RNA Biology最新文献_第9页

Small RNA-big impact: exosomal miRNAs in mitochondrial dysfunction in various diseases. 小 RNA 大影响：外泌体 miRNA 在各种疾病的线粒体功能障碍中的作用。

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-01-04 DOI: 10.1080/15476286.2023.2293343

Xiaqing Li, Yi Han, Yu Meng, Lianghong Yin

{"title":"Small RNA-big impact: exosomal miRNAs in mitochondrial dysfunction in various diseases.","authors":"Xiaqing Li, Yi Han, Yu Meng, Lianghong Yin","doi":"10.1080/15476286.2023.2293343","DOIUrl":"10.1080/15476286.2023.2293343","url":null,"abstract":"Mitochondria are multitasking organelles involved in maintaining the cell homoeostasis. Beyond its well-established role in cellular bioenergetics, mitochondria also function as signal organelles to propagate various cellular outcomes. However, mitochondria have a self-destructive arsenal of factors driving the development of diseases caused by mitochondrial dysfunction. Extracellular vesicles (EVs), a heterogeneous group of membranous nano-sized vesicles, are present in a variety of bodily fluids. EVs serve as mediators for intercellular interaction. Exosomes are a class of small EVs (30-100 nm) released by most cells. Exosomes carry various cargo including microRNAs (miRNAs), a class of short noncoding RNAs. Recent studies have closely associated exosomal miRNAs with various human diseases, including diseases caused by mitochondrial dysfunction, which are a group of complex multifactorial diseases and have not been comprehensively described. In this review, we first briefly introduce the characteristics of EVs. Then, we focus on possible mechanisms regarding exosome-mitochondria interaction through integrating signalling networks. Moreover, we summarize recent advances in the knowledge of the role of exosomal miRNAs in various diseases, describing how mitochondria are changed in disease status. Finally, we propose future research directions to provide a novel therapeutic strategy that could slow the disease progress mediated by mitochondrial dysfunction.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10773649/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139088169","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

TBP facilitates RNA Polymerase I transcription following mitosis. TBP 有助于有丝分裂后的 RNA 聚合酶 I 转录。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-07-03 DOI: 10.1080/15476286.2024.2375097

James Z J Kwan, Thomas F Nguyen, Sheila S Teves

{"title":"TBP facilitates RNA Polymerase I transcription following mitosis.","authors":"James Z J Kwan, Thomas F Nguyen, Sheila S Teves","doi":"10.1080/15476286.2024.2375097","DOIUrl":"10.1080/15476286.2024.2375097","url":null,"abstract":"The TATA-box binding protein (TBP) is the sole transcription factor common in the initiation complexes of the three major eukaryotic RNA Polymerases (Pol I, II and III). Although TBP is central to transcription by the three RNA Pols in various species, the emergence of TBP paralogs throughout evolution has expanded the complexity in transcription initiation. Furthermore, recent studies have emerged that questioned the centrality of TBP in mammalian cells, particularly in Pol II transcription, but the role of TBP and its paralogs in Pol I transcription remains to be re-evaluated. In this report, we show that in murine embryonic stem cells TBP localizes onto Pol I promoters, whereas the TBP paralog TRF2 only weakly associates to the Spacer Promoter of rDNA, suggesting that it may not be able to replace TBP for Pol I transcription. Importantly, acute TBP depletion does not fully disrupt Pol I occupancy or activity on ribosomal RNA genes, but TBP binding in mitosis leads to efficient Pol I reactivation following cell division. These findings provide a more nuanced role for TBP in Pol I transcription in murine embryonic stem cells.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11225926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141493161","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

Transcriptional landscape of small non-coding RNAs reveals diversity of categories and functions in molluscs. 小非编码 RNA 的转录景观揭示了软体动物中类别和功能的多样性。

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-05-01 DOI: 10.1080/15476286.2024.2348893

Songqian Huang, Kazutoshi Yoshitake, Shigeharu Kinoshita, Shuichi Asakawa

{"title":"Transcriptional landscape of small non-coding RNAs reveals diversity of categories and functions in molluscs.","authors":"Songqian Huang, Kazutoshi Yoshitake, Shigeharu Kinoshita, Shuichi Asakawa","doi":"10.1080/15476286.2024.2348893","DOIUrl":"https://doi.org/10.1080/15476286.2024.2348893","url":null,"abstract":"Small non-coding RNAs (sncRNAs) are non-coding RNA molecules that play various roles in metazoans. Among the sncRNAs, microRNAs (miRNAs) guide post-translational gene regulation during cellular development, proliferation, apoptosis, and differentiation, while PIWI-interacting RNAs (piRNAs) suppress transposon activity to safeguard the genome from detrimental insertion mutagenesis. While an increasing number of piRNAs are being identified in the soma and germlines of various organisms, they are scarcely reported in molluscs. To unravel the small RNA (sRNA) expression patterns and genomic function in molluscs, we generated a comprehensive sRNA dataset by sRNA sequencing (sRNA-seq) of eight mollusc species. Abundant miRNAs were identified and characterized in all investigated molluscs, and ubiquitous piRNAs were discovered in both somatic and gonadal tissues in six of the investigated molluscs, which are more closely associated with transposon silencing. Tens of piRNA clusters were also identified based on the genomic mapping results, which varied among different tissues and species. Our dataset serves as important reference data for future genomic and genetic studies on sRNAs in these molluscs and related species, especially in elucidating the ancestral state of piRNAs in bilaterians.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11067994/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140854753","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

HNRNPD regulates the biogenesis of circRNAs and the ratio of mRNAs to circRNAs for a set of genes. HNRNPD 可调节 circRNA 的生物生成以及一组基因的 mRNA 与 circRNA 的比例。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-08-24 DOI: 10.1080/15476286.2024.2386500

Shuhui Chang, Yucong Wang, Xiaolin Wang, Hanyuan Liu, Tao Zhang, Yangge Zheng, Xueren Wang, Ge Shan, Liang Chen

{"title":"HNRNPD regulates the biogenesis of circRNAs and the ratio of mRNAs to circRNAs for a set of genes.","authors":"Shuhui Chang, Yucong Wang, Xiaolin Wang, Hanyuan Liu, Tao Zhang, Yangge Zheng, Xueren Wang, Ge Shan, Liang Chen","doi":"10.1080/15476286.2024.2386500","DOIUrl":"10.1080/15476286.2024.2386500","url":null,"abstract":"Exonic circular RNAs (ecircRNAs) in animal cells are generated by backsplicing, and the biogenesis of ecircRNAs is regulated by an array of RNA binding proteins (RBPs). HNRNPD is a heterogeneous nuclear ribonucleoprotein family member with both cytoplasmic and nuclear roles, and whether HNRNPD regulates the biogenesis of circRNAs remains unknown. In this study, we examine the role of HNRNPD in the biogenesis of ecircRNAs. The levels of ecircRNAs are primarily increased upon depletion of HNRNPD. HNRNPD preferentially binds to motifs enriched with A and U nucleotides, and the flanking introns of ecircRNAs tend to have more numbers and higher intensity of HNRNPD binding sites. The levels of mRNAs are generally not significantly altered in HNRNPD knockout cells. For a small set of genes, the circRNA:mRNA ratio is substantially affected, and the mRNA levels of some of these genes demonstrate a significant decrease in HNRNPD knockout cells. CDK1 is identified as a key gene modulated by HNRNPD in the context of circRNA biogenesis. HNRNPD suppresses the biogenesis of circCDK1 and favours the generation of CDK1 mRNA, and the CDK1 protein is a critical regulator of the cell cycle and apoptosis. HNRNPD can participate in cellular physiology, including the cell cycle and apoptosis, and plays roles in clear cell renal cell carcinoma (ccRCC) by modulating circRNA biogenesis and the mRNA levels of key genes, such as CDK1.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11346550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142047127","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 role of the 5' sensing function of ribonuclease E in cyanobacteria. 蓝藻中核糖核酸酶 E 的 5'感应功能的作用。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-03-12 DOI: 10.1080/15476286.2024.2328438

Ute A Hoffmann, Elisabeth Lichtenberg, Said N Rogh, Raphael Bilger, Viktoria Reimann, Florian Heyl, Rolf Backofen, Claudia Steglich, Wolfgang R Hess, Annegret Wilde

{"title":"The role of the 5' sensing function of ribonuclease E in cyanobacteria.","authors":"Ute A Hoffmann, Elisabeth Lichtenberg, Said N Rogh, Raphael Bilger, Viktoria Reimann, Florian Heyl, Rolf Backofen, Claudia Steglich, Wolfgang R Hess, Annegret Wilde","doi":"10.1080/15476286.2024.2328438","DOIUrl":"10.1080/15476286.2024.2328438","url":null,"abstract":"RNA degradation is critical for synchronising gene expression with changing conditions in prokaryotic and eukaryotic organisms. In bacteria, the preference of the central ribonucleases RNase E, RNase J and RNase Y for 5'-monophosphorylated RNAs is considered important for RNA degradation. For RNase E, the underlying mechanism is termed 5' sensing, contrasting to the alternative 'direct entry' mode, which is independent of monophosphorylated 5' ends. Cyanobacteria, such as Synechocystis sp. PCC 6803 (Synechocystis), encode RNase E and RNase J homologues. Here, we constructed a Synechocystis strain lacking the 5' sensing function of RNase E and mapped on a transcriptome-wide level 283 5'-sensing-dependent cleavage sites. These included so far unknown targets such as mRNAs encoding proteins related to energy metabolism and carbon fixation. The 5' sensing function of cyanobacterial RNase E is important for the maturation of rRNA and several tRNAs, including tRNAGluUUC. This tRNA activates glutamate for tetrapyrrole biosynthesis in plant chloroplasts and in most prokaryotes. Furthermore, we found that increased RNase activities lead to a higher copy number of the major Synechocystis plasmids pSYSA and pSYSM. These results provide a first step towards understanding the importance of the different target mechanisms of RNase E outside Escherichia coli.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10939160/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140102384","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

Low dose ribosomal DNA P-loop mutation affects development and enforces autophagy in Arabidopsis 低剂量核糖体 DNA P 环突变影响拟南芥的生长发育并强化自噬作用

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-12-29 DOI: 10.1080/15476286.2023.2298532

Thiruvenkadam Shanmugam, Palak Chaturvedi, Deniz Streit, Arindam Ghatak, Thorsten Bergelt, Stefan Simm, Wolfram Weckwerth, Enrico Schleiff