RNA Biology最新文献_第9页

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

FMRP cooperates with miRISC components to repress translation and regulate neurite morphogenesis in Drosophila. FMRP与miRISC成分合作抑制翻译并调控果蝇的神经元形态发生。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-08-27 DOI: 10.1080/15476286.2024.2392304

Navneeta Kaul, Sarala J Pradhan, Nathan G Boin, Madeleine M Mason, Julian Rosales, Emily L Starke, Emily C Wilkinson, Erich G Chapman, Scott A Barbee

{"title":"FMRP cooperates with miRISC components to repress translation and regulate neurite morphogenesis in Drosophila.","authors":"Navneeta Kaul, Sarala J Pradhan, Nathan G Boin, Madeleine M Mason, Julian Rosales, Emily L Starke, Emily C Wilkinson, Erich G Chapman, Scott A Barbee","doi":"10.1080/15476286.2024.2392304","DOIUrl":"10.1080/15476286.2024.2392304","url":null,"abstract":"Fragile X Syndrome (FXS) is the most common inherited form of intellectual disability and is caused by mutations in the gene encoding the Fragile X messenger ribonucleoprotein (FMRP). FMRP is an evolutionarily conserved and neuronally enriched RNA-binding protein (RBP) with functions in RNA editing, RNA transport, and protein translation. Specific target RNAs play critical roles in neurodevelopment, including the regulation of neurite morphogenesis, synaptic plasticity, and cognitive function. The different biological functions of FMRP are modulated by its cooperative interaction with distinct sets of neuronal RNA and protein-binding partners. Here, we focus on interactions between FMRP and components of the microRNA (miRNA) pathway. Using the Drosophila S2 cell model system, we show that the Drosophila ortholog of FMRP (dFMRP) can repress translation when directly tethered to a reporter mRNA. This repression requires the activity of AGO1, GW182, and MOV10/Armitage, conserved proteins associated with the miRNA-containing RNA-induced silencing complex (miRISC). Additionally, we find that untagged dFMRP can interact with a short stem-loop sequence in the translational reporter, a prerequisite for repression by exogenous miR-958. Finally, we demonstrate that dFmr1 interacts genetically with GW182 to control neurite morphogenesis. These data suggest that dFMRP may recruit the miRISC to nearby miRNA binding sites and repress translation via its cooperative interactions with evolutionarily conserved components of the miRNA pathway.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"11-22"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11352701/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142081388","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 polymerase III transcription and regulation in ischaemic stroke. RNA 聚合酶 III 转录和调节在缺血性中风中的作用。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-10-03 DOI: 10.1080/15476286.2024.2409554

Chi Kwan Tsang, X F Steven Zheng

{"title":"Role of RNA polymerase III transcription and regulation in ischaemic stroke.","authors":"Chi Kwan Tsang, X F Steven Zheng","doi":"10.1080/15476286.2024.2409554","DOIUrl":"10.1080/15476286.2024.2409554","url":null,"abstract":"Ischaemic stroke is a leading cause of death and life-long disability due to neuronal cell death resulting from interruption of glucose and oxygen supplies. RNA polymerase III (Pol III)-dependent transcription plays a central role in protein synthesis that is necessary for normal cerebral neuronal functions, and the survival and recovery under pathological conditions. Notably, Pol III transcription is highly sensitive to ischaemic stress that is known to rapidly shut down Pol III transcriptional activity. However, its precise role in ischaemic stroke, especially during the acute and recovery phases, remains poorly understood. The microenvironment within the ischaemic brain undergoes dynamic changes in different phases after stroke. Emerging evidence highlights the distinct roles of Pol III transcription in neuroprotection during the acute phase and repair during the recovery phase of stroke. Additionally, investigations into the mTOR-MAF1 signalling pathway, a conserved regulator of Pol-III transcription, reveal its therapeutic potential in enhancing acute phase neuroprotection and recovery phase repair.","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/PMC11457610/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142372755","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

Post-transcriptional regulation of BIRC5/survivin expression and induction of apoptosis in breast cancer cells by tristetraprolin. Tristetraprolin对BIRC5/survivin表达的转录后调控以及对乳腺癌细胞凋亡的诱导。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2023-12-18 DOI: 10.1080/15476286.2023.2286101

Suhad Al-Yahya, Maher Al-Saif, Maha Al-Ghamdi, Walid Moghrabi, Khalid S A Khabar, Norah Al-Souhibani

{"title":"Post-transcriptional regulation of BIRC5/survivin expression and induction of apoptosis in breast cancer cells by tristetraprolin.","authors":"Suhad Al-Yahya, Maher Al-Saif, Maha Al-Ghamdi, Walid Moghrabi, Khalid S A Khabar, Norah Al-Souhibani","doi":"10.1080/15476286.2023.2286101","DOIUrl":"10.1080/15476286.2023.2286101","url":null,"abstract":"Inhibition of apoptosis is one of the hallmarks of cancer and is a target of various therapeutic interventions. BIRC5 is an inhibitor of apoptosis that is aberrantly expressed in cancer leading to sustained growth of tumours. Post-transcriptional control mechanisms involving RNA-binding proteins and AU-rich elements (AREs) are fundamental to many cellular processes and changes in the expression or function of these proteins can promote an aberrant and pathological phenotype. BIRC5 mRNA has an ARE in its 3' UTR making it a candidate for regulation by the RNA binding proteins tristetraprolin (TTP) and HuR (ELAVL1). In this study, we investigated the binding of TTP and HuR by RNA-immunoprecipitation assays and found that these proteins were associated with BIRC5 mRNA to varying extents. Consequently, BIRC5 expression decreased when TTP was overexpressed and apoptosis was induced. In the absence of TTP, BIRC5 mRNA was stabilized, protein expression increased and the number of apoptotic cells declined. As an ARE-mRNA stabilizing protein, recombinant HuR led to upregulation of BIRC5 expression, whereas HuR silencing was concomitant with downregulation of BIRC5 mRNA and protein and increased cell death. Survival analyses demonstrated that increased TTP and low BIRC5 expression predicted an overall better prognosis compared to dysregulated TTP and high BIRC5. Thus, the results present a novel target of ARE-mediated post-transcriptional regulation.","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/PMC10761079/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138809127","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

Programmable RNA targeting with CRISPR-Cas13. 利用 CRISPR-Cas13 进行可编程 RNA 靶向。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-05-19 DOI: 10.1080/15476286.2024.2351657

Peiguo Shi, Xuebing Wu

引用次数: 0

Decoding the genome of SARS-CoV-2: a pathway to drug development through translation inhibition. 解码SARS-CoV-2基因组：通过翻译抑制的药物开发途径

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-12-04 DOI: 10.1080/15476286.2024.2433830

Shan-Na Wu, Ting Xiao, Hui Chen, Xiao-Hong Li

{"title":"Decoding the genome of SARS-CoV-2: a pathway to drug development through translation inhibition.","authors":"Shan-Na Wu, Ting Xiao, Hui Chen, Xiao-Hong Li","doi":"10.1080/15476286.2024.2433830","DOIUrl":"10.1080/15476286.2024.2433830","url":null,"abstract":"The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease 2019 (COVID-19) pandemic and is continuously spreading globally. The continuous emergence of new SARS-CoV-2 variants keeps posing threats, highlighting the need for fast-acting, mutation-resistant broad-spectrum therapeutics. Protein translation is vital for SARS-CoV-2 replication, producing early non-structural proteins for RNA replication and transcription, and late structural proteins for virion assembly. Targeted blocking of viral protein translation is thus a potential approach to developing effective anti-SARS-CoV-2 drugs. SARS-CoV-2, as an obligate parasite, utilizes the host's translation machinery. Translation-blocking strategies that target the SARS-CoV-2 mRNA, especially those that target its conserved elements are generally preferred. In this review, we discuss the current understanding of SARS-CoV-2 translation, highlighting the important conserved motifs and structures involved in its regulation. We also discuss the current strategies for blocking SARS-CoV-2 translation through viral RNA degradation or RNA element dysfunction.","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/PMC11632750/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142772090","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