RNA Biology最新文献_第8页

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

The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking. EMT过程中的替代多聚腺苷酸化及其受RNA结合蛋白Quaking的调控。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2023-12-19 DOI: 10.1080/15476286.2023.2294222

Daniel P Neumann, Katherine A Pillman, B Kate Dredge, Andrew G Bert, Caroline A Phillips, Rachael Lumb, Yesha Ramani, Cameron P Bracken, Brett G Hollier, Luke A Selth, Traude H Beilharz, Gregory J Goodall, Philip A Gregory

{"title":"The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking.","authors":"Daniel P Neumann, Katherine A Pillman, B Kate Dredge, Andrew G Bert, Caroline A Phillips, Rachael Lumb, Yesha Ramani, Cameron P Bracken, Brett G Hollier, Luke A Selth, Traude H Beilharz, Gregory J Goodall, Philip A Gregory","doi":"10.1080/15476286.2023.2294222","DOIUrl":"10.1080/15476286.2023.2294222","url":null,"abstract":"Epithelial-mesenchymal transition (EMT) plays important roles in tumour progression and is orchestrated by dynamic changes in gene expression. While it is well established that post-transcriptional regulation plays a significant role in EMT, the extent of alternative polyadenylation (APA) during EMT has not yet been explored. Using 3' end anchored RNA sequencing, we mapped the alternative polyadenylation (APA) landscape following Transforming Growth Factor (TGF)-β-mediated induction of EMT in human mammary epithelial cells and found APA generally causes 3'UTR lengthening during this cell state transition. Investigation of potential mediators of APA indicated the RNA-binding protein Quaking (QKI), a splicing factor induced during EMT, regulates a subset of events including the length of its own transcript. Analysis of QKI crosslinked immunoprecipitation (CLIP)-sequencing data identified the binding of QKI within 3' untranslated regions (UTRs) was enriched near cleavage and polyadenylation sites. Following QKI knockdown, APA of many transcripts is altered to produce predominantly shorter 3'UTRs associated with reduced gene expression. These findings reveal the changes in APA that occur during EMT and identify a potential role for QKI in this process.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"1-11"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10732628/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138809129","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 high-density lipoprotein binding protein HDLBP is an unusual RNA-binding protein with multiple roles in cancer and disease. 高密度脂蛋白结合蛋白 HDLBP 是一种不寻常的 RNA 结合蛋白，在癌症和疾病中有多种作用。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-03-13 DOI: 10.1080/15476286.2024.2313881

Jonathan Feicht, Ralf-Peter Jansen

引用次数: 0

Nm-Nano: a machine learning framework for transcriptome-wide single-molecule mapping of 2´-O-methylation (Nm) sites in nanopore direct RNA sequencing datasets. Nm-Nano：纳米孔直接 RNA 测序数据集中 2´-O-methylation (Nm) 位点的全转录组单分子图谱的机器学习框架。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-05-17 DOI: 10.1080/15476286.2024.2352192

Doaa Hassan, Aditya Ariyur, Swapna Vidhur Daulatabad, Quoseena Mir, Sarath Chandra Janga

{"title":"Nm-Nano: a machine learning framework for transcriptome-wide single-molecule mapping of 2´-O-methylation (Nm) sites in nanopore direct RNA sequencing datasets.","authors":"Doaa Hassan, Aditya Ariyur, Swapna Vidhur Daulatabad, Quoseena Mir, Sarath Chandra Janga","doi":"10.1080/15476286.2024.2352192","DOIUrl":"10.1080/15476286.2024.2352192","url":null,"abstract":"2´-O-methylation (Nm) is one of the most abundant modifications found in both mRNAs and noncoding RNAs. It contributes to many biological processes, such as the normal functioning of tRNA, the protection of mRNA against degradation by the decapping and exoribonuclease (DXO) protein, and the biogenesis and specificity of rRNA. Recent advancements in single-molecule sequencing techniques for long read RNA sequencing data offered by Oxford Nanopore technologies have enabled the direct detection of RNA modifications from sequencing data. In this study, we propose a bio-computational framework, Nm-Nano, for predicting the presence of Nm sites in direct RNA sequencing data generated from two human cell lines. The Nm-Nano framework integrates two supervised machine learning (ML) models for predicting Nm sites: Extreme Gradient Boosting (XGBoost) and Random Forest (RF) with K-mer embedding. Evaluation on benchmark datasets from direct RNA sequecing of HeLa and HEK293 cell lines, demonstrates high accuracy (99% with XGBoost and 92% with RF) in identifying Nm sites. Deploying Nm-Nano on HeLa and HEK293 cell lines reveals genes that are frequently modified with Nm. In HeLa cell lines, 125 genes are identified as frequently Nm-modified, showing enrichment in 30 ontologies related to immune response and cellular processes. In HEK293 cell lines, 61 genes are identified as frequently Nm-modified, with enrichment in processes like glycolysis and protein localization. These findings underscore the diverse regulatory roles of Nm modifications in metabolic pathways, protein degradation, and cellular processes. The source code of Nm-Nano can be freely accessed at https://github.com/Janga-Lab/Nm-Nano.","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/PMC11110688/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140958988","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

Innovative construction of the first reliable catalogue of bovine circular RNAs. 创新性地构建了首个可靠的牛环状 RNA 目录。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-07-11 DOI: 10.1080/15476286.2024.2375090

Annie Robic, Frieder Hadlich, Gabriel Costa Monteiro Moreira, Emily Louise Clark, Graham Plastow, Carole Charlier, Christa Kühn

{"title":"Innovative construction of the first reliable catalogue of bovine circular RNAs.","authors":"Annie Robic, Frieder Hadlich, Gabriel Costa Monteiro Moreira, Emily Louise Clark, Graham Plastow, Carole Charlier, Christa Kühn","doi":"10.1080/15476286.2024.2375090","DOIUrl":"10.1080/15476286.2024.2375090","url":null,"abstract":"The aim of this study was to compare the circular transcriptome of divergent tissues in order to understand: i) the presence of circular RNAs (circRNAs) that are not exonic circRNAs, i.e. originated from backsplicing involving known exons and, ii) the origin of artificial circRNA (artif_circRNA), i.e. circRNA not generated in-vivo. CircRNA identification is mostly an in-silico process, and the analysis of data from the BovReg project (https://www.bovreg.eu/) provided an opportunity to explore new ways to identify reliable circRNAs. By considering 117 tissue samples, we characterized 23,926 exonic circRNAs, 337 circRNAs from 273 introns (191 ciRNAs, 146 intron circles), 108 circRNAs from small non-coding genes and nearly 36.6K circRNAs classified as other_circRNAs. Furthermore, for 63 of those samples we analysed in parallel data from total-RNAseq (ribosomal RNAs depleted prior to library preparation) with paired mRNAseq (library prepared with poly(A)-selected RNAs). The high number of circRNAs detected in mRNAseq, and the significant number of novel circRNAs, mainly other_circRNAs, led us to consider all circRNAs detected in mRNAseq as artificial. This study provided evidence of 189 false entries in the list of exonic circRNAs: 103 artif_circRNAs identified by total RNAseq/mRNAseq comparison using two circRNA tools, 26 probable artif_circRNAs, and 65 identified by deep annotation analysis. Extensive benchmarking was performed (including analyses with CIRI2 and CIRCexplorer-2) and confirmed 94% of the 23,737 reliable exonic circRNAs. Moreover, this study demonstrates the effectiveness of a panel of highly expressed exonic circRNAs (5-8%) in analysing the tissue specificity of the bovine circular transcriptome.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"52-74"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11244336/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141580690","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

If the 5' cap fits (wear it) - Non-canonical RNA capping. 如果 5'盖帽合适（戴上它）--非规范 RNA 盖帽。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-07-15 DOI: 10.1080/15476286.2024.2372138

Jiří František Potužník, Hana Cahova

引用次数: 0