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EIciRNAs in focus: current understanding and future perspectives. 关注eicirna:当前的理解和未来的观点。
IF 3.6 3区 生物学
RNA Biology Pub Date : 2025-12-01 Epub Date: 2024-12-23 DOI: 10.1080/15476286.2024.2443876
Yan Yang, Yinchun Zhong, Liang Chen
{"title":"EIciRNAs in focus: current understanding and future perspectives.","authors":"Yan Yang, Yinchun Zhong, Liang Chen","doi":"10.1080/15476286.2024.2443876","DOIUrl":"10.1080/15476286.2024.2443876","url":null,"abstract":"<p><p>Circular RNAs (circRNAs) are a unique class of covalently closed single-stranded RNA molecules that play diverse roles in normal physiology and pathology. Among the major types of circRNA, exon-intron circRNA (EIciRNA) distinguishes itself by its sequence composition and nuclear localization. Recent RNA-seq technologies and computational methods have facilitated the detection and characterization of EIciRNAs, with features like circRNA intron retention (CIR) and tissue-specificity being characterized. EIciRNAs have been identified to exert their functions via mechanisms such as regulating gene transcription, and the physiological relevance of EIciRNAs has been reported. Within this review, we present a summary of the current understanding of EIciRNAs, delving into their identification and molecular functions. Additionally, we emphasize factors regulating EIciRNA biogenesis and the physiological roles of EIciRNAs based on recent research. We also discuss the future challenges in EIciRNA exploration, underscoring the potential for novel functions and functional mechanisms of EIciRNAs for further investigation.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"22 1","pages":"1-12"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142877855","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
Alternative splicing of the Snap23 microexon is regulated by MBNL, QKI, and RBFOX2 in a tissue-specific manner and is altered in striated muscle diseases. Snap23微外显子的选择性剪接由MBNL、QKI和RBFOX2以组织特异性方式调节,并在横纹肌疾病中发生改变。
IF 3.6 3区 生物学
RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-05-06 DOI: 10.1080/15476286.2025.2491160
Gabrielle M Gentile, R Eric Blue, Grant A Goda, Bryan B Guzman, Rachel A Szymanski, Eunice Y Lee, Nichlas M Engels, Emma R Hinkle, Hannah J Wiedner, Aubriana N Bishop, Jonathan T Harrison, Hua Zhang, Xander H T Wehrens, Daniel Dominguez, Jimena Giudice
{"title":"Alternative splicing of the Snap23 microexon is regulated by MBNL, QKI, and RBFOX2 in a tissue-specific manner and is altered in striated muscle diseases.","authors":"Gabrielle M Gentile, R Eric Blue, Grant A Goda, Bryan B Guzman, Rachel A Szymanski, Eunice Y Lee, Nichlas M Engels, Emma R Hinkle, Hannah J Wiedner, Aubriana N Bishop, Jonathan T Harrison, Hua Zhang, Xander H T Wehrens, Daniel Dominguez, Jimena Giudice","doi":"10.1080/15476286.2025.2491160","DOIUrl":"https://doi.org/10.1080/15476286.2025.2491160","url":null,"abstract":"<p><p>The reprogramming of alternative splicing networks during development is a hallmark of tissue maturation and identity. Alternative splicing of microexons (small, genomic regions ≤ 51 nucleotides) functionally regulate protein-protein interactions in the brain and is altered in several neuronal diseases. However, little is known about the regulation and function of alternatively spliced microexons in striated muscle. Here, we investigated alternative splicing of a microexon in the synaptosome-associated protein 23 (<i>Snap23</i>) encoded gene. We found that inclusion of this microexon is developmentally regulated and tissue-specific, as it occurs exclusively in adult heart and skeletal muscle. The alternative region is highly conserved in mammalian species and encodes an in-frame sequence of 11 amino acids. Furthermore, we showed that alternative splicing of this microexon is mis-regulated in mouse models of heart and skeletal muscle diseases. We identified the RNA-binding proteins (RBPs) quaking (QKI) and RNA binding fox-1 homolog 2 (RBFOX2) as the primary splicing regulators of the Snap23 microexon. We found that QKI and RBFOX2 bind downstream of the Snap23 microexon to promote its inclusion, and this regulation can be escaped when the weak splice donor is mutated to the consensus 5' splice site. Finally, we uncovered the interplay between QKI and muscleblind-like splicing regulator (MBNL) as an additional, but minor layer of Snap23 microexon splicing control. Our results are one of the few reports detailing microexon alternative splicing regulation during mammalian striated muscle development.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"22 1","pages":"1-20"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12064062/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144023816","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
LncRNA HOTAIR promotes aerobic glycolysis by recruiting Lin28 to induce inflammation and apoptosis in acute lung injury. LncRNA HOTAIR通过募集Lin28诱导急性肺损伤中的炎症和细胞凋亡,促进有氧糖酵解。
IF 3.6 3区 生物学
RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-03-07 DOI: 10.1080/15476286.2025.2475255
Junjie Xie, Zhicong Zheng, Bin Wang, Jianfang Zhang, Junqi Jiang, Fengde Wu, Xiangming Zhong, Jianfeng Chen
{"title":"LncRNA HOTAIR promotes aerobic glycolysis by recruiting Lin28 to induce inflammation and apoptosis in acute lung injury.","authors":"Junjie Xie, Zhicong Zheng, Bin Wang, Jianfang Zhang, Junqi Jiang, Fengde Wu, Xiangming Zhong, Jianfeng Chen","doi":"10.1080/15476286.2025.2475255","DOIUrl":"10.1080/15476286.2025.2475255","url":null,"abstract":"<p><p>Acute lung injury (ALI) is a life-threatening condition with high rates of morbidity and mortality. Recently, there has been growing evidence suggesting a link between lncRNA HOTAIR and ALI. Nonetheless, the precise role and mechanism of lncRNA HOTAIR in ALI remain to be fully elucidated. siHOTAIR transfection, qPCR detection (HOTAIR), ELISA (TNF-α, IL-6, and IL-1β), Lactate detection, Glucose uptake experiment, Cell Apoptosis Analysis, Fluorescence in situ hybridization (FISH) assay. Through siHOTAIR transfection, we discovered that HOTAIR plays a role in the secretion of inflammatory factors in ALI and further regulates glucose uptake and metabolism in lung epithelial cells. Moreover, a comparison between HOTAIR knockdown cells and HOTAIR overexpression cells revealed that HOTAIR promotes cellular aerobic sugar metabolism, leading to increased secretion of inflammatory factors and cell apoptosis. Our in-depth research also identified an interaction between HOTAIR and the LIN28 protein. Knocking down HOTAIR resulted in the downregulation of LIN28 protein expression, which subsequently inhibited the expression of the glucose transporter GLUT1. This indicates that HOTAIR facilitates glucose uptake and boosts cellular aerobic glycolysis by modulating the LIN28 protein, thereby promoting inflammation and apoptosis in acute lung injury. The research findings presented in this article offer significant insights into the function of HOTAIR in ALI and suggest a potential therapeutic target for the treatment of this condition.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"22 1","pages":"1-12"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11901367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143573924","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 LARP6 La module from Tetrabaena socialis reveals structural and functional differences from plant and animal LARP6 homologues. 社会四鳃鱼的LARP6 La模块揭示了植物和动物LARP6同源物在结构和功能上的差异。
IF 3.6 3区 生物学
RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-04-09 DOI: 10.1080/15476286.2025.2489303
Emily M Lewis, Olga Becker, Alexis N Symons, Cora LaCoss, A Jasmine Baclig, Avery Guzman, Charles Sanders, Leticia Gonzalez, Lisa R Warner, Karen A Lewis
{"title":"The LARP6 La module from <i>Tetrabaena socialis</i> reveals structural and functional differences from plant and animal LARP6 homologues.","authors":"Emily M Lewis, Olga Becker, Alexis N Symons, Cora LaCoss, A Jasmine Baclig, Avery Guzman, Charles Sanders, Leticia Gonzalez, Lisa R Warner, Karen A Lewis","doi":"10.1080/15476286.2025.2489303","DOIUrl":"10.1080/15476286.2025.2489303","url":null,"abstract":"<p><p>This study identified the LARP6 La Module from <i>Tetrabaena socialis</i> (<i>T. socialis</i>), a four-celled green algae, in an effort to better understand the evolution of LARP6 structure and RNA-binding activity in multicellular eukaryotes. Using a combination of sequence alignments, domain boundary screens, and structural modelling, we recombinantly expressed and isolated the <i>Ts</i>LARP6 La Module to > 98% purity for <i>in vitro</i> biochemical characterization. The La Module is stably folded and exerts minimal RNA binding activity against single-stranded homopolymeric RNAs. Surprisingly, it exhibits low micromolar binding affinity for the vertebrate LARP6 cognate ligand, a bulged-stem loop found in the 5'UTR of collagen type I mRNA, but does not bind double-stranded RNAs of similar size. These result suggests that the <i>Ts</i>LARP6 La Module may prefer structured RNA ligands. In contrast, however, the <i>Ts</i>LARP6 La Module does not exhibit the RNA chaperone activity that is observed in vertebrate homologs. Therefore, we conclude that protist LARP6 may have both distinct RNA ligands and binding mechanisms from the previously characterized LARP6 proteins of animals and vascular plants, thus establishing a distinct third class of the LARP6 protein family.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-9"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11988235/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143780999","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
6S-1 pRNA 9-mers are a prominent length species during outgrowth of Bacillus subtilis cells from extended stationary phase. S-1 pRNA 9-mers是枯草芽孢杆菌延长固定期生长过程中的一个突出的长度物种。
IF 3.6 3区 生物学
RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-04-14 DOI: 10.1080/15476286.2025.2484519
Katrin Damm, Paul Klemm, Marcus Lechner, Dominik Helmecke, Roland K Hartmann
{"title":"6S-1 pRNA 9-mers are a prominent length species during outgrowth of <i>Bacillus subtilis</i> cells from extended stationary phase.","authors":"Katrin Damm, Paul Klemm, Marcus Lechner, Dominik Helmecke, Roland K Hartmann","doi":"10.1080/15476286.2025.2484519","DOIUrl":"10.1080/15476286.2025.2484519","url":null,"abstract":"<p><p>Bacterial RNA polymerases (RNAP) utilize 6S RNAs as templates to synthesize ultrashort transcripts (up to ~14 nt), termed product RNAs (pRNAs), that play a key role in reversing the blockage of RNAP by 6S RNA. Here, we resolved the pRNA length profile of 6S-1 RNA from <i>B. subtilis</i>, a major model system for the study of 6S RNA biology, during outgrowth of cells from extended stationary phase. 9-mers were found to be a particularly abundant pRNA length species, followed by 8-/10-/11-mers and 13-/14-mers. Consistent with <i>in vitro</i> data from the <i>Escherichia coli</i> system, these findings support the mechanistic model according to which the housekeeping sigma factor (σ<sup>70</sup> or σ<sup>A</sup>) dissociates from 6S RNA:RNAP complexes upon synthesis of pRNA 9-mers, followed by final dissociation of 6S RNA and RNAP upon synthesis of longer pRNAs (13-/14-mers). Methodologically, the identification of such ultrashort RNAs in total cellular extracts by RNA-Seq is inefficient with standard protocols using adapter ligation to RNA 3'-ends for reverse transcription and PCR-based cDNA sequencing. Here, we demonstrate that ultrashort RNAs can instead be incorporated into RNA-Seq libraries by polyA-, polyC- and potentially also polyU-tailing of their 3'-ends. At positions where a non-tailing nucleotide is followed by one or more tailing nucleotides, an algorithm that integrates RNA-Seq results from at least two different 3'-end tailings allows one to approximate the fraction of read counts at such ambiguous positions. Finally, methodological biases and potential applications of our approach to other short RNAs are discussed.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-14"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12005410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710720","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
AUGcontext DB: a comprehensive catalog of the mRNA AUG initiator codon context across eukaryotes. AUGcontext DB:真核生物中mRNA AUG启动子密码子上下文的综合目录。
IF 3.6 3区 生物学
RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-02-13 DOI: 10.1080/15476286.2025.2465196
Vincent G Osnaya, Laura Gómez-Romero, Gabriel Moreno-Hagelsieb, Greco Hernández
{"title":"AUGcontext DB: a comprehensive catalog of the mRNA AUG initiator codon context across eukaryotes.","authors":"Vincent G Osnaya, Laura Gómez-Romero, Gabriel Moreno-Hagelsieb, Greco Hernández","doi":"10.1080/15476286.2025.2465196","DOIUrl":"10.1080/15476286.2025.2465196","url":null,"abstract":"<p><p>The mRNA translation defines the composition of the cell proteome in all forms of life and diseases. In this process, precise selection of the mRNA translation initiation site (TIS) is crucial, as it establishes the correct open reading frame for triplet decoding. We have gathered and curated all published TIS consensus context sequences. We also included the TIS consensus context from novel 538 fungal genomes available from NCBI's RefSeq database. To do so, we wrote ad hoc programs in PERL to find and extract the TIS for each annotated gene, plus ten bases upstream and three downstream. For each genome, the sequences around the TIS of each gene were obtained, and the consensus was further calculated according to the Cavener rules and by the LOGOS algorithm. We created AUGcontext DB, a portal with a comprehensive collection of TIS context sequences across eukaryotes in a range from -10 to + 6. The compilation covers species of 30 vertebrates, 17 invertebrates, 25 plants, 14 fungi, and 11 protists studied in silico; 23 experimental studies; data on biotechnology; and the discovery of 8 diseases associated with specific mutations. Additionally, TIS context sequences of cellular IRESs were included. AUGcontext DB belongs to the National Institute of Cancer (Instituto Nacional de Cancerología, INCan), Mexico, and is freely available at http://108.161.138.77:8096/. Our catalogue allows us to do comparative studies between species, may help improve the diagnosis of certain diseases, and will be key to maximize the production of recombinant proteins.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-5"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834415/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143399899","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 differentially expressed non-coding RNAs in the plasma of women with preterm birth. 早产妇女血浆中差异表达的非编码rna的鉴定。
IF 3.6 3区 生物学
RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-01-13 DOI: 10.1080/15476286.2024.2449278
Waqasuddin Khan, Samiah Kanwar, Mohammad Mohsin Mannan, Furqan Kabir, Naveed Iqbal, Mehdia Nadeem Rajab Ali, Syeda Rehana Zia, Sharmeen Mian, Fatima Aziz, Sahrish Muneer, Adil Kalam, Akram Hussain, Iqra Javed, Muhammad Farrukh Qazi, Javairia Khalid, Muhammad Imran Nisar, Fyezah Jehan
{"title":"Identification of differentially expressed non-coding RNAs in the plasma of women with preterm birth.","authors":"Waqasuddin Khan, Samiah Kanwar, Mohammad Mohsin Mannan, Furqan Kabir, Naveed Iqbal, Mehdia Nadeem Rajab Ali, Syeda Rehana Zia, Sharmeen Mian, Fatima Aziz, Sahrish Muneer, Adil Kalam, Akram Hussain, Iqra Javed, Muhammad Farrukh Qazi, Javairia Khalid, Muhammad Imran Nisar, Fyezah Jehan","doi":"10.1080/15476286.2024.2449278","DOIUrl":"10.1080/15476286.2024.2449278","url":null,"abstract":"<p><p>This study aimed to identify differentially expressed non-coding RNAs (ncRNAs) associated with preterm birth (PTB) and determine biological pathways being influenced in the context of PTB. We processed cell-free RNA sequencing data and identified seventeen differentially expressed (DE) ncRNAs that could be involved in the onset of PTB. Per the validation via customized RT-qPCR, the recorded variations in expressions of eleven ncRNAs were concordant with the <i>in-silico</i> analyses. The results of this study provide insights into the role of DE ncRNAs and their impact on pregnancy-related biological pathways that could lead to PTB. Further studies are required to elucidate the precise mechanisms by which these DE ncRNAs contribute to adverse pregnancy outcomes (APOs) and their potential as diagnostic biomarkers.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"22 1","pages":"1-8"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11730358/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142971981","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
miRNA-mRNA integrated analysis reveals candidate genes associated with salt stress response in Halophytic Sonneratia apetala. miRNA-mRNA整合分析揭示了盐生植物无瓣海桑盐胁迫响应的候选基因。
IF 3.6 3区 生物学
RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-04-28 DOI: 10.1080/15476286.2025.2496097
Beibei Chen, Lishan Zhen, Zhuanying Yang, Tingting Liu, Shaoxia Yang, Wei Mu, Xiao Xiao, Jinhui Chen
{"title":"miRNA-mRNA integrated analysis reveals candidate genes associated with salt stress response in Halophytic <i>Sonneratia apetala</i>.","authors":"Beibei Chen, Lishan Zhen, Zhuanying Yang, Tingting Liu, Shaoxia Yang, Wei Mu, Xiao Xiao, Jinhui Chen","doi":"10.1080/15476286.2025.2496097","DOIUrl":"10.1080/15476286.2025.2496097","url":null,"abstract":"<p><p><i>Sonneratia apetala</i> is a pioneering species of mangrove plants, which has evolved various mechanisms to tolerate salt-stress due to their long-term exposure to a salinized environment as compared to the of terrestrial freshwater plants. However, limited attempt has been made to uncover the underlying molecular mechanism of their saline adaptation. Here, we integrated mRNA and microRNA (miRNA) sequencing to identify the genes and pathways that may be involved in salt stress-response in the roots of <i>S. apetala</i>. A comprehensive full‑length transcriptome containing 295,501 high‑quality unigenes was obtained by PacBio sequencing technology. Of these, 6,686 genes exhibited significantly differential accumulation after salt stress treatment (<i>p</i> < 0.001, <i>Q</i> < 0.01). They were mainly implicated in plant signal transduction and diverse metabolic pathways, such as those involving phenylpropanoid biosynthesis, plant-pathogen interaction and protein processing. Also, our results identified the regulatory interaction between miRNA-target counterparts during salt stress. Taken together, we present the first global overview of the transcriptome of <i>S. apetala</i> roots, and identify potentially important genes and pathways associated with salt tolerance for further investigation. This study is expected to deliver novel insights in understanding the regulatory mechanism in <i>S. apetala</i> response to salt stress.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"22 1","pages":"1-13"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12045576/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144012653","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
Carrot and stick: how RNase R contributes to function and destruction of the translation machinery. 胡萝卜加大棒:RNase R如何促进翻译机制的功能和破坏。
IF 3.4 3区 生物学
RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-07-29 DOI: 10.1080/15476286.2025.2535846
Helge Paternoga, Lyudmila Dimitrova-Paternoga
{"title":"Carrot and stick: how RNase R contributes to function and destruction of the translation machinery.","authors":"Helge Paternoga, Lyudmila Dimitrova-Paternoga","doi":"10.1080/15476286.2025.2535846","DOIUrl":"10.1080/15476286.2025.2535846","url":null,"abstract":"<p><p>RNA is fundamental for life, and its homoeostasis is a critical contributor to cellular growth and adaptation to stress. Key RNA species include messenger RNA (mRNA) and non-coding RNAs, such as transfer RNA (tRNA), or ribosomal RNA (rRNA), that are essential for ribosome formation and translation of the genetic code. Furthermore, various other non-coding RNAs are expressed at each growth stage. Given RNA's abundance and its role in all cellular processes, RNases - enzymes responsible for RNA degradation and processing - are central to RNA metabolism. In this review, we discuss the pivotal contribution of the 3' exonuclease RNase R to bacterial RNA homoeostasis. We focus on its functions in regulating and degrading components of the translation machinery, including the trans-translation system, and we take a look at recent structural studies that shed new light on the activities of this important enzyme.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"22 1","pages":"1-22"},"PeriodicalIF":3.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12320835/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144744569","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 deleterious non-synonymous single nucleotide polymorphisms in the mRNA decay activator ZFP36L2. mRNA衰变激活子ZFP36L2中有害非同义单核苷酸多态性的鉴定。
IF 3.6 3区 生物学
RNA Biology Pub Date : 2025-12-01 Epub Date: 2024-12-13 DOI: 10.1080/15476286.2024.2437590
Betül Akçeşme, Hilal Hekimoğlu, Venkat R Chirasani, Şeyma İş, Habibe Nur Atmaca, Justin M Waldern, Silvia B V Ramos
{"title":"Identification of deleterious non-synonymous single nucleotide polymorphisms in the mRNA decay activator ZFP36L2.","authors":"Betül Akçeşme, Hilal Hekimoğlu, Venkat R Chirasani, Şeyma İş, Habibe Nur Atmaca, Justin M Waldern, Silvia B V Ramos","doi":"10.1080/15476286.2024.2437590","DOIUrl":"10.1080/15476286.2024.2437590","url":null,"abstract":"<p><p>More than 4,000 single nucleotide polymorphisms (SNP) variants have been identified in the human <i>ZFP36L2</i> gene, however only a few have been studied in the context of protein function. The tandem zinc finger domain of ZFP36L2, an RNA binding protein, is the functional domain that binds to its target mRNAs. This protein/RNA interaction triggers mRNA degradation, controlling gene expression. We identified 32 non-synonymous SNPs (nsSNPs) in the tandem zinc finger domain of ZFP36L2 that could have possible deleterious impacts in humans. Using different bioinformatic strategies, we prioritized five among these 32 nsSNPs, namely rs375096815, rs1183688047, rs1214015428, rs1215671792 and rs920398592 to be validated. When we experimentally tested the functionality of these protein variants using gel shift assays, all five (Y154H, R160W, R184C, G204D, and C206F) resulted in a dramatic reduction in RNA binding compared to the WT protein. To understand the mechanistic effect of these variants on the protein/RNA interaction, we employed DUET, DynaMut and PyMOL to investigate structural changes in the protein. Additionally, we conducted Molecular Docking and Molecular Dynamics Simulations to fine tune the active behaviour of this biomolecular system at an atomic level. Our results propose atomic explanations for the impact of each of these five genetic variants identified.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"22 1","pages":"1-15"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142819035","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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