RNA Biology最新文献_第3页

Silencing LINC00663 inhibits inflammation and angiogenesis through downregulation of NR2F1 via EBF1 in bladder cancer 沉默 LINC00663 可通过下调 EBF1 抑制膀胱癌中的 NR2F1，从而抑制炎症和血管生成

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-06-18 DOI: 10.1080/15476286.2024.2368304

Xiulong Zhong, Lijiang Sun, Junxiang Liu, Xiaokun Yang, Minghui Hou, Xinning Wang, Huifeng Diao

引用次数: 0

Mistranslating the genetic code with leucine in yeast and mammalian cells 在酵母和哺乳动物细胞中用亮氨酸错译遗传密码

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-04-17 DOI: 10.1080/15476286.2024.2340297

Josephine Davey-Young, Farah Hasan, Rasangi Tennakoon, Peter Rozik, Henry Moore, Peter Hall, Ecaterina Cozma, Julie Genereaux, Kyle S. Hoffman, Patricia P. Chan, Todd M. Lowe, Christopher J. Brandl, Patrick O’Donoghue

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The regulatory roles of small nucleolar RNAs within their host locus 小核仁核糖核酸在宿主基因座内的调控作用

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-04-16 DOI: 10.1080/15476286.2024.2342685

Étienne Fafard-Couture, Stéphane Labialle, Michelle S Scott

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Synthetic RNA biology 合成 RNA 生物学

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-04-14 DOI: 10.1080/15476286.2024.2335746

Beatrix Suess

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Global and single-nucleotide resolution detection of 7-methylguanosine in RNA 全局和单核苷酸分辨率检测 RNA 中的 7-甲基鸟苷

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-04-02 DOI: 10.1080/15476286.2024.2337493

Silvia D’Ambrosi, Raquel García-Vílchez, Darek Kedra, Patrice Vitali, Nuria Macias-Cámara, Laura Bárcena, Monika Gonzalez-Lopez, Ana M. Aransay, Sabine Dietmann, Antonio Hurtado, Sandra Blanco

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MiRNAs differentially expressed in vegetative and reproductive organs of Marchantia polymorpha – insights into their expression pattern, gene structures and function 在马钱子无性器官和生殖器官中表达不同的 MiRNAs--洞察其表达模式、基因结构和功能

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-02-01 DOI: 10.1080/15476286.2024.2303555

Bharti Aggarwal, Wojciech Maciej Karlowski, Przemyslaw Nuc, Artur Jarmolowski, Zofia Szweykowska-Kulinska, Halina Pietrykowska

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Recent progress in miRNA biogenesis and decay. miRNA生物发生与衰变研究进展。

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2023-11-29 DOI: 10.1080/15476286.2023.2288741

Xavier Bofill-De Ros, Ulf Andersson Vang Ørom

引用次数: 0

Extracellular RNA in oncogenesis, metastasis and drug resistance. 肿瘤发生、转移和耐药性中的细胞外 RNA。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-08-06 DOI: 10.1080/15476286.2024.2385607

Hannah Nelson, Sherman Qu, Jeffrey L Franklin, Qi Liu, Heather H Pua, Kasey C Vickers, Alissa M Weaver, Robert J Coffey, James G Patton

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CCAR-1 works together with the U2AF large subunit UAF-1 to regulate alternative splicing. CCAR-1 与 U2AF 大亚基 UAF-1 共同调节替代剪接。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2023-12-21 DOI: 10.1080/15476286.2023.2289707

Doreen I Lugano, Lindsey N Barrett, Dale Chaput, Margaret A Park, Sandy D Westerheide

{"title":"CCAR-1 works together with the U2AF large subunit UAF-1 to regulate alternative splicing.","authors":"Doreen I Lugano, Lindsey N Barrett, Dale Chaput, Margaret A Park, Sandy D Westerheide","doi":"10.1080/15476286.2023.2289707","DOIUrl":"10.1080/15476286.2023.2289707","url":null,"abstract":"The Cell Division Cycle and Apoptosis Regulator (CCAR) protein family members have recently emerged as regulators of alternative splicing and transcription, as well as having other key physiological functions. For example, mammalian CCAR2/DBC1 forms a complex with the zinc factor protein ZNF326 to integrate alternative splicing with RNA polymerase II transcriptional elongation in AT-rich regions of the DNA. Additionally, Caenorhabditis elegans CCAR-1, a homolog to mammalian CCAR2, facilitates the alternative splicing of the perlecan unc-52 gene. However, much about the CCAR family's role in alternative splicing is unknown. Here, we have examined the role of CCAR-1 in genome-wide alternative splicing in Caenorhabditis elegans and have identified new alternative splicing targets of CCAR-1 using RNA sequencing. Also, we found that CCAR-1 interacts with the spliceosome factors UAF-1 and UAF-2 using mass spectrometry, and that knockdown of ccar-1 affects alternative splicing patterns, motility, and proteostasis of UAF-1 mutant worms. Collectively, we demonstrate the role of CCAR-1 in regulating global alternative splicing in C. elegans and in conjunction with UAF-1.","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/PMC10761121/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138831335","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

BioDeepfuse: a hybrid deep learning approach with integrated feature extraction techniques for enhanced non-coding RNA classification. BioDeepfuse：一种集成特征提取技术的混合深度学习方法，用于增强非编码 RNA 分类。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-03-25 DOI: 10.1080/15476286.2024.2329451

Anderson P Avila Santos, Breno L S de Almeida, Robson P Bonidia, Peter F Stadler, Polonca Stefanic, Ines Mandic-Mulec, Ulisses Rocha, Danilo S Sanches, André C P L F de Carvalho

{"title":"BioDeepfuse: a hybrid deep learning approach with integrated feature extraction techniques for enhanced non-coding RNA classification.","authors":"Anderson P Avila Santos, Breno L S de Almeida, Robson P Bonidia, Peter F Stadler, Polonca Stefanic, Ines Mandic-Mulec, Ulisses Rocha, Danilo S Sanches, André C P L F de Carvalho","doi":"10.1080/15476286.2024.2329451","DOIUrl":"10.1080/15476286.2024.2329451","url":null,"abstract":"The accurate classification of non-coding RNA (ncRNA) sequences is pivotal for advanced non-coding genome annotation and analysis, a fundamental aspect of genomics that facilitates understanding of ncRNA functions and regulatory mechanisms in various biological processes. While traditional machine learning approaches have been employed for distinguishing ncRNA, these often necessitate extensive feature engineering. Recently, deep learning algorithms have provided advancements in ncRNA classification. This study presents BioDeepFuse, a hybrid deep learning framework integrating convolutional neural networks (CNN) or bidirectional long short-term memory (BiLSTM) networks with handcrafted features for enhanced accuracy. This framework employs a combination of k-mer one-hot, k-mer dictionary, and feature extraction techniques for input representation. Extracted features, when embedded into the deep network, enable optimal utilization of spatial and sequential nuances of ncRNA sequences. Using benchmark datasets and real-world RNA samples from bacterial organisms, we evaluated the performance of BioDeepFuse. Results exhibited high accuracy in ncRNA classification, underscoring the robustness of our tool in addressing complex ncRNA sequence data challenges. The effective melding of CNN or BiLSTM with external features heralds promising directions for future research, particularly in refining ncRNA classifiers and deepening insights into ncRNAs in cellular processes and disease manifestations. In addition to its original application in the context of bacterial organisms, the methodologies and techniques integrated into our framework can potentially render BioDeepFuse effective in various and broader domains.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"1-12"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10968306/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140288892","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