IF 4.1 3区生物学

RNA Biology Pub Date : 2026-12-31 Epub Date: 2026-05-12 DOI: 10.1080/15476286.2026.2667707

Laveena Kansara, Georg Wolfstetter, Daniel Wintermayr, Ioannis Alexopoulos, Alejandra Escos, Marc Friedländer, Ylva Engström

{"title":"The mRNA architecture of the translation termination site primes programmed stop codon readthrough events in Drosophila.","authors":"Laveena Kansara, Georg Wolfstetter, Daniel Wintermayr, Ioannis Alexopoulos, Alejandra Escos, Marc Friedländer, Ylva Engström","doi":"10.1080/15476286.2026.2667707","DOIUrl":"10.1080/15476286.2026.2667707","url":null,"abstract":"Programmed stop codon readthrough (SCR) is a form of genetic re-coding, in which a near-cognate tRNA base-pairs with a stop codon, leading to the translation of a C-terminally extended protein. Recent studies revealed that SCR represents an evolutionarily conserved, spatio-temporally controlled mechanism of posttranscriptional gene regulation that requires cis-regulatory elements as well as trans-acting factors. In this study, we characterized cis-regulatory elements controlling programmed SCR of the Drosophila POU3-family member drifter/ventral veins lacking (dfr/vvl). Using S2 cell-based luciferase assays, we show that stop codon identity and the +4 to +9 nucleotide sequence are required but not sufficient for dfr SCR regulation. Phylogenetic prediction identified an mRNA stem-loop in the 3' UTR, proximal to the readthrough UAG codon. Mutational analysis revealed that the distance from the stop codon as well as stem-loop stability, but not the underlying sequence identity, critically impact dfr SCR. Similarly, the mRNA stem-loop promoted SCR in an in vivo Drosophila model. We applied this information to refine computational prediction of SCR-associated mRNA stem-loops and show that these elements effectively promote SCR of heterologous mRNAs. These findings increase our understanding of SCR and the underlying regulatory mechanisms.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-21"},"PeriodicalIF":4.1,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13170385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147842295","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

A transformer-based method for the cap analysis of gene expression and gene expression tag associated capping region prediction in RNA. 基于变压器的RNA基因表达Cap分析及基因表达标签相关capping区域预测方法。

IF 4.1 3区生物学

RNA Biology Pub Date : 2026-12-31 Epub Date: 2026-02-16 DOI: 10.1080/15476286.2026.2629530

Dibya Kanti Haldar, Avik Pramanick, Chandrama Mukherjee, Pralay Mitra

{"title":"A transformer-based method for the cap analysis of gene expression and gene expression tag associated capping region prediction in RNA.","authors":"Dibya Kanti Haldar, Avik Pramanick, Chandrama Mukherjee, Pralay Mitra","doi":"10.1080/15476286.2026.2629530","DOIUrl":"10.1080/15476286.2026.2629530","url":null,"abstract":"5' RNA capping is one of the major post-transcriptional modifications for the mobility and stability of RNA molecules. Measuring 5' caps of RNAs can help quantify expression levels of mRNAs and lncRNAs. One of the most successful RNAseq methods that has used capping as a tool to quantify expression of transcription is Cap Analysis of Gene Expression (CAGE). Computational prediction of capping can therefore be used as a precursor to the prediction of transcriptional expression. Unfortunately, there is hardly any computational technique that has focused purely on predicting 5' capping. We have developed a transformer-based method for computational prediction of capping from DNA sequences. Our Llama and ReLoRA-based pre-training model, and Llama and LoRA-based fine-tuning model predict capping associated regions. We have used Leave-one-chromosome-out-cross-validation for our model. The average accuracy, and F1-score after fine-tuning the human genome hg19 (mouse genome mm9) for sequence classification is 79.12% (78.09%) and 78.11% (76.17%), respectively. We noted attention peak-based motifs having an aggregate Wilcoxon rank-sum p-value of 1.075e-10 between the attention peak region and the entire context window for the predicted positive motifs; an aggregate p-value of 7.17e-18 for the predicted negative motifs; and an aggregate p-value of 6.70e-08 between the attention peaks of the predicted positive and the predicted negative motifs. Our Llama-based approach aims to create a sequence-based framework to identify capping associated regions corresponding to CAGE peaks. Our analysis reveals statistically significant motifs from the regions of peak attention scores, which demonstrates biological relevance for some through their resident sites matching with known TF motifs.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-15"},"PeriodicalIF":4.1,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12915862/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146158588","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

Hsa_circ_0000711 can serve as a novel biomarker for primary biliary cholangitis by promoting disease progression through the regulation of miR-185-5p and NFATc3. Hsa_circ_0000711可以通过调节miR-185-5p和NFATc3促进疾病进展，作为原发性胆道炎的新型生物标志物。

IF 4.1 3区生物学

RNA Biology Pub Date : 2026-12-31 Epub Date: 2026-03-25 DOI: 10.1080/15476286.2026.2638278

Wenlong Lu, Wenshuai Li, Pan Wang, Peishan Cong, Zhan Wang, Weize Gao, Guirong Sun, Mingjun Liu

{"title":"Hsa_circ_0000711 can serve as a novel biomarker for primary biliary cholangitis by promoting disease progression through the regulation of miR-185-5p and NFATc3.","authors":"Wenlong Lu, Wenshuai Li, Pan Wang, Peishan Cong, Zhan Wang, Weize Gao, Guirong Sun, Mingjun Liu","doi":"10.1080/15476286.2026.2638278","DOIUrl":"10.1080/15476286.2026.2638278","url":null,"abstract":"Primary biliary cholangitis (PBC) is a chronic cholestatic liver disease characterized by autoimmune-mediated destruction of intrahepatic bile ducts. Emerging evidence suggests that circular RNAs (circRNAs) play regulatory roles in autoimmune diseases, but their involvement in PBC remains unclear. This study focused on the hsa_circ_0000711 and its potential mechanism in PBC pathogenesis. The study included 46 PBC patients, 40 healthy controls, and 40 patients with other liver diseases. Human intrahepatic biliary epithelial cells (HiBEpic) were treated with 1 mM glycochenodeoxycholic acid (GCDCA) to establish a PBC cell model. Hsa_circ_0000711 was overexpressed or knocked down using plasmid transfection and siRNA, respectively. Expression levels were analysed by qPCR/Western blot, cell viability by CCK-8, and hsa_circ_0000711-miR-185-5p interaction by luciferase assay. Serum hsa_circ_0000711 levels were significantly higher in PBC patients compared to healthy controls and other liver disease groups (p < 0.0001). GCDCA-treated HiBEpic cells showed increased expression of the E2 subunit of the pyruvate dehydrogenase complex (PDC-E2) and nuclear factor of activated T cells 3 (NFATc3), along with decreased cell viability. Overexpression of hsa_circ_0000711 increased PDC-E2 and NFATc3 expression and worsened cellular injury, while its knockdown reversed these effects. The dual luciferase assay confirmed that hsa_circ_0000711 directly binds to miR-185-5p, suppressing its activity and thereby relieving the repression of NFATc3. Hsa_circ_0000711 promotes PBC progression by sponging miR-185-5p and upregulating NFATc3, leading to bile duct epithelial cell injury. These findings highlight its potential as a novel diagnostic biomarker and therapeutic target for PBC.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"23 1","pages":"1-13"},"PeriodicalIF":4.1,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13020888/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147514496","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

Long non-coding RNA transcripts in crucian carp brain - annotation and expression patterns in anoxia and reoxygenation. 鲫鱼脑长链非编码RNA转录物在缺氧和复氧条件下的注释和表达模式。

IF 4.1 3区生物学

RNA Biology Pub Date : 2026-12-31 Epub Date: 2026-03-25 DOI: 10.1080/15476286.2026.2643366

Magdalena Winklhofer, Göran Erik Nilsson, Sjannie Lefevre

{"title":"Long non-coding RNA transcripts in crucian carp brain - annotation and expression patterns in anoxia and reoxygenation.","authors":"Magdalena Winklhofer, Göran Erik Nilsson, Sjannie Lefevre","doi":"10.1080/15476286.2026.2643366","DOIUrl":"10.1080/15476286.2026.2643366","url":null,"abstract":"Long non-coding RNAs (lncRNAs) regulate diverse cellular processes, yet their role in anoxia-induced transcriptomic changes in crucian carp (Carassius carassius) - a species that endures months without oxygen at low temperatures - remains unclear. Because existing genome annotations focus on protein-coding genes, we aimed to annotate lncRNAs in crucian carp, assess their potential for involvement in mRNA regulation during anoxia and reoxygenation, and characterize differentially regulated lncRNAs and nearby putative interaction partners (IPs). Using next-generation RNA sequencing of the brain across normoxia, anoxia, and reoxygenation (n = 10 per group), we assembled 145,264 transcripts with a reference-guided approach. With CPC2, CNCI, CPAT, and FEELnc, we identified 6072 lncRNAs. Anoxia elicited a robust transcriptomic response: 56,440 transcripts were differentially expressed (adjusted p-value < 0.05; |log2(fold change)| > 0.38), including 1321 lncRNAs. FEELnc classification highlighted proximal RNA transcripts suggestive of cis-acting lncRNA functions. Most (60%) DElncRNA - IP interaction sites were intergenic, predominantly on the same strand within intergenic subtypes, with many features nested within genic contexts. Notably, log2-fold changes in RNA abundance of predicted DE IPs positively correlated with those of their corresponding DElncRNAs. These results provide a comprehensive lncRNA annotation for crucian carp and reveal extensive lncRNA co-expression with nearby genes during anoxia and reoxygenation, supporting a potential cis-regulatory role in the adaptive transcriptomic response to oxygen deprivation.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-21"},"PeriodicalIF":4.1,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13023002/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147390871","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

HyLnc: a hybrid deep learning and feature-based approach for long non-coding RNA prediction. HyLnc：用于长链非编码RNA预测的混合深度学习和基于特征的方法。

IF 4.1 3区生物学

RNA Biology Pub Date : 2026-12-31 Epub Date: 2026-09-16 DOI: 10.1080/15476286.2026.2731913

Amrit Venkatesan, Prashasti Sinha, Jolly Basak, Ranjit Prasad Bahadur

{"title":"HyLnc: a hybrid deep learning and feature-based approach for long non-coding RNA prediction.","authors":"Amrit Venkatesan, Prashasti Sinha, Jolly Basak, Ranjit Prasad Bahadur","doi":"10.1080/15476286.2026.2731913","DOIUrl":"10.1080/15476286.2026.2731913","url":null,"abstract":"Long non-coding RNAs (lncRNAs) play important roles in gene regulation, development and disease, yet accurate identification of lncRNAs from transcriptomic data remains a major computational challenge. Existing methods often rely either on handcrafted sequence features or deep learning approaches, each with their inherent limitations in capturing the full complexity of RNA sequences. In this study, we proposed HyLnc, a computational framework that integrates transformer-based contextual embeddings with biologically meaningful sequence features for improved lncRNA prediction. A custom BERT-based model was first pre-trained on a large corpus of metazoan RNA sequences using a masked language modelling strategy to learn contextual nucleotide dependencies. The model was subsequently fine-tuned on curated datasets of lncRNAs and protein-coding transcripts and 256-dimensional deep sequence embeddings were extracted. Parallelly, 348 handcrafted features, including ORF characteristics, untranslated region (UTR) properties, nucleotide composition and Fickett scores, were computed. A multi-stage feature selection strategy was applied to identify the most informative features, resulting in optimized hybrid feature sets. Multiple machine learning classifiers were evaluated, with the RF model achieving the best performance. The proposed framework attained an accuracy of 91.30%, F1-score of 91.23% and MCC of 82.60 on an independent validation dataset, outperforming several existing lncRNA prediction tools. Thus, HyLnc demonstrates that integrating deep contextual representations with biologically interpretable features enhances lncRNA prediction. This approach provides a robust and scalable solution for large-scale transcriptome annotation and can be extended to other sequence-based prediction.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-18"},"PeriodicalIF":4.1,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13596925/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148920921","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

Identification of proteins interacting with the N-terminal half of endoribonuclease RNase E in Escherichia coli. 大肠杆菌核糖核酸内切酶RNase E n端相互作用蛋白的鉴定。

IF 4.1 3区生物学

RNA Biology Pub Date : 2026-12-31 Epub Date: 2026-06-02 DOI: 10.1080/15476286.2026.2678028

Yvonne Göpel, Svetlana Durica-Mitic, Solomiia Boyko, Przemyslaw Dudys, Fabian Amman, Karin Schnetz, Boris Görke

{"title":"Identification of proteins interacting with the N-terminal half of endoribonuclease RNase E in Escherichia coli.","authors":"Yvonne Göpel, Svetlana Durica-Mitic, Solomiia Boyko, Przemyslaw Dudys, Fabian Amman, Karin Schnetz, Boris Görke","doi":"10.1080/15476286.2026.2678028","DOIUrl":"10.1080/15476286.2026.2678028","url":null,"abstract":"In E. coli endoribonuclease RNase E (Rne) plays a central role in RNA processing and decay. Rne consists of an N-terminal catalytic domain (NTD) and a C-terminal scaffolding domain, separated by a membrane targeting sequence (MTS). While the scaffolding domain represents a hub for interaction, only few proteins are known to bind the Rne-NTD. One example is protein RapZ, which forms a transient complex with the Rne-NTD to target a small RNA to decay. Here, we screened a genomic bacterial two-hybrid library for proteins binding to the Rne N-terminal half including the MTS. We identified fragments of 43 proteins, of which 15 were validated to bind Rne as full-length proteins. We distinguished three groups: Group I likely uses a membrane domain to bind a segment in Rne that contains the MTS. Group II proteins are cytoplasmic and bind the Rne-NTD. Group III proteins bind the Rne-NTD and additionally the MTS region, indicating two distinct interaction surfaces. RNA-seq revealed that overproduction of three group II proteins including YegJ generates similar effects on the transcriptome. Genes carrying Rne cleavage sites were enriched among downregulated genes but depleted from upregulated genes, suggesting altered RNA decay. Interestingly, strong overexpression of yegJ destabilizes rRNA and arrests growth. Apparently, YegJ damages the membrane, granting periplasmic RNase I and presumably also Rne access to cytoplasmic rRNA. We present a catalogue of proteins likely binding the Rne N-terminal half, which may provide a valuable resource for further investigation of these interactions and their roles.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-28"},"PeriodicalIF":4.1,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13232886/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147988957","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

Mechanistic studies on HNRNPA2B1 suggest binding but not selective recognition of m⁶A. HNRNPA2B1的机制研究表明其结合而非选择性识别m6A。

IF 4.1 3区生物学

RNA Biology Pub Date : 2026-12-31 Epub Date: 2026-03-02 DOI: 10.1080/15476286.2026.2627781

Raeyeon Park, Madeline Demny, Lucas G Miller, Cristian Pedraza, Xenophon Xenophontos, Ryleigh K Hunt, Asuka A Orr, Lisa M Perez, Mauro Montalbano, Lydia M Contreras, Phanourios Tamamis

{"title":"Mechanistic studies on HNRNPA2B1 suggest binding but not selective recognition of m6A.","authors":"Raeyeon Park, Madeline Demny, Lucas G Miller, Cristian Pedraza, Xenophon Xenophontos, Ryleigh K Hunt, Asuka A Orr, Lisa M Perez, Mauro Montalbano, Lydia M Contreras, Phanourios Tamamis","doi":"10.1080/15476286.2026.2627781","DOIUrl":"10.1080/15476286.2026.2627781","url":null,"abstract":"HNRNPA2B1 contains two RRM domains and has been investigated for its possible role as an m6A reader protein. The targetome of HNRNPA2B1 was shown to overlap with the m6A methylation motif, but further investigations of its binding affinity for m6A-containing RNAs have been less clear on the relative selectivity of HNRNPA2B1 for methylated transcripts. Our computational and experimental studies depict that when an m6A modification is positioned in between the two RRM domains, and in the context of the GGACU motif that can be written by methyltransferases, the binding affinity is nearly identical and slightly less favourable to the unmodified sequence. Our study suggests that HNRNPA2B1 is not a (selective) reader but has high affinity for m6A in a sequence-dependent manner. This can be attributed to the strong interactions conferred by AGG and UAG motifs rather than adenine or m6A in the GGACU motif which are predicted to interact weakly, intercalating between the two RRMs or positioned outwards. Overall, our findings highlight the higher complexity of HNRNPA2B1 and RRM recognition properties compared to well-studied YTH domains in the recognition of m6A, as well as modified and unmodified sequences.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-28"},"PeriodicalIF":4.1,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12962277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146150440","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

Sequence and ionic requirements of pUG fold quadruplexes. pUG折叠四联体的序列和离子要求。

IF 4.1 3区生物学

RNA Biology Pub Date : 2026-12-31 Epub Date: 2026-03-03 DOI: 10.1080/15476286.2026.2638283

Saeed Roschdi, Takuma Kume, Riley J Petersen, Abby McCann, Cristian A Escobar Bravo, Anika Richard, Samuel Butcher

{"title":"Sequence and ionic requirements of pUG fold quadruplexes.","authors":"Saeed Roschdi, Takuma Kume, Riley J Petersen, Abby McCann, Cristian A Escobar Bravo, Anika Richard, Samuel Butcher","doi":"10.1080/15476286.2026.2638283","DOIUrl":"10.1080/15476286.2026.2638283","url":null,"abstract":"Poly(UG) repeats or pUG RNAs can fold into a left-handed parallel quadruplex, the pUG fold. The pUG fold directs the epigenetic amplification of RNAi in Caenorhabditis elegans, and pUG sequences are abundant in eukaryotic transcriptomes. Here, we report the sequence and ionic requirements for pUG folding. The pUG fold preferentially incorporates 12 guanosines but has an otherwise flexible sequence requirement. The uridines can be substituted with other nucleotides, with some sequence variants folding better than pUG RNA. The GA repeat sequence (GA)12 also forms a pUG-like fold, albeit with lower thermodynamic stability than (GU)12. The pUG fold can tolerate multiple deoxyribose substitutions but does not fold when the backbone is entirely deoxyribose. It has a high affinity and specificity for potassium ions (K1/2 = 6 mM) and does not fold in sodium or ammonium. Addition of 2 mM Mg2+ does not further stabilize the pUG fold, and the polyamines spermine and spermidine do not affect its stability. Finally, the pUG fold is sensitive to surrounding sequence context and complementary flanking sequences can stabilize pUG folds, while other sequences can interfere with folding. These data provide an improved ability to understand and predict pUG folds.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-16"},"PeriodicalIF":4.1,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12962679/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147309758","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 RNA exosome: mechanisms of RNA surveillance, regulation, and disease. RNA外泌体：RNA监视、调控和疾病的机制。

IF 4.1 3区生物学

RNA Biology Pub Date : 2026-12-31 Epub Date: 2026-06-11 DOI: 10.1080/15476286.2026.2685379

Priyanka Upadhyai, Neha Quadri, Divya Chandran

{"title":"The RNA exosome: mechanisms of RNA surveillance, regulation, and disease.","authors":"Priyanka Upadhyai, Neha Quadri, Divya Chandran","doi":"10.1080/15476286.2026.2685379","DOIUrl":"10.1080/15476286.2026.2685379","url":null,"abstract":"The RNA exosome is a conserved multi-subunit ribonuclease complex with pivotal roles in RNA biogenesis, surveillance, and processing. It comprises a nine-subunit scaffold that associates with distinct ribonucleases in a cell compartment-specific manner, contributing to the processing and turnover of a broad spectrum of nuclear and cytoplasmic transcripts, including pervasively transcribed and short-lived RNAs, precursors, and abortive and aberrant transcripts. In this review, we examine how the RNA exosome engages a wide spectrum of RNAs via differential adaptor usage and intrinsic substrate features, such as transcript length and 3' end structure. This also modulates the entry routes of the recruited transcripts. We highlight conserved principles and major differences between yeast and metazoans. We assimilate emerging evidence that suggests that the RNA exosome localization and activity are dynamically regulated in response to cellular context and external stimuli. Finally, drawing on findings from studies in S. cerevisiae, Drosophila, zebrafish, and mice, we discuss how perturbations in RNA surveillance can result in abnormalities in organismal development and homoeostasis. Together, these studies not only enhance our knowledge of the broader relevance of RNA quality control and metabolism but also provide mechanistic insights into pathomechanisms, particularly the tissue-specific vulnerabilities noted in RNA exosome-linked diseases.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"23 1","pages":"1-24"},"PeriodicalIF":4.1,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13271354/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148219489","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

Crosstalk between RNA secondary and three-dimensional structure prediction: a comprehensive study. RNA二级串扰与三维结构预测的综合研究。

IF 4.1 3区生物学

RNA Biology Pub Date : 2026-12-31 Epub Date: 2026-04-13 DOI: 10.1080/15476286.2026.2655096

Deyin Wang, Yangwei Jiang, Linli He, Linxi Zhang, Ruhong Zhou, Dong Zhang

{"title":"Crosstalk between RNA secondary and three-dimensional structure prediction: a comprehensive study.","authors":"Deyin Wang, Yangwei Jiang, Linli He, Linxi Zhang, Ruhong Zhou, Dong Zhang","doi":"10.1080/15476286.2026.2655096","DOIUrl":"10.1080/15476286.2026.2655096","url":null,"abstract":"In recent years, various computational methods have been developed to predict the three-dimensional (3D) structures of RNAs. Due to its hierarchical folding property, RNA secondary (2D) structure is often used as input for 3D structure prediction to improve accuracy and efficiency. However, the extent to which the accuracy of input 2D structure affects the performance of 3D structure prediction remains to be further investigated. Additionally, whether and how the input base-pairing interactions are modified during the 3D structure modelling process is another question worth exploring. To address these issues, here we comprehensively benchmark six representative 3D structure prediction models on extensive datasets, using 2D structures of varied accuracies as input. Our results indicate that there is a pervasive crosstalk between RNA 2D and 3D structure predictions, where the performance dependence of 3D structure prediction on the accuracy of input 2D structure is closely associated with the 3D model's ability to modify the input base-pairing interactions during structure modelling. Furthermore, we also observed that RNA 3D structure prediction performance is more sensitive to the occurrence of false positive base pairs in the input 2D structure than to true positive base pairs, suggesting a worthy direction to further improve the model performance.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-18"},"PeriodicalIF":4.1,"publicationDate":"2026-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13078229/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147594438","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

RNA Biology最新文献