RNA Biology最新文献_第7页

Correction. 修正。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-12-12 DOI: 10.1080/15476286.2024.2437203

引用次数: 0

RNA-dependent proteome solubility maintenance in Escherichia coli lysates analysed by quantitative mass spectrometry: Proteomic characterization in terms of isoelectric point, structural disorder, functional hub, and chaperone network. 通过定量质谱分析大肠杆菌裂解物中依赖于 RNA 的蛋白质组溶解度维持：等电点、结构紊乱、功能枢纽和伴侣网络方面的蛋白质组特征。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-02-15 DOI: 10.1080/15476286.2024.2315383

Chan Park, Bitnara Han, Yura Choi, Yoontae Jin, Kwang Pyo Kim, Seong Il Choi, Baik L Seong

{"title":"RNA-dependent proteome solubility maintenance in Escherichia coli lysates analysed by quantitative mass spectrometry: Proteomic characterization in terms of isoelectric point, structural disorder, functional hub, and chaperone network.","authors":"Chan Park, Bitnara Han, Yura Choi, Yoontae Jin, Kwang Pyo Kim, Seong Il Choi, Baik L Seong","doi":"10.1080/15476286.2024.2315383","DOIUrl":"10.1080/15476286.2024.2315383","url":null,"abstract":"Protein aggregation, a consequence of misfolding and impaired proteostasis, can lead to cellular malfunctions such as various proteinopathies. The mechanisms protecting proteins from aggregation in complex cellular environments have long been investigated, often from a protein-centric viewpoint. However, our study provides insights into a crucial, yet overlooked actor: RNA. We found that depleting RNAs from Escherichia coli lysates induces global protein aggregation. Our quantitative mass spectrometry analysis identified over 900 statistically significant proteins from the Escherichia coli proteome whose solubility depends on RNAs. Proteome-wide characterization showed that the RNA dependency is particularly enriched among acidic proteins, intrinsically disordered proteins, and structural hub proteins. Moreover, we observed distinct differences in RNA-binding mode and Gene Ontology categories between RNA-dependent acidic and basic proteins. Notably, the solubility of key molecular chaperones [Trigger factor, DnaJ, and GroES] is largely dependent on RNAs, suggesting a yet-to-be-explored hierarchical relationship between RNA-based chaperone (termed as chaperna) and protein-based chaperones, both of which constitute the whole chaperone network. These findings provide new insights into the RNA-centric role in maintaining healthy proteome solubility in vivo, where proteins associate with a variety of RNAs, either stably or transiently.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"1-18"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10878026/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139741894","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

Skin treatment with non-thermal plasma modulates the immune system through miR-223-3p and its target genes. 用非热等离子体进行皮肤治疗可通过 miR-223-3p 及其靶基因调节免疫系统。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-06-03 DOI: 10.1080/15476286.2024.2361571

Annika Engel, Nicole Ludwig, Friederike Grandke, Viktoria Wagner, Fabian Kern, Tobias Fehlmann, Georges P Schmartz, Ernesto Aparicio-Puerta, Dominic Henn, Barbara Walch-Rückheim, Matthias Hannig, Stefan Rupf, Eckart Meese, Matthias W Laschke, Andreas Keller

{"title":"Skin treatment with non-thermal plasma modulates the immune system through miR-223-3p and its target genes.","authors":"Annika Engel, Nicole Ludwig, Friederike Grandke, Viktoria Wagner, Fabian Kern, Tobias Fehlmann, Georges P Schmartz, Ernesto Aparicio-Puerta, Dominic Henn, Barbara Walch-Rückheim, Matthias Hannig, Stefan Rupf, Eckart Meese, Matthias W Laschke, Andreas Keller","doi":"10.1080/15476286.2024.2361571","DOIUrl":"10.1080/15476286.2024.2361571","url":null,"abstract":"Non-thermal plasma, a partially ionized gas, holds significant potential for clinical applications, including wound-healing support, oral therapies, and anti-tumour treatments. While its applications showed promising outcomes, the underlying molecular mechanisms remain incompletely understood. We thus apply non-thermal plasma to mouse auricular skin and conducted non-coding RNA sequencing, as well as single-cell blood sequencing. In a time-series analysis (five timepoints spanning 2 hours), we compare the expression of microRNAs in the plasma-treated left ears to the unexposed right ears of the same mice as well as to the ears of unexposed control mice. Our findings indicate specific effects in the treated ears for a set of five miRNAs: mmu-miR-144-5p, mmu-miR-144-3p, mmu-miR-142a-5p, mmu-miR-223-3p, and mmu-miR-451a. Interestingly, mmu-miR-223-3p also exhibits an increase over time in the right non-treated ear of the exposed mice, suggesting systemic effects. Notably, this miRNA, along with mmu-miR-142a-5p and mmu-miR-144-3p, regulates genes and pathways associated with wound healing and tissue regeneration (namely ErbB, FoxO, Hippo, and PI3K-Akt signalling). This co-regulation is particularly remarkable considering the significant seed dissimilarities among the miRNAs. Finally, single-cell sequencing of PBMCs reveals the downregulation of 12 from 15 target genes in B-cells, Cd4+ and Cd8+ T-cells. Collectively, our data provide evidence for a systemic effect of non-thermal plasma.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"31-44"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11152102/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141200882","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

Significance of VLPs in Vlp-circRNA vaccines: a vaccine candidate or delivery vehicle? VLPs在Vlp-circRNA疫苗中的意义：候选疫苗还是输送载体？

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-09-06 DOI: 10.1080/15476286.2024.2399307

Reeshu Gupta, Kajal Arora, Nupur Mehrotra Arora, Prabuddha Kundu

{"title":"Significance of VLPs in Vlp-circRNA vaccines: a vaccine candidate or delivery vehicle?","authors":"Reeshu Gupta, Kajal Arora, Nupur Mehrotra Arora, Prabuddha Kundu","doi":"10.1080/15476286.2024.2399307","DOIUrl":"10.1080/15476286.2024.2399307","url":null,"abstract":"Circular RNAs (circRNAs) are a class of single-stranded RNAs with a closed loop lacking 5' and 3' ends. These circRNAs are translatable and, therefore, have a potential in developing vaccine. CircRNA vaccines have been shown to be more stable, safe, easy to manufacture and scale-up production when compared to mRNA vaccines. However, these vaccines also suffer from several drawbacks such as low circularization efficiency for longer RNA precursor and usage of lipid nano particles (LNPs) in their delivery. LNPs have been shown to require large amounts of RNA due to their indirect delivery from endosome to cytosol. Besides, individual components of LNPs provide reactogenicity. Usage of virus like particles (VLPs) can improve the increased production and targeted delivery of circRNA vaccines and show no reactogenicity. Moreover, VLPs has also been used to produce vaccines against several diseases such as hepatitis C virus (HCV) etc. In this article, we will discuss about the methods used to enhance synthesis or circularization efficiency of circRNA. Moreover, we will also discuss about the significance of VLPs as the delivery vehicle for circRNA and their possible usage as the dual vaccine.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"17-28"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11382717/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142140940","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

Regulation and mechanisms of action of RNA helicases. RNA 螺旋酶的调控和作用机制。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-10-22 DOI: 10.1080/15476286.2024.2415801

Nina Lang, Pravin Kumar Ankush Jagtap, Janosch Hennig

引用次数: 0

Tissue-specific silencing of integrated transgenes achieved through endogenous RNA interference in Caenorhabditis elegans. 在秀丽隐杆线虫体内通过内源性 RNA 干扰实现整合转基因的组织特异性沉默。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-03-26 DOI: 10.1080/15476286.2024.2332856

Siyu Chen, Weihong Liu, Lei Xiong, Zhiju Tao, Di Zhao

{"title":"Tissue-specific silencing of integrated transgenes achieved through endogenous RNA interference in Caenorhabditis elegans.","authors":"Siyu Chen, Weihong Liu, Lei Xiong, Zhiju Tao, Di Zhao","doi":"10.1080/15476286.2024.2332856","DOIUrl":"10.1080/15476286.2024.2332856","url":null,"abstract":"Transgene silencing is a common phenomenon observed in Caenorhabditis elegans, particularly in the germline, but the precise mechanisms underlying this process remain elusive. Through an analysis of the transcription factors profile of C. elegans, we discovered that the expression of several transgenic reporter lines exhibited tissue-specific silencing, specifically in the intestine of C. elegans. Notably, this silencing could be reversed in mutants defective in endogenous RNA interference (RNAi). Further investigation using knock-in strains revealed that these intestine-silent genes were indeed expressed in vivo, indicating that the organism itself regulates the intestine-specific silencing. This tissue-specific silencing appears to be mediated through the endo-RNAi pathway, with the main factors of this pathway, mut-2 and mut-16, are significantly enriched in the intestine. Additionally, histone modification factors, such as met-2, are involved in this silencing mechanism. Given the crucial role of the intestine in reproduction alongside the germline, the transgene silencing observed in the intestine reflects the self-protective mechanisms employed by the organisms. In summary, our study proposed that compared to other tissues, the transgenic silencing of intestine is specifically regulated by the endo-RNAi pathway.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"1-10"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10978027/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140294387","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

Role of RNA binding proteins of the Drosophila behavior and human splicing (DBHS) family in health and cancer. 果蝇行为和人类剪接（DBHS）家族的 RNA 结合蛋白在健康和癌症中的作用。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-03-29 DOI: 10.1080/15476286.2024.2332855

Toshihiko Takeiwa, Kazuhiro Ikeda, Kuniko Horie, Satoshi Inoue

引用次数: 0

Decoding LINC00052 role in breast cancer by bioinformatic and experimental analyses. 通过生物信息学和实验分析解码 LINC00052 在乳腺癌中的作用。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-06-04 DOI: 10.1080/15476286.2024.2355393

Jose Manuel Sanchez-Lopez, Miguel Angel Juarez-Mancera, Benjamin Bustamante, Araceli Ruiz-Silvestre, Magali Espinosa, Gretel Mendoza-Almanza, Gisela Ceballos-Cancino, Jorge Melendez-Zajgla, Vilma Maldonado, Floria Lizarraga

{"title":"Decoding LINC00052 role in breast cancer by bioinformatic and experimental analyses.","authors":"Jose Manuel Sanchez-Lopez, Miguel Angel Juarez-Mancera, Benjamin Bustamante, Araceli Ruiz-Silvestre, Magali Espinosa, Gretel Mendoza-Almanza, Gisela Ceballos-Cancino, Jorge Melendez-Zajgla, Vilma Maldonado, Floria Lizarraga","doi":"10.1080/15476286.2024.2355393","DOIUrl":"10.1080/15476286.2024.2355393","url":null,"abstract":"LncRNA is a group of transcripts with a length exceeding 200 nucleotides that contribute to tumour development. Our research group found that LINC00052 expression was repressed during the formation of breast cancer (BC) multicellular spheroids. Intriguingly, LINC00052 precise role in BC remains uncertain. We explored LINC00052 expression in BC patients` RNA samples (TCGA) in silico, as well as in an in-house patient cohort, and inferred its cellular and molecular mechanisms. In vitro studies evaluated LINC00052 relevance in BC cells viability, cell cycle and DNA damage. Results. Bioinformatic RNAseq analysis of BC patients showed that LINC00052 is overexpressed in samples from all BC molecular subtypes. A similar LINC00052 expression pattern was observed in an in-house patient cohort. In addition, higher LINC00052 levels are related to better BC patient´s overall survival. Remarkably, MCF-7 and ZR-75-1 cells treated with estradiol showed increased LINC00052 expression compared to control, while these changes were not observed in MDA-MB-231 cells. In parallel, bioinformatic analyses indicated that LINC00052 influences DNA damage and cell cycle. MCF-7 cells with low LINC00052 levels exhibited increased cellular protection against DNA damage and diminished growth capacity. Furthermore, in cisplatin-resistant MCF-7 cells, LINC00052 expression was downregulated. Conclusion. This work shows that LINC00052 expression is associated with better BC patient survival. Remarkably, LINC00052 expression can be regulated by Estradiol. Additionally, assays suggest that LINC00052 could modulate MCF-7 cells growth and DNA damage repair. Overall, this study highlights the need for further research to unravel LINC00052 molecular mechanisms and potential clinical applications in BC.","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/PMC11152094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141238301","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

Circular at the very beginning: on the initial genomes in the RNA world. 最初的循环：关于 RNA 世界中最初的基因组。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-07-17 DOI: 10.1080/15476286.2024.2380130

Yufan Luo, Minglun Liang, Chunwu Yu, Wentao Ma

{"title":"Circular at the very beginning: on the initial genomes in the RNA world.","authors":"Yufan Luo, Minglun Liang, Chunwu Yu, Wentao Ma","doi":"10.1080/15476286.2024.2380130","DOIUrl":"10.1080/15476286.2024.2380130","url":null,"abstract":"It is likely that an RNA world existed in early life, when RNA played both the roles of the genome and functional molecules, thereby undergoing Darwinian evolution. However, even with only one type of polymer, it seems quite necessary to introduce a labour division concerning these two roles because folding is required for functional molecules (ribozymes) but unfavourable for the genome (as a template in replication). Notably, while ribozymes tend to have adopted a linear form for folding without constraints, a circular form, which might have been topologically hindered in folding, seems more suitable for an RNA template. Another advantage of involving a circular genome could have been to resist RNA's end-degradation. Here, we explore the scenario of a circular RNA genome plus linear ribozyme(s) at the precellular stage of the RNA world through computer modelling. The results suggest that a one-gene scene could have been 'maintained', albeit with rather a low efficiency for the circular genome to produce the ribozyme, which required precise chain-break or chain-synthesis. This strict requirement may have been relieved by introducing a 'noncoding' sequence into the genome, which had the potential to derive a second gene through mutation. A two-gene scene may have 'run well' with the two corresponding ribozymes promoting the replication of the circular genome from different respects. Circular genomes with more genes might have arisen later in RNA-based protocells. Therefore, circular genomes, which are common in the modern living world, may have had their 'root' at the very beginning of life.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"17-31"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11259081/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141627575","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 polymerase I mutant affects ribosomal RNA processing and ribosomal DNA stability. RNA 聚合酶 I 突变体影响核糖体 RNA 处理和核糖体 DNA 的稳定性。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-07-24 DOI: 10.1080/15476286.2024.2381910

Christophe Normand, Christophe Dez, Lise Dauban, Sophie Queille, Sarah Danché, Sarra Abderrahmane, Frederic Beckouet, Olivier Gadal

{"title":"RNA polymerase I mutant affects ribosomal RNA processing and ribosomal DNA stability.","authors":"Christophe Normand, Christophe Dez, Lise Dauban, Sophie Queille, Sarah Danché, Sarra Abderrahmane, Frederic Beckouet, Olivier Gadal","doi":"10.1080/15476286.2024.2381910","DOIUrl":"10.1080/15476286.2024.2381910","url":null,"abstract":"Transcription is a major contributor to genomic instability. The ribosomal RNA (rDNA) gene locus consists of a head-to-tail repeat of the most actively transcribed genes in the genome. RNA polymerase I (RNAPI) is responsible for massive rRNA production, and nascent rRNA is co-transcriptionally assembled with early assembly factors in the yeast nucleolus. In Saccharomyces cerevisiae, a mutant form of RNAPI bearing a fusion of the transcription factor Rrn3 with RNAPI subunit Rpa43 (CARA-RNAPI) has been described previously. Here, we show that the CARA-RNAPI allele results in a novel type of rRNA processing defect, associated with rDNA genomic instability. A fraction of the 35S rRNA produced in CARA-RNAPI mutant escapes processing steps and accumulates. This accumulation is increased in mutants affecting exonucleolytic activities of the exosome complex. CARA-RNAPI is synthetic lethal with monopolin mutants that are known to affect the rDNA condensation. CARA-RNAPI strongly impacts rDNA organization and increases rDNA copy number variation. Reduced rDNA copy number suppresses lethality, suggesting that the chromosome segregation defect is caused by genomic rDNA instability. We conclude that a constitutive association of Rrn3 with transcribing RNAPI results in the accumulation of rRNAs that escape normal processing, impacting rDNA organization and affecting rDNA stability.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"1-16"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11275518/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141760616","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