IF 4.1 3区生物学

RNA Biology Pub Date : 2024-09-10 DOI: 10.1080/15476286.2024.2397757

Jiyao Liu,Tianyou Zhao,Caiqing Zheng,Ling Ma,Fan Song,Li Tian,Wanzhi Cai,Hu Li,Yuange Duan

{"title":"An orthology-based methodology as a complementary approach to retrieve evolutionarily conserved A-to-I RNA editing sites.","authors":"Jiyao Liu,Tianyou Zhao,Caiqing Zheng,Ling Ma,Fan Song,Li Tian,Wanzhi Cai,Hu Li,Yuange Duan","doi":"10.1080/15476286.2024.2397757","DOIUrl":"https://doi.org/10.1080/15476286.2024.2397757","url":null,"abstract":"Adar-mediated adenosine-to-inosine (A-to-I) mRNA editing is a conserved mechanism that exerts diverse regulatory functions during the development, evolution, and adaptation of metazoans. The accurate detection of RNA editing sites helps us understand their biological significance. In this work, with an improved genome assembly of honeybee (Apis mellifera), we used a new orthology-based methodology to complement the traditional pipeline of (de novo) RNA editing detection. Compared to the outcome of traditional pipeline, we retrieved many novel editing sites in CDS that are deeply conserved between honeybee and other distantly related insects. The newly retrieved sites were missed by the traditional de novo identification due to the stringent criteria for controlling false-positive rate. Caste-specific editing sites are identified, including an Ile>Met auto-recoding site in Adar. This recoding was even conserved between honeybee and bumblebee, suggesting its putative regulatory role in shaping the phenotypic plasticity of eusocial Hymenoptera. In summary, we proposed a complementary approach to the traditional pipeline and retrieved several previously unnoticed CDS editing sites. From both technical and biological aspects, our works facilitate future researches on finding the functional editing sites and advance our understanding on the connection between RNA editing and the great phenotypic diversity of organisms.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142193451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A systematic analysis of circRNAs in subnuclear compartments. 系统分析核下区室中的 circRNA。

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-09-10 DOI: 10.1080/15476286.2024.2395718

Andre Brezski,Justin Murtagh,Marcel H Schulz,Kathi Zarnack

{"title":"A systematic analysis of circRNAs in subnuclear compartments.","authors":"Andre Brezski,Justin Murtagh,Marcel H Schulz,Kathi Zarnack","doi":"10.1080/15476286.2024.2395718","DOIUrl":"https://doi.org/10.1080/15476286.2024.2395718","url":null,"abstract":"CircRNAs are an important class of RNAs with diverse cellular functions in human physiology and disease. A thorough knowledge of circRNAs including their biogenesis and subcellular distribution is important to understand their roles in a wide variety of processes. However, the analysis of circRNAs from total RNA sequencing data remains challenging. Therefore, we developed Calcifer, a versatile workflow for circRNA annotation. Using Calcifer, we analysed APEX-Seq data to compare circRNA occurrence between whole cells, nucleus and subnuclear compartments. We generally find that circRNAs show higher abundance in whole cells compared to nuclear samples, consistent with their accumulation in the cytoplasm. The notable exception is the single-exon circRNA circCANX(9), which is unexpectedly enriched in the nucleus. In addition, we observe that circFIRRE prevails over the linear lncRNA FIRRE in both the cytoplasm and the nucleus. Zooming in on the subnuclear compartments, we show that circRNAs are strongly depleted from nuclear speckles, indicating that excess splicing factors in this compartment counteract back-splicing. Our results thereby provide valuable insights into the subnuclear distribution of circRNAs. Regarding circRNA function, we surprisingly find that the majority of all detected circRNAs possess complete open reading frames with potential for cap-independent translation. Overall, we show that Calcifer is an easy-to-use, versatile and sustainable workflow for the annotation of circRNAs which expands the repertoire of circRNA tools and allows to gain new insights into circRNA distribution and function.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142193452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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

引用次数: 0

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

引用次数: 0

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

引用次数: 0

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

引用次数: 0

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

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 4.1 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":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/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

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

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