RNA Biology最新文献_第5页

Mature microRNA-binding protein QKI promotes microRNA-mediated gene silencing. 成熟的 microRNA 结合蛋白 QKI 可促进 microRNA 介导的基因沉默。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-02-19 DOI: 10.1080/15476286.2024.2314846

Kyung-Won Min, Myung Hyun Jo, Minseok Song, Ji Won Lee, Min Ji Shim, Kyungmin Kim, Hyun Bong Park, Shinwon Ha, Hyejin Mun, Ahsan Polash, Markus Hafner, Jung-Hyun Cho, Dongsan Kim, Ji-Hoon Jeong, Seungbeom Ko, Sungchul Hohng, Sung-Ung Kang, Je-Hyun Yoon

{"title":"Mature microRNA-binding protein QKI promotes microRNA-mediated gene silencing.","authors":"Kyung-Won Min, Myung Hyun Jo, Minseok Song, Ji Won Lee, Min Ji Shim, Kyungmin Kim, Hyun Bong Park, Shinwon Ha, Hyejin Mun, Ahsan Polash, Markus Hafner, Jung-Hyun Cho, Dongsan Kim, Ji-Hoon Jeong, Seungbeom Ko, Sungchul Hohng, Sung-Ung Kang, Je-Hyun Yoon","doi":"10.1080/15476286.2024.2314846","DOIUrl":"10.1080/15476286.2024.2314846","url":null,"abstract":"Although Argonaute (AGO) proteins have been the focus of microRNA (miRNA) studies, we observed AGO-free mature miRNAs directly interacting with RNA-binding proteins, implying the sophisticated nature of fine-tuning gene regulation by miRNAs. To investigate microRNA-binding proteins (miRBPs) globally, we analyzed PAR-CLIP data sets to identify RBP quaking (QKI) as a novel miRBP for let-7b. Potential existence of AGO-free miRNAs were further verified by measuring miRNA levels in genetically engineered AGO-depleted human and mouse cells. We have shown that QKI regulates miRNA-mediated gene silencing at multiple steps, and collectively serves as an auxiliary factor empowering AGO2/let-7b-mediated gene silencing. Depletion of QKI decreases interaction of AGO2 with let-7b and target mRNA, consequently controlling target mRNA decay. This finding indicates that QKI is a complementary factor in miRNA-mediated mRNA decay. QKI, however, also suppresses the dissociation of let-7b from AGO2, and slows the assembly of AGO2/miRNA/target mRNA complexes at the single-molecule level. We also revealed that QKI overexpression suppresses cMYC expression at post-transcriptional level, and decreases proliferation and migration of HeLa cells, demonstrating that QKI is a tumour suppressor gene by in part augmenting let-7b activity. Our data show that QKI is a new type of RBP implicated in the versatile regulation of miRNA-mediated gene silencing.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"1-15"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10878027/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139900373","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

WDR33 alternative polyadenylation is dependent on stochastic poly(a) site usage and splicing efficiencies. WDR33 的替代多腺苷酸化取决于随机多聚（a）位点的使用和剪接效率。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-09-26 DOI: 10.1080/15476286.2024.2408708

Lizhi Liu, Takahiro Seimiya, James L Manley

{"title":"WDR33 alternative polyadenylation is dependent on stochastic poly(a) site usage and splicing efficiencies.","authors":"Lizhi Liu, Takahiro Seimiya, James L Manley","doi":"10.1080/15476286.2024.2408708","DOIUrl":"10.1080/15476286.2024.2408708","url":null,"abstract":"Transcripts from the human WDR33 gene, which encodes a central component of the mRNA polyadenylation (PA) machinery, are subject to alternative polyadenylation (APA) within promoter-proximal introns/exons. This APA, which itself involves usage of multiple PA sites, results in the production of two non-canonical protein isoforms, V2 and V3, that are functionally completely unrelated to the full-length protein, with roles in innate immunity. The mechanism and regulation of WDR33 APA are unclear. Here, we report that levels of the PA factor CFIm25 modulate V2 and V3 expression, and that PA site usage of both V2 and V3 varies in distinct immune responses. Using newly developed assays to measure splicing and PA site strength, we show that splicing of V2-associated intron 6 is inefficient, allowing V2 to be produced using weak PA sites. Usage of V3's strong PA sites, on the other hand, is relatively low, reflecting the high efficiency of intron 7 splicing coupled with dependency on usage of an alternative 3' splice site within the intron. Overall, our findings demonstrate that usage of WDR33 alternative PA sites is stochastic, dependent on a complex interplay between splicing and PA, and thus provide new insights into mechanisms underlying APA.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"25-35"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11445923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142353014","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

LncRNAs in melanoma phenotypic plasticity: emerging targets for promising therapies. 黑色素瘤表型可塑性中的 LncRNAs：有望成为疗法的新兴靶点。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-11-05 DOI: 10.1080/15476286.2024.2421672

Tonin Beatriz Cristina Biz, Castro-Silva Carolina de Sousa, Slack Frank John, Jasiulionis Miriam Galvonas

{"title":"LncRNAs in melanoma phenotypic plasticity: emerging targets for promising therapies.","authors":"Tonin Beatriz Cristina Biz, Castro-Silva Carolina de Sousa, Slack Frank John, Jasiulionis Miriam Galvonas","doi":"10.1080/15476286.2024.2421672","DOIUrl":"10.1080/15476286.2024.2421672","url":null,"abstract":"Long non-coding RNAs (lncRNAs) have received growing attention due to their diverse regulatory roles in cancer, including in melanoma, an aggressive type of skin cancer. The plasticity and phenotypic adaptability of melanoma cells are crucial factors contributing to therapeutic resistance. The identification of molecules playing key roles in melanoma cell plasticity could unravel novel and more effective therapeutic targets. This review presents current concepts of melanoma cell plasticity, illustrating its fluidity and dismissing the outdated notion of epithelial-mesenchymal-like transition as a simplistic binary process. Emphasis is placed on the pivotal role of lncRNAs in orchestrating cell plasticity, employing various mechanisms recently elucidated and unveiling their potential as promising targets for novel therapeutic strategies. Insights into the molecular mechanisms coordinated by lncRNAs in melanoma pave the way for the development of RNA-based therapies, holding great promise for enhancing treatment outcomes and offering a glimpse into a more effective approach to melanoma treatment.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"81-93"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540095/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142584259","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

Rapid and scalable detection of synthetic mRNA byproducts using polynucleotide phosphorylase and polythymidine oligonucleotides. 使用多核苷酸磷酸化酶和多胸苷寡核苷酸快速、可扩展地检测合成 mRNA 副产品。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-06-05 DOI: 10.1080/15476286.2024.2363029

Francis Combes, Thanh-Huong Bui, Frida J Pettersson, Sjoerd Hak

{"title":"Rapid and scalable detection of synthetic mRNA byproducts using polynucleotide phosphorylase and polythymidine oligonucleotides.","authors":"Francis Combes, Thanh-Huong Bui, Frida J Pettersson, Sjoerd Hak","doi":"10.1080/15476286.2024.2363029","DOIUrl":"10.1080/15476286.2024.2363029","url":null,"abstract":"Production and storage of synthetic mRNA can introduce a variety of byproducts which reduce the overall integrity and functionality of mRNA vaccines and therapeutics. mRNA integrity is therefore designated as a critical quality attribute which must be evaluated with state-of-the-art analytical methods before clinical use. The current study first demonstrates the effect of heat degradation on transcript translatability and then describes a novel enzymatic approach to assess the integrity of conventional mRNA and long self-amplifying mRNA. By first hybridizing oligo-T to the poly(A) tail of intact mRNA and subsequently digesting the unhybridized RNA fragments with a 3'-5' exoribonuclease, individual nucleotides can be selectively released from RNA fragments. The adenosine-based fraction of these nucleotides can then be converted into ATP and detected by luminescence as a sensitive indicator of mRNA byproducts. We developed a polynucleotide phosphorylase (PNPase)-based assay that offers fast and sensitive evaluation of mRNA integrity, regardless of its length, thus presenting a novel and fully scalable alternative to chromatographic-, electrophoresis-, or sequencing-based techniques.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"1-8"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11155706/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141248427","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

Expression of RNautophagy/DNautophagy-related genes is regulated under control of an innate immune receptor. RNautophagy/DNautophagy 相关基因的表达受先天性免疫受体的调控。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-01-10 DOI: 10.1080/15476286.2023.2291610

Yuuki Fujiwara, Kazuki Oroku, Yinping Zhou, Masayuki Takahashi, Taiichi Katayama, Keiji Wada, Nobuyuki Tsutsumi, Tetsuo Sato, Tomohiro Kabuta

{"title":"Expression of RNautophagy/DNautophagy-related genes is regulated under control of an innate immune receptor.","authors":"Yuuki Fujiwara, Kazuki Oroku, Yinping Zhou, Masayuki Takahashi, Taiichi Katayama, Keiji Wada, Nobuyuki Tsutsumi, Tetsuo Sato, Tomohiro Kabuta","doi":"10.1080/15476286.2023.2291610","DOIUrl":"10.1080/15476286.2023.2291610","url":null,"abstract":"Double-stranded RNA (dsRNA) is a molecular pattern uniquely produced in cells infected with various viruses as a product or byproduct of replication. Cells detect such molecules, which indicate non-self invasion, and induce diverse immune responses to eliminate them. The degradation of virus-derived molecules can also play a role in the removal of pathogens and suppression of their replication. RNautophagy and DNautophagy are cellular degradative pathways in which RNA and DNA are directly imported into a hydrolytic organelle, the lysosome. Two lysosomal membrane proteins, SIDT2 and LAMP2C, mediate nucleic acid uptake via this pathway. Here, we showed that the expression of both SIDT2 and LAMP2C is selectively upregulated during the intracellular detection of poly(I:C), a synthetic analog of dsRNA that mimics viral infection. The upregulation of these two gene products upon poly(I:C) introduction was transient and synchronized. We also observed that the induction of SIDT2 and LAMP2C expression by poly(I:C) was dependent on MDA5, a cytoplasmic innate immune receptor that directly recognizes poly(I:C) and induces various antiviral responses. Finally, we showed that lysosomes can target viral RNA for degradation via RNautophagy and may suppress viral replication. Our results revealed a novel degradative pathway in cells as a downstream component of the innate immune response and provided evidence suggesting that the degradation of viral nucleic acids via RNautophagy/DNautophagy contributes to the suppression of viral replication.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"1-9"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10793664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139417980","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 nanostructures for targeted drug delivery and imaging. 用于靶向给药和成像的 RNA 纳米结构。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-03-31 DOI: 10.1080/15476286.2024.2328440

Laura Teodori, Marjan Omer, Jørgen Kjems

{"title":"RNA nanostructures for targeted drug delivery and imaging.","authors":"Laura Teodori, Marjan Omer, Jørgen Kjems","doi":"10.1080/15476286.2024.2328440","DOIUrl":"10.1080/15476286.2024.2328440","url":null,"abstract":"The RNA molecule plays a pivotal role in many biological processes by relaying genetic information, regulating gene expression, and serving as molecular machines and catalyzers. This inherent versatility of RNA has fueled significant advancements in the field of RNA nanotechnology, driving the engineering of complex nanoscale architectures toward biomedical applications, including targeted drug delivery and bioimaging. RNA polymers, serving as building blocks, offer programmability and predictability of Watson-Crick base pairing, as well as non-canonical base pairing, for the construction of nanostructures with high precision and stoichiometry. Leveraging the ease of chemical modifications to protect the RNA from degradation, researchers have developed highly functional and biocompatible RNA architectures and integrated them into preclinical studies for the delivery of payloads and imaging agents. This review offers an educational introduction to the use of RNA as a biopolymer in the design of multifunctional nanostructures applied to targeted delivery in vivo, summarizing physical and biological barriers along with strategies to overcome them. Furthermore, we highlight the most recent progress in the development of both small and larger RNA nanostructures, with a particular focus on imaging reagents and targeted cancer therapeutics in pre-clinical models and provide insights into the prospects of this rapidly evolving field.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"1-19"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10984137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140330105","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

Circadian regulation of translation. 翻译的昼夜节律调节

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-09-26 DOI: 10.1080/15476286.2024.2408524

Jiali Lyu, Yanrong Zhuang, Yi Lin

{"title":"Circadian regulation of translation.","authors":"Jiali Lyu, Yanrong Zhuang, Yi Lin","doi":"10.1080/15476286.2024.2408524","DOIUrl":"10.1080/15476286.2024.2408524","url":null,"abstract":"Most, if not all organisms exhibit robust rhythmicity of their biological functions, allowing a perpetual adaptation to external clues within the daily 24 hours-cycle. Studies on circadian rhythm regulation primarily focused on transcriptional level, considering mRNA levels to represent the primary determinant of oscillations of intracellular protein levels. However, a plethora of emerging evidence suggests that post-transcriptional regulation, particularly rhythmic mRNA translation, is not solely reliant on the oscillation of transcription. Instead, the circadian regulation of mRNA translation plays a critical role as well. A comprehensive understanding of these mechanisms underlying rhythmic translation and its regulation should bridge the gap in rhythm regulation beyond RNA fluctuations in research, and greatly enhance our comprehension of rhythm generation and maintenance. In this review, we summarize the major mechanisms of circadian regulation of translation, including regulation of translation initiation, elongation, and the alteration in rhythmic translation to external stresses, such as endoplasmic reticulum (ER) stress and ageing. We also illuminate the complex interplay between phase separation and mRNA translation. Together, we have summarized various facets of mRNA translation in circadian regulation, to set on forthcoming studies into the intricate regulatory mechanisms underpinning circadian rhythms and their implications for associated disorders.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"14-24"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11441039/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142353016","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

Representation of non-coding RNA-mediated regulation of gene expression using the Gene Ontology. 使用基因本体对非编码 RNA 介导的基因表达调控进行表述。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-10-07 DOI: 10.1080/15476286.2024.2408523

Giulia Antonazzo, Pascale Gaudet, Ruth C Lovering, Helen Attrill

引用次数: 0

The nexus of long noncoding RNAs, splicing factors, alternative splicing and their modulations. 长链非编码rna，剪接因子，选择性剪接及其调节的联系。

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2023-11-28 DOI: 10.1080/15476286.2023.2286099

Pushkar Malakar, Sudhanshu Shukla, Meghna Mondal, Rajesh Kumar Kar, Jawed Akhtar Siddiqui

引用次数: 0

Correction. 校正

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2023-09-30 DOI: 10.1080/15476286.2023.2264666

引用次数: 0