IF 5 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":"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.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"584-595"},"PeriodicalIF":5.0,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Development of Universal Mass Exclusion List (UMEL) for RNA modification mapping. 用于RNA修饰定位的通用质量排除表（UMEL）的开发。

IF 5 3区生物学

RNA Pub Date : 2026-04-16 DOI: 10.1261/rna.080901.125

Asif Rayhan, Patrick A Limbach, Balasubrahmanyam Addepalli

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 5 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":"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 m6A and CCR4-NOT 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, en4528, shows that it regulates CDKN2C and FAF1 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.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"704-723"},"PeriodicalIF":5.0,"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

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 5 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 Drosophila Pumilio.","authors":"Tammy H Wharton, Robin P Wharton","doi":"10.1261/rna.080791.125","DOIUrl":"10.1261/rna.080791.125","url":null,"abstract":"The PUF domain of Drosophila 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.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"596-611"},"PeriodicalIF":5.0,"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

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 5 3区生物学

RNA Pub Date : 2026-04-16 DOI: 10.1261/rna.080931.125

Cody J S Hecht, Roy R Parker

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 5 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":"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.","PeriodicalId":21401,"journal":{"name":"RNA","volume":"32 5","pages":"568-583"},"PeriodicalIF":5.0,"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

Localized regulation of cell junction mRNAs is required for epithelial cell integrity. 细胞连接mrna的局部调控是上皮细胞完整性所必需的。

IF 5 3区生物学

RNA Pub Date : 2026-04-16 DOI: 10.1261/rna.080898.125

Ashley Chin, Jonathan Bergeman, Laudine Communal, Seda Barutcu, Jonathan Boulais, Gene W Yeo, Anne-Marie Mes-Masson, Eric Lécuyer

{"title":"Localized regulation of cell junction mRNAs is required for epithelial cell integrity.","authors":"Ashley Chin, Jonathan Bergeman, Laudine Communal, Seda Barutcu, Jonathan Boulais, Gene W Yeo, Anne-Marie Mes-Masson, Eric Lécuyer","doi":"10.1261/rna.080898.125","DOIUrl":"10.1261/rna.080898.125","url":null,"abstract":"Epithelial cells exhibit a highly polarized organization along their apico-basal axis, a feature that is critical to their function and is frequently perturbed in cancer. One less explored process modulating epithelial cell polarity is the subcellular localization of mRNA molecules. In this study, we report that several mRNAs encoding evolutionarily conserved epithelial polarity regulatory proteins, including Zo-1, Afdn, and Scrib, are localized to cell junction regions in Drosophila epithelial tissues and human epithelial cells. Targeting of these mRNAs coincides with robust junctional distribution of their encoded proteins, and these transcripts are translated in proximity to cell junction regions. Through systematic immunolabeling, we identify a collection of RNA binding proteins with cell junction distribution patterns, several of which associate with junctional transcripts and are functionally required for proper targeting of ZO-1 and SCRIB proteins. Loss of function of two candidate factors, MAGOH and PCBP3, differentially impacts junctional mRNA, with MAGOH knockdown reducing Zo-1 and Scrib transcript targeting and localized translation, while PCBP3 knockdown only perturbs local translation. Depletion of Drosophila MAGO in vivo in follicular epithelial cells also disrupts the distribution of junctional transcripts and proteins. Finally, through tissue microarray analysis of ovarian cancer tumor specimens, we find that the expression of MAGOH and ZO-1 is positively correlated and that both proteins are potential biomarkers of good prognosis. We conclude that localized mRNA regulation at cell junction regions is important for modulating epithelial cell integrity.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"635-653"},"PeriodicalIF":5.0,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145985434","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

Corrigendum: Aminoacyl-tRNA synthetases. 更正：氨基酰基- trna合成酶。

IF 5 3区生物学

RNA Pub Date : 2026-04-16 DOI: 10.1261/rna.080972.126

Miguel Angel Rubio Gomez, Michael Ibba

引用次数: 0

Identification of 3D motifs in Rfam with JAR3D. 用JAR3D识别Rfam中的三维图案。

IF 5 3区生物学

RNA Pub Date : 2026-04-16 DOI: 10.1261/rna.080764.125

James Roll, Craig L Zirbel

{"title":"Identification of 3D motifs in Rfam with JAR3D.","authors":"James Roll, Craig L Zirbel","doi":"10.1261/rna.080764.125","DOIUrl":"10.1261/rna.080764.125","url":null,"abstract":"Many non-protein-coding RNAs are being discovered each year. At first we know them only by their sequences in a few organisms, but to understand their function and interactions, we need to understand what 3D structures they may form, in whole or in part. Many hairpin and internal loops are known to form recurrent structured 3D motifs, for example, kink turn and sarcin-ricin internal loops, and GNRA and T-loop hairpin loops. A new non-protein-coding RNA may have one or more known structured 3D loop motifs. Here we introduce a tool which identifies loops in Rfam seed alignments that match known 3D loop motifs and makes those identifications easily accessible. JAR3D was developed to map sequences of hairpin and internal loops to known 3D motifs, and was extended for this work to three-way and four-way junction motifs. We applied JAR3D to 4166 Rfam seed alignments from Rfam 15.0 and made the results accessible on the JAR3D web page, making it easy to evaluate the possible matches for each loop in each Rfam family. We provide several examples which validate JAR3D's ability to identify the correct loop motif, using 3D structures of RNAs outside of the training set. We created a page to search for instances of a particular loop motif across all Rfam families, to study how widespread the occurrence of each motif is. We provide statistics on how many Rfam loops appear to match well to a known 3D motif. Match rates are much higher for internal loops than for hairpins or multihelix junctions.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"555-567"},"PeriodicalIF":5.0,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13085918/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146053679","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

Distribution and structural diversity of type IV internal ribosome entry sites. IV型内部核糖体进入位点的分布和结构多样性。

IF 5 3区生物学

RNA Pub Date : 2026-04-16 DOI: 10.1261/rna.080638.125

Katherine E Segar, Madeline E Sherlock, Jeffrey S Kieft

{"title":"Distribution and structural diversity of type IV internal ribosome entry sites.","authors":"Katherine E Segar, Madeline E Sherlock, Jeffrey S Kieft","doi":"10.1261/rna.080638.125","DOIUrl":"10.1261/rna.080638.125","url":null,"abstract":"Internal ribosome entry sites (IRESs) are RNA sequences that facilitate cap- and end-independent translation initiation in eukaryotes. Type IV IRESs, which include the hepatitis C virus IRES, directly bind the 40S ribosomal subunit and require only a subset of canonical initiation factors to function. As the full extent of diversity and species distribution of type IV IRESs was unknown, we sought to identify and classify the architectural variation of all members. Using a secondary structure homology-based search method, we identified 163 putative type IV IRESs from viruses with diverse hosts and phylogeny, including the first example in a double-stranded viral genome. Clustering analysis based on the presence and overall size of secondary structure elements yielded three distinct groups, differentiated by substantial expansions and deletions. Chemical probing of representative IRES RNAs from each cluster confirmed predicted secondary structures. Subsequent in vitro translation assays suggested that structural differences produce functional variation. Our findings reveal distinct structural adaptations and patterns within the type IV IRESs that may influence IRES function and mechanism.","PeriodicalId":21401,"journal":{"name":"RNA","volume":" ","pages":"622-634"},"PeriodicalIF":5.0,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146114136","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

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