RNA Biology最新文献_第10页

Correction. 校正

IF 4.1 3区生物学

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

引用次数: 0

RNA therapeutics. RNA 疗法。

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-01-11 DOI: 10.1080/15476286.2022.2161704

Tony Gutschner

引用次数: 0

A beneficial fungal root endophyte triggers systemic RNA silencing and DNA methylation of a host reporter gene. 有益的真菌根内生菌触发宿主报告基因的系统性RNA沉默和DNA甲基化。

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-01-01 DOI: 10.1080/15476286.2022.2159158

Athanasios Dalakouras, Afrodite Katsaouni, Marianna Avramidou, Elena Dadami, Olga Tsiouri, Sotirios Vasileiadis, Athanasios Makris, Maria Eleni Georgopoulou, Kalliope K Papadopoulou

{"title":"A beneficial fungal root endophyte triggers systemic RNA silencing and DNA methylation of a host reporter gene.","authors":"Athanasios Dalakouras, Afrodite Katsaouni, Marianna Avramidou, Elena Dadami, Olga Tsiouri, Sotirios Vasileiadis, Athanasios Makris, Maria Eleni Georgopoulou, Kalliope K Papadopoulou","doi":"10.1080/15476286.2022.2159158","DOIUrl":"https://doi.org/10.1080/15476286.2022.2159158","url":null,"abstract":"A growing body of evidence suggests that RNA interference (RNAi) plays a pivotal role in the communication between plants and pathogenic fungi, where a bi-directional trans-kingdom RNAi is established to the advantage of either the host or the pathogen. Similar mechanisms acting during plant association with non-pathogenic symbiotic microorganisms have been elusive to this date. To determine whether root endophytes can induce systemic RNAi responses to their host plants, we designed an experimental reporter-based system consisting of the root-restricted, beneficial fungal endophyte, Fusarium solani strain K (FsK) and its host Nicotiana benthamiana. Since not all fungi encode the RNAi machinery, we first needed to validate that FsK does so, by identifying its core RNAi enzymes (2 Dicer-like genes, 2 Argonautes and 4 RNA-dependent RNA polymerases) and by showing its susceptibility to in vitro RNAi upon exogenous application of double stranded RNAs (dsRNAs). Upon establishing this, we transformed FsK with a hairpin RNA (hpRNA) construct designed to target a reporter gene in its host N. benthamiana. The hpRNA was processed by FsK RNAi machinery predominantly into 21-24-nt small RNAs that triggered RNA silencing but not DNA methylation in the fungal hyphae. Importantly, when the hpRNA-expressing FsK was used to inoculate N. benthamiana, systemic RNA silencing and DNA methylation of the host reporter gene was recorded. Our data suggest that RNAi signals can be translocated by root endophytes to their hosts and can modulate gene expression during mutualism, which may be translated to beneficial phenotypes.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/52/c8/KRNB_20_2159158.PMC9809956.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9167589","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: 4

L1CAM immunocapture generates a unique extracellular vesicle population with a reproducible miRNA fingerprint. L1CAM免疫捕获产生独特的细胞外囊泡群，具有可复制的miRNA指纹。

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-01-01 DOI: 10.1080/15476286.2023.2198805

Rachael Anne Dunlop, Sandra Anne Banack, Paul Alan Cox

{"title":"L1CAM immunocapture generates a unique extracellular vesicle population with a reproducible miRNA fingerprint.","authors":"Rachael Anne Dunlop, Sandra Anne Banack, Paul Alan Cox","doi":"10.1080/15476286.2023.2198805","DOIUrl":"https://doi.org/10.1080/15476286.2023.2198805","url":null,"abstract":"Micro RNAs (miRNAs) are short, non-coding RNAs with significant potential as diagnostic and prognostic biomarkers. However, a lack of reproducibility across studies has hindered their introduction into clinical settings. Inconsistencies between studies include a lack of consensus on the miRNAs associated with a specific disease and the direction of regulation. These differences may reflect the heterogenous nature of pathologies with multiple phenotypes, such as amyotrophic lateral sclerosis (ALS). It is also possible that discrepancies are due to different sampling, processing, and analysis protocols across labs. Using miRNA extracted from L1CAM immunoaffinity purified extracellular vesicles (neural-enriched extracellular vesicles or NEE), we thrice replicated an 8-miRNA fingerprint diagnostic of ALS, which includes the miRNA species and direction of regulation. We aimed to determine if the extra purification steps required to generate NEE created a unique extracellular vesicle (EV) fraction that might contribute to the robustness and replicability of our assay. We compared three fractions from control human plasma: 1) total heterogenous EVs (T), 2) L1CAM/neural enriched EVs (NEE), and 3) the remaining total-minus-NEE fraction (T-N). Each fraction was characterized for size, total protein content, and protein markers, then total RNA was extracted, and qPCR was run on 20 miRNAs. We report that the miRNA expression within NEE was different enough compared to T and T-N to justify the extra steps required to generate this fraction. We conclude that L1CAM immunocapture generates a unique fraction of EVs that consistently and robustly replicates a miRNA fingerprint which differentiates ALS patients from controls.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/08/88/KRNB_20_2198805.PMC10101655.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9333197","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: 3

Translational control of murine adiponectin expression by an upstream open reading frame element. 上游开放阅读框元件对小鼠脂联素表达的翻译控制。

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-01-01 DOI: 10.1080/15476286.2023.2256094

Kommireddy Vasu, Iyappan Ramachandiran, Aayushi Chechi, Krishnendu Khan, Debjit Khan, Randall Kaufman, Paul L Fox

{"title":"Translational control of murine adiponectin expression by an upstream open reading frame element.","authors":"Kommireddy Vasu, Iyappan Ramachandiran, Aayushi Chechi, Krishnendu Khan, Debjit Khan, Randall Kaufman, Paul L Fox","doi":"10.1080/15476286.2023.2256094","DOIUrl":"https://doi.org/10.1080/15476286.2023.2256094","url":null,"abstract":"ABSTRACT Adiponectin, an adipocyte-specific secretory protein encoded by the ADIPOQ gene has a causal role in insulin resistance. Anti-diabetic drugs increase plasma adiponectin by a poorly understood, post-transcriptional mechanism enhancing insulin sensitivity. Deletion analysis of a reporter bearing the mouse Adipoq mRNA 5’-leader identified an inhibitory cis-regulatory sequence. The 5’-leader harbours two potential upstream open reading frames (uORFs) overlapping the principal downstream ORF. Mutation of the uORF ATGs increased reporter translation ~3-fold, indicative of a functional uORF. uORFs are common in mammalian mRNAs; however, only a select group resist translational repression by the integrated stress response (ISR). Thapsigargin (TG), which induces endoplasmic reticulum (ER) stress and the ISR, enhanced expression of a reporter bearing the Adipoq 5’-leader; polysome profiling verified translation-stimulation. TG-stimulated translation was absent in cells defective in Ser51 phosphorylation of eukaryotic initiation factor 2α (eIF2α), required for the ISR. To determine its role in expression and function of endogenous adiponectin, the upstream uORF was disrupted by CRISPR-Cas9-mediated mutagenesis of differentiated mouse 3T3-L1 adipocytes. uORF disruption in adipocytes increased adiponectin expression, triacylglycerol accumulation, and glucose uptake, and inhibited paracrine muscle and liver cell expression of gluconeogenic enzymes, establishing an important role of the uORF in adiponectin-mediated responses to stress.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/db/bb/KRNB_20_2256094.PMC10501164.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10259496","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

Cup is essential for oskar mRNA translational repression during early Drosophila oogenesis. 在果蝇早期卵发生过程中，Cup对oskar mRNA翻译抑制至关重要。

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-01-01 DOI: 10.1080/15476286.2023.2242650

Livia V Bayer, Samantha Milano, Stephen K Formel, Harpreet Kaur, Rishi Ravichandran, Juan A Cambeiro, Lizaveta Slinko, Irina E Catrina, Diana P Bratu

{"title":"Cup is essential for oskar mRNA translational repression during early Drosophila oogenesis.","authors":"Livia V Bayer, Samantha Milano, Stephen K Formel, Harpreet Kaur, Rishi Ravichandran, Juan A Cambeiro, Lizaveta Slinko, Irina E Catrina, Diana P Bratu","doi":"10.1080/15476286.2023.2242650","DOIUrl":"https://doi.org/10.1080/15476286.2023.2242650","url":null,"abstract":"Study of the timing and location for mRNA translation across model systems has begun to shed light on molecular events fundamental to such processes as intercellular communication, morphogenesis, and body pattern formation. In D. melanogaster, the posterior mRNA determinant, oskar, is transcribed maternally but translated only when properly localized at the oocyte's posterior cortex. Two effector proteins, Bruno1 and Cup, mediate steps of oskar mRNA regulation. The current model in the field identifies Bruno1 as necessary for Cup's recruitment to oskar mRNA and indispensable for oskar's translational repression. We now report that this Bruno1-Cup interaction leads to precise oskar mRNA regulation during early oogenesis and, importantly, the two proteins mutually influence each other's mRNA expression and protein distribution in the egg chamber. We show that these factors stably associate with oskar mRNA in vivo. Cup associates with oskar mRNA without Bruno1, while surprisingly Bruno1's stable association with oskar mRNA depends on Cup. We demonstrate that the essential factor for oskar mRNA repression in early oogenesis is Cup, not Bruno1. Furthermore, we find that Cup is a key P-body component that maintains functional P-body morphology during oogenesis and is necessary for oskar mRNA's association with P-bodies. Therefore, Cup drives the translational repression and stability of oskar mRNA. These experimental results point to a regulatory feedback loop between Bruno 1 and Cup in early oogenesis that appears crucial for oskar mRNA to reach the posterior pole and its expression in the egg chamber for accurate embryo development.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/84/e1/KRNB_20_2242650.PMC10413924.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10032029","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 paralogues MAGOH and MAGOHB are oncogenic factors in high-grade gliomas and safeguard the splicing of cell division and cell cycle genes. MAGOH 和 MAGOHB 的对映体是高级别胶质瘤的致癌因子，可保护细胞分裂和细胞周期基因的剪接。

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-01-01 DOI: 10.1080/15476286.2023.2221511

Rodrigo A S Barreiro, Gabriela D A Guardia, Fabiana M Meliso, Xiufen Lei, Wei-Qing Li, Andre Savio, Martin Fellermeyer, Helena B Conceição, Rafael L V Mercuri, Tesha Landry, Mei Qiao, Lorea Blazquez, Jernej Ule, Luiz O F Penalva, Pedro A F Galante

{"title":"The paralogues MAGOH and MAGOHB are oncogenic factors in high-grade gliomas and safeguard the splicing of cell division and cell cycle genes.","authors":"Rodrigo A S Barreiro, Gabriela D A Guardia, Fabiana M Meliso, Xiufen Lei, Wei-Qing Li, Andre Savio, Martin Fellermeyer, Helena B Conceição, Rafael L V Mercuri, Tesha Landry, Mei Qiao, Lorea Blazquez, Jernej Ule, Luiz O F Penalva, Pedro A F Galante","doi":"10.1080/15476286.2023.2221511","DOIUrl":"10.1080/15476286.2023.2221511","url":null,"abstract":"The exon junction complex (EJC) plays key roles throughout the lifespan of RNA and is particularly relevant in the nervous system. We investigated the roles of two EJC members, the paralogs MAGOH and MAGOHB, with respect to brain tumour development. High MAGOH/MAGOHB expression was observed in 14 tumour types; glioblastoma (GBM) showed the greatest difference compared to normal tissue. Increased MAGOH/MAGOHB expression was associated with poor prognosis in glioma patients, while knockdown of MAGOH/MAGOHB affected different cancer phenotypes. Reduced MAGOH/MAGOHB expression in GBM cells caused alterations in the splicing profile, including re-splicing and skipping of multiple exons. The binding profiles of EJC proteins indicated that exons affected by MAGOH/MAGOHB knockdown accumulated fewer complexes on average, providing a possible explanation for their sensitivity to MAGOH/MAGOHB knockdown. Transcripts (genes) showing alterations in the splicing profile are mainly implicated in cell division, cell cycle, splicing, and translation. We propose that high MAGOH/MAGOHB levels are required to safeguard the splicing of genes in high demand in scenarios requiring increased cell proliferation (brain development and GBM growth), ensuring efficient cell division, cell cycle regulation, and gene expression (splicing and translation). Since differentiated neuronal cells do not require increased MAGOH/MAGOHB expression, targeting these paralogs is a potential option for treating GBM.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10259345/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10065214","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

Discovering microproteins: making the most of ribosome profiling data. 发现微蛋白:充分利用核糖体分析数据。

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-01-01 Epub Date: 2023-11-27 DOI: 10.1080/15476286.2023.2279845

Sonia Chothani, Lena Ho, Sebastian Schafer, Owen Rackham

{"title":"Discovering microproteins: making the most of ribosome profiling data.","authors":"Sonia Chothani, Lena Ho, Sebastian Schafer, Owen Rackham","doi":"10.1080/15476286.2023.2279845","DOIUrl":"10.1080/15476286.2023.2279845","url":null,"abstract":"Building a reference set of protein-coding open reading frames (ORFs) has revolutionized biological process discovery and understanding. Traditionally, gene models have been confirmed using cDNA sequencing and encoded translated regions inferred using sequence-based detection of start and stop combinations longer than 100 amino-acids to prevent false positives. This has led to small ORFs (smORFs) and their encoded proteins left un-annotated. Ribo-seq allows deciphering translated regions from untranslated irrespective of the length. In this review, we describe the power of Ribo-seq data in detection of smORFs while discussing the major challenge posed by data-quality, -depth and -sparseness in identifying the start and end of smORF translation. In particular, we outline smORF cataloguing efforts in humans and the large differences that have arisen due to variation in data, methods and assumptions. Although current versions of smORF reference sets can already be used as a powerful tool for hypothesis generation, we recommend that future editions should consider these data limitations and adopt unified processing for the community to establish a canonical catalogue of translated smORFs.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10730196/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138446075","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

Dynamic and static circulating cancer microRNA biomarkers - a validation study. 动态和静态循环癌症 microRNA 生物标记物--一项验证研究。

IF 3.6 3区生物学

RNA Biology Pub Date : 2023-01-01 DOI: 10.1080/15476286.2022.2154470

Masood Abu-Halima, Andreas Keller, Lea Simone Becker, Ulrike Fischer, Annika Engel, Nicole Ludwig, Fabian Kern, Trine B Rounge, Hilde Langseth, Eckart Meese, Verena Keller

{"title":"Dynamic and static circulating cancer microRNA biomarkers - a validation study.","authors":"Masood Abu-Halima, Andreas Keller, Lea Simone Becker, Ulrike Fischer, Annika Engel, Nicole Ludwig, Fabian Kern, Trine B Rounge, Hilde Langseth, Eckart Meese, Verena Keller","doi":"10.1080/15476286.2022.2154470","DOIUrl":"10.1080/15476286.2022.2154470","url":null,"abstract":"For cancers and other pathologies, early diagnosis remains the most promising path to survival. Profiling of longitudinal cohorts facilitates insights into trajectories of biomarkers. We measured microRNA expression in 240 serum samples from patients with colon, lung, and breast cancer and from cancer-free controls. Each patient provided at least two serum samples, one prior to diagnosis and one following diagnosis. The median time interval between the samples was 11.6 years. Using computational models, we evaluated the circulating profiles of 21 microRNAs. The analysis yielded two sets of biomarkers, static ones that show an absolute difference between certain cancer types and controls and dynamic ones where the level over time provided higher diagnostic information content. In the first group, miR-99a-5p stands out for all three cancer types. In the second group, miR-155-5p allows to predict lung cancers and colon cancers. Classification in samples from cancer and non-cancer patients using gradient boosted trees reached an average accuracy of 79.9%. The results suggest that individual change over time or an absolute value at one time point may predict a disease with high specificity and sensitivity.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9754110/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10051537","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-targeted small-molecule drug discoveries: a machine-learning perspective. RNA靶向小分子药物发现：机器学习视角。

IF 3.6 3区生物学

RNA Biology Pub Date : 2023-01-01 DOI: 10.1080/15476286.2023.2223498

Huan Xiao, Xin Yang, Yihao Zhang, Zongkang Zhang, Ge Zhang, Bao-Ting Zhang

引用次数: 0