUrl":"10.1261/rna.080892.125","url":null,"abstract":"<p><p>RNA-binding proteins (RBPs) are essential modulators in the regulation of mRNA processing. The binding patterns, interactions, and functions of most RBPs are not well-characterized. Previous studies have shown that motif context is an important contributor to RBP binding specificity, but its precise role remains unclear. Despite recent computational advances to predict RBP binding, existing methods are challenging to interpret and largely lack a categorical focus on RBP motif contexts and RBP-RBP interactions. There remains a need for interpretable predictive models to disambiguate the contextual determinants of RBP binding specificity in vivo. Here, we present a novel and comprehensive pipeline to address these knowledge gaps. We devise a natural language processing-based method to deconstruct sequences into entities comprising a target <i>k</i>-mer and its flanking regions, then use this representation to formulate RBP binding prediction as a weakly supervised multiple instance learning problem. To interpret our predictions, we introduce a deterministic motif discovery algorithm to leverage our data structure, recapitulating the established motifs of numerous RBPs as validation. Importantly, we characterize the binding motifs and binding contexts for 71 RBPs in HepG2 and 74 RBPs in K562, with many of them being novel. Finally, through feature integration, transitive inference, and a new cross-prediction approach, we propose novel cooperative and competitive RBP-RBP interaction partners and hypothesize their potential regulatory functions. In summary, we present a complete framework for investigating the contextual determinants of specific RBP binding, and we demonstrate the significance of our findings in delineating RBP binding patterns, interactions, and functions.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"885-914"},"PeriodicalIF":4.3,"publicationDate":"2026-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13182611/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146228431","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
MiSiPi.Rna: an integrated tool for characterizing small regulatory RNA processing. MiSiPi。Rna:用于表征小调控Rna加工的集成工具。
IF 4.3 3区 生物学
RNA Pub Date : 2026-04-16 DOI: 10.1261/rna.080864.125
Taiya Jarva, Chris Baugh, Jialin Zhang, Eric C Lai, Alex Flynt
{"title":"MiSiPi.Rna: an integrated tool for characterizing small regulatory RNA processing.","authors":"Taiya Jarva, Chris Baugh, Jialin Zhang, Eric C Lai, Alex Flynt","doi":"10.1261/rna.080864.125","DOIUrl":"10.1261/rna.080864.125","url":null,"abstract":"<p><p>Argonaute proteins mediate gene silencing via small regulatory RNAs that are generated by distinctive biogenesis pathways. In animals, three main classes are recognized: ∼21-24 nucleotide (nt) microRNAs (miRNAs), ∼21-24 nt small-interfering RNAs (siRNAs), and ∼24-32 nt Piwi-interacting RNAs (piRNAs). Mechanistic understanding of these pathways was gained from genetic, biochemical, and genomic studies in a handful of model systems, where key ribonucleolytic events were identified that specify stereotyped positioning of small RNAs relative to their precursor transcripts. With burgeoning availability of assembled genomes and small RNA data, there are abundant opportunities to characterize the diversity of small RNAs across nonmodel organisms. While several tools are well-suited to analyze specific small RNA pathways, an integrated package that can help classify and interpret all three major classes of small RNAs is wanting. To address this need, we developed a simple and efficient R package (MiSiPi.Rna) that can generate a variety of plots and statistics for preselected loci, which enable the characterization of diverse biogenesis features of miRNAs, siRNAs, and piRNAs. MiSiPi.Rna requires minimal computational expertise to run and will facilitate efforts to annotate and analyze the major classes of Argonaute-based small regulatory RNAs in arbitrary species of choice.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"584-595"},"PeriodicalIF":4.3,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13418560/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146053734","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 repertoire of binding specificities for two repeats in the RNA-binding domain of Drosophila Pumilio. 果蝇rna结合域两个重复序列的结合特异性。
IF 4.3 3区 生物学
RNA Pub Date : 2026-04-16 DOI: 10.1261/rna.080791.125
Tammy H Wharton, Robin P Wharton
{"title":"The repertoire of binding specificities for two repeats in the RNA-binding domain of <i>Drosophila</i> Pumilio.","authors":"Tammy H Wharton, Robin P Wharton","doi":"10.1261/rna.080791.125","DOIUrl":"10.1261/rna.080791.125","url":null,"abstract":"<p><p>The PUF domain of <i>Drosophila</i> Pumilio consists of eight homologous repeats that act in a modular fashion to recognize Nanos response elements (NREs) in targeted mRNAs, each repeat interacting with a single base of the NRE. Most of the sequence specificity of binding is thought to be driven by interactions between residues 12 and 16 of each repeat with the edge of the appropriate RNA base. In this report, we investigate the repertoire of amino acids at positions 12 and 16 that are capable of mediating high-affinity binding for two of the PUF repeats, R6 and R5. We generate plasmid libraries in which the codons for residues 12 and 16 are randomized, transform these into a suitable yeast strain, and screen for variants that recognize an NRE in three-hybrid RNA-binding experiments. We find that the two repeats have very different capabilities. Relatively few amino acid combinations in R6 are functional, and these exhibit a limited array of binding specificities; in contrast, ∼24% of the edge-on amino acid combinations in R5 are functional, and these exhibit a variety of novel specificities. These results support the idea that R6 (in part) defines NRE target sites, while R5 selects among NREs to allow differential regulation in vivo. We also show that R5 binding modules generally cannot be functionally swapped into R6. Thus, although binding of the Pumilio PUF domain is modular, the R6 and R5 modules are not readily interchangeable, consistent with studies of other PUF domains.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"596-611"},"PeriodicalIF":4.3,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146119922","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
eRNAs modulate mRNA stability and translation efficiency to bridge transcriptional and post-transcriptional gene regulation. erna调节mRNA的稳定性和翻译效率,以架起转录和转录后基因调控的桥梁。
IF 4.3 3区 生物学
RNA Pub Date : 2026-04-16 DOI: 10.1261/rna.080681.125
Rene Kuklinkova, Natalia Benova, Chinedu A Anene
{"title":"eRNAs modulate mRNA stability and translation efficiency to bridge transcriptional and post-transcriptional gene regulation.","authors":"Rene Kuklinkova, Natalia Benova, Chinedu A Anene","doi":"10.1261/rna.080681.125","DOIUrl":"10.1261/rna.080681.125","url":null,"abstract":"<p><p>Enhancer RNAs (eRNAs) are best known for their role in transcriptional regulation, where they facilitate enhancer-promoter communication and chromatin remodeling. Yet growing evidence suggests that their function may extend beyond the nucleus. Here, we systematically characterize the decay kinetics of eRNAs across human cell types using time-resolved transcriptomics and kinetic modeling. While most eRNAs undergo canonical exponential decay, a subset displays nonlinear dynamics, suggesting context-dependent degradation mechanisms. Perturbation of core decay regulators, including components of the m<sup>6</sup>A and <i>CCR4-NOT</i> pathways, reveals that eRNA stability is modulated by a patchwork of pathways governing mRNA turnover. Integrating transcriptome-wide ribosome profiling, RNA-seq, and half-life data, we identify eRNAs associated with changes in mRNA stability and translation efficiency of their target protein-coding transcripts. Functional validation of one such eRNA, <i>en4528</i>, shows that it regulates <i>CDKN2C</i> and <i>FAF1</i> mRNA independently of transcription and impacts cell migration. These findings redefine the regulatory scope of eRNAs, positioning them as active participants in post-transcriptional gene control and cellular behavior. The resulting decay profiles and regulatory annotations have been incorporated into the eRNAkit database, available at https://github.com/AneneLab/eRNAkit, enhancing its capacity for integrative systems-level analysis of eRNA function.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"704-723"},"PeriodicalIF":4.3,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146114093","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
RK-33 inhibits the OC43 coronavirus and induces stress granules via DDX3X-independent mechanisms. RK-33通过不依赖ddx3x的机制抑制OC43冠状病毒并诱导应激颗粒。
IF 4.3 3区 生物学
RNA Pub Date : 2026-04-16 DOI: 10.1261/rna.080931.125
Cody J S Hecht, Roy R Parker
{"title":"RK-33 inhibits the OC43 coronavirus and induces stress granules via DDX3X-independent mechanisms.","authors":"Cody J S Hecht, Roy R Parker","doi":"10.1261/rna.080931.125","DOIUrl":"10.1261/rna.080931.125","url":null,"abstract":"<p><p>DDX3X is a human DEAD-box RNA helicase with multiple functions in RNA metabolism. Previous studies have suggested that DDX3X is an important proviral host factor for numerous RNA viruses, including HIV, HCV, and SARS-CoV-2, and may be targetable with inhibitors such as RK-33 for therapeutic benefit. In exploring the role of DDX3X and its homolog DDX3Y in coronavirus replication, we found that the DDX3X inhibitor RK-33 inhibits propagation of the OC43 coronavirus through a DDX3X/DDX3Y-independent mechanism. Knockdowns of DDX3X or DDX3X and DDX3Y had little effect on OC43 growth in multiple cell lines, yet RK-33 treatment reduced OC43 replication in the presence or absence of DDX3 proteins. We observed that RK-33 stimulates the integrated stress response independently of DDX3 proteins to cause stress granule formation, although this is not the primary mechanism by which RK-33 suppresses OC43. Together, our results show that DDX3 proteins are likely not general pro-coronaviral host factors, and caution should be used in interpreting results with RK-33 given its off-target activity.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"724-735"},"PeriodicalIF":4.3,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13085917/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146093855","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
Codon bias shapes bacterial small RNA binding sites within protein-coding sequences. 密码子偏倚在蛋白质编码序列中形成细菌小RNA结合位点。
IF 4.3 3区 生物学
RNA Pub Date : 2026-04-16 DOI: 10.1261/rna.080839.125
Shira Fisher, Hanah Margalit
{"title":"Codon bias shapes bacterial small RNA binding sites within protein-coding sequences.","authors":"Shira Fisher, Hanah Margalit","doi":"10.1261/rna.080839.125","DOIUrl":"10.1261/rna.080839.125","url":null,"abstract":"<p><p>Bacterial small RNAs (sRNAs) regulate gene expression by base-pairing with target mRNAs, affecting their stability and translation. While sRNA binding sites were initially identified in 5' untranslated regions of mRNAs, consistent with their role as translation-initiation regulators, recent large-scale studies have revealed sRNA binding sites within protein-coding sequences, suggesting additional regulatory mechanisms. It is intriguing to explore how the latter sRNA binding sites are adjusted with the reading frame and what selection forces maintain them within the coding sequence through evolution. Using RIL-seq data, we determined prime sRNA binding positions within coding sequences, which are positions within the inferred binding-site motif that show exceptionally high conservation across target sequences (≥95%), indicating their putative importance for sRNA-mRNA base-pairing. We found that these positions are mostly adjusted with the reading frame and correspond to the most frequent codons, high above random expectation. This suggests that frequent codons may facilitate sRNA-mRNA encounters and that codon usage bias influences binding site formation via selective pressures. Conservation analysis across genomes in the Enterobacterales order revealed that prime positions show relatively high conservation of base-pairing interactions. However, in some genomes base-pairing in these positions may be hampered due to the degeneracy of the genetic code. This is often compensated for by other positions that conserve the base-pairing interactions, ensuring the maintenance of a requisite number of base pairs for sustaining the sRNA-target interaction. Our findings highlight the importance of distinct interacting positions as well as an adequate number of base pairs for sustaining sRNA-target interactions.</p>","PeriodicalId":21401,"journal":{"name":"RNA","volume":"32 5","pages":"568-583"},"PeriodicalIF":4.3,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13085923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147699635","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
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