RNA Biology最新文献

筛选
英文 中文
RNA diagnostics and therapeutics: a comprehensive review. RNA诊断和治疗:综述。
IF 3.6 3区 生物学
RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-01-03 DOI: 10.1080/15476286.2024.2449277
Adeela Fathima Saju, Aditi Mukundan, Divyashree Ms, Raghu Chandrashekhar, Archana Mahadev Rao
{"title":"RNA diagnostics and therapeutics: a comprehensive review.","authors":"Adeela Fathima Saju, Aditi Mukundan, Divyashree Ms, Raghu Chandrashekhar, Archana Mahadev Rao","doi":"10.1080/15476286.2024.2449277","DOIUrl":"10.1080/15476286.2024.2449277","url":null,"abstract":"<p><p>RNA-focused therapy and diagnostics have been making waves in molecular biology due to the advantages RNA has over DNA; for instance, the ability of RNA to target nearly any genetic component in the cell is a big step in treating disorders. Moreover, RNA-based diagnosis of diseases is only becoming increasingly popular, especially after the COVID-19 pandemic, which brought up the need for cost-effective and efficient diagnosing kits for the vast majority. RNA-based techniques also have close to no risk of genotoxicity and can efficiently target undruggable regions of the cell. RNA treatments have effectively shown the future of the medical industry in the past couple of decades, and they will only be seen to improve. This review paper provides an overview on the different techniques that use RNA-based approaches in the field of diagnostics and therapeutics.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-11"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142915525","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
Relevance of RNA to the therapeutic efficacy of mesenchymal stromal/stem cells extracellular vesicles. RNA与间充质间质/干细胞细胞外囊泡治疗效果的相关性
IF 3.6 3区 生物学
RNA Biology Pub Date : 2025-12-01 Epub Date: 2024-12-24 DOI: 10.1080/15476286.2024.2446868
Thong Teck Tan, Sai Kiang Lim
{"title":"Relevance of RNA to the therapeutic efficacy of mesenchymal stromal/stem cells extracellular vesicles.","authors":"Thong Teck Tan, Sai Kiang Lim","doi":"10.1080/15476286.2024.2446868","DOIUrl":"10.1080/15476286.2024.2446868","url":null,"abstract":"<p><p>Mesenchymal Stromal/Stem Cells (MSCs) are among the most frequently studied cell types in clinical trials, and their small extracellular vesicles (sEVs) are now being extensively investigated for therapeutic applications. The RNA cargo of MSC-sEVs, particularly miRNAs and mRNAs, is widely believed to be a key therapeutic component of these vesicles. In this review, we critically examine using first principles and peer-reviewed literature, whether MSC- extracellular vesicles (MSC-EVs) can deliver sufficient quantity of functional miRNA or mRNA to target compartments within recipient cells to elicit a pharmacological response. Several RNA sequencing studies reveal that miRNAs are underrepresented in the small RNA population of MSC-sEVs compared to the parent MSCs. Additionally, the majority of miRNAs are mature forms that are not associated with Argonaute (AGO) proteins, essential for their function in RNA-induced silencing complexes (RISCs). Compounding this, cellular uptake of EVs is generally inefficient, with less than 1% being internalized, and only a fraction of these reaching the cytosol. This suggests that EVs may not deliver miRNAs in sufficient quantities to meaningfully interact with AGO proteins, either through canonical or non-canonical pathways, or with other proteins like Toll-like receptors (TLRs). Further, MSC-sEV RNAs are generally small, with sizes less than 500 nucleotides indicating that any mRNA present is likely fragmented as the average mammalian mRNA is approximately 2000 nucleotides, a fact confirmed by RNA sequencing data. Together, these findings challenge the notion that RNA, particularly miRNAs and mRNAs, are primary therapeutic attributes of MSC-sEVs.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"22 1","pages":"1-7"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142885343","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
RNase P cleavage of pseudoknot substrates reveals differences in active site architecture that depend on residue N-1 in the 5' leader. 伪结底物的RNase P切割揭示了活性位点结构的差异,这取决于5'先导物中的残基N-1。
IF 3.6 3区 生物学
RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-01-20 DOI: 10.1080/15476286.2024.2427906
David M Kosek, J Luis Leal, Ema Kikovska-Stojanovska, Guanzhong Mao, Shiying Wu, Samuel C Flores, Leif A Kirsebom
{"title":"RNase P cleavage of pseudoknot substrates reveals differences in active site architecture that depend on residue N-1 in the 5' leader.","authors":"David M Kosek, J Luis Leal, Ema Kikovska-Stojanovska, Guanzhong Mao, Shiying Wu, Samuel C Flores, Leif A Kirsebom","doi":"10.1080/15476286.2024.2427906","DOIUrl":"https://doi.org/10.1080/15476286.2024.2427906","url":null,"abstract":"<p><p>We show that a small biotin-binding RNA aptamer that folds into a pseudoknot structure acts as a substrate for bacterial RNase P RNA (RPR) with and without the RNase P C5 protein. Cleavage in the single-stranded region in loop 1 was shown to depend on the presence of a RCCA-motif at the 3' end of the substrate. The nucleobase and the 2'hydroxyl at the position immediately 5' of the cleavage site contribute to both cleavage efficiency and site selection, where C at this position induces significant cleavage at an alternative site, one base upstream of the main cleavage site. The frequencies of cleavage at these two sites and Mg<sup>2+</sup> binding change upon altering the structural topology in the vicinity of the cleavage site as well as by replacing Mg<sup>2+</sup> with other divalent metal ions. Modelling studies of RPR in complex with the pseudoknot substrates suggest alternative structural topologies for cleavage at the main and the alternative site and a shift in positioning of Mg<sup>2+</sup> that activates the H<sub>2</sub>O nucleophile. Together, our data are consistent with a model where the organization of the active site structure and positioning of Mg<sup>2+</sup> is influenced by the identities of residues at and in the vicinity of the site of cleavage.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"22 1","pages":"1-19"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010860","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
The role and function of lncRNA in ageing-associated liver diseases. lncRNA在衰老相关肝脏疾病中的作用和功能
IF 3.6 3区 生物学
RNA Biology Pub Date : 2025-12-01 Epub Date: 2024-12-19 DOI: 10.1080/15476286.2024.2440678
Peyman Kheirandish Zarandi, Mohsen Ghiasi, Mohammad Heiat
{"title":"The role and function of lncRNA in ageing-associated liver diseases.","authors":"Peyman Kheirandish Zarandi, Mohsen Ghiasi, Mohammad Heiat","doi":"10.1080/15476286.2024.2440678","DOIUrl":"10.1080/15476286.2024.2440678","url":null,"abstract":"<p><p>Liver diseases are a significant global health issue, characterized by elevated levels of disorder and death. The substantial impact of ageing on liver diseases and their prognosis is evident. Multiple processes are involved in the ageing process, which ultimately leads to functional deterioration of this organ. The process of liver ageing not only renders the liver more susceptible to diseases but also compromises the integrity of other organs due to the liver's critical function in metabolism regulation. A growing body of research suggests that long non-coding RNAs (lncRNAs) play a significant role in the majority of pathophysiological pathways. They regulate gene expression through a variety of interactions with microRNAs (miRNAs), messenger RNAs (mRNAs), DNA, or proteins. LncRNAs exert a major influence on the progression of age-related liver diseases through the regulation of cell proliferation, necrosis, apoptosis, senescence, and metabolic reprogramming. A concise overview of the current understanding of lncRNAs and their potential impact on the development of age-related liver diseases will be provided in this mini-review.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"22 1","pages":"1-8"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11660375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142855134","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
Two complementing in vivo selection systems based on CCA-trimming exonucleases as a tool to monitor, select and evaluate enzymatic features of tRNA nucleotidyltransferases. 基于cca修饰外切酶的两种互补的体内选择系统,作为监测、选择和评估tRNA核苷酸转移酶酶学特征的工具。
IF 3.6 3区 生物学
RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-01-29 DOI: 10.1080/15476286.2025.2453963
Karolin Wellner, Josefine Gnauck, Dorian Bernier, Stephan H Bernhart, Heike Betat, Mario Mörl
{"title":"Two complementing <i>in vivo</i> selection systems based on CCA-trimming exonucleases as a tool to monitor, select and evaluate enzymatic features of tRNA nucleotidyltransferases.","authors":"Karolin Wellner, Josefine Gnauck, Dorian Bernier, Stephan H Bernhart, Heike Betat, Mario Mörl","doi":"10.1080/15476286.2025.2453963","DOIUrl":"10.1080/15476286.2025.2453963","url":null,"abstract":"<p><p>tRNA nucleotidyltransferase represents a ubiquitous and essential activity that adds the indispensable CCA triplet to the 3'-end of tRNAs. To fulfill this function, the enzyme contains a set of highly conserved motifs whose coordinated interplay is crucial for the sequence-specific CCA polymerization. In the human enzyme, alterations within these regions have been shown to lead to the manifestation of disease. Recently, we developed an <i>in vivo</i> screening system that allows for the selection and analysis of tRNA nucleotidyltransferase variants by challenging terminal AMP incorporation into tRNA during induced RNase T-catalyzed CCA-decay. Here, we extend this method for screening of full CCA-end repair by utilizing the CCA-trimming activity of exonuclease LCCR4. To demonstrate the combined potential of these two <i>in vivo</i> selection systems, we applied a semi-rational library design to investigate the mode of operation of catalytically important motifs in the human CCA-adding enzyme. This approach revealed unexpected requirements for amino acid composition in two motifs and gives new insights into the mechanism of CCA addition. The data show the potential of these RNase-based screening systems, as they allow the detection of enzyme variations that would not have been identified by a conventional rational approach. Furthermore, the combination of both RNase T and LCCR4 systems can be used to investigate and dissect the effects of pathogenic mutations on C- and A-addition.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-14"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784652/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010861","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
Translational regulation of PKD1 by evolutionarily conserved upstream open reading frames. 进化保守的上游开放阅读框对PKD1的翻译调控。
IF 3.6 3区 生物学
RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-01-05 DOI: 10.1080/15476286.2024.2448387
Lei Chen, Xia Gao, Xiangshen Liu, Ye Zhu, Dong Wang
{"title":"Translational regulation of PKD1 by evolutionarily conserved upstream open reading frames.","authors":"Lei Chen, Xia Gao, Xiangshen Liu, Ye Zhu, Dong Wang","doi":"10.1080/15476286.2024.2448387","DOIUrl":"10.1080/15476286.2024.2448387","url":null,"abstract":"<p><p>Mutations in <i>PKD1</i> coding sequence and abnormal PKD1 expression levels contribute to the development of autosomal-dominant polycystic kidney disease, the most common genetic disorder. Regulation of PKD1 expression by factors located in the promoter and 3´ UTR have been extensively studied. Less is known about its regulation by 5´ UTR elements. In this study, we investigated the effects of uORFs and uORF-affecting variants by combining bioinformatic analyses, luciferase reporter assays, RT-qPCR and immunoblotting experiments. Our analyses demonstrate that <i>PKD1</i> mRNA contains two evolutionarily conserved translation-inhibitory uORFs. uORF1 is translatable, and uORF2 is likely not translatable. The 5´ UTR and uORFs do not modulate downstream protein output under endoplasmic reticulum stress and oxidative stress conditions. Some of uORF-perturbing variants in the SNP database are predicted to affect gene translation. Luciferase reporter assays and RT-qPCR results reveal that rs2092942382 and rs1596636969 increase, while rs2092942900 decreases main gene translation without affecting transcription. Antisense oligos targeting the uORFs reduce luciferase protein levels without altering luciferase mRNA levels. Our results establish <i>PKD1</i> as a novel target of uORF-mediated translational regulation and mutations that perturb uORFs may dysregulate PKD1 protein level.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"22 1","pages":"1-12"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11810096/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142932624","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
AUGcontext DB: a comprehensive catalogue of the mRNA AUG initiator codon context across eukaryotes.
IF 3.6 3区 生物学
RNA Biology Pub Date : 2025-02-12 DOI: 10.1080/15476286.2025.2465196
Vincent G Osnaya, Laura Gómez-Romero, Gabriel Moreno-Hagelsieb, Greco Hernández
{"title":"AUGcontext DB: a comprehensive catalogue of the mRNA AUG initiator codon context across eukaryotes.","authors":"Vincent G Osnaya, Laura Gómez-Romero, Gabriel Moreno-Hagelsieb, Greco Hernández","doi":"10.1080/15476286.2025.2465196","DOIUrl":"https://doi.org/10.1080/15476286.2025.2465196","url":null,"abstract":"<p><strong>Introduction: </strong>The mRNA translation defines the composition of the cell proteome in all forms of life and diseases. In this process, precise selection of the mRNA translation initiation site (TIS) is crucial, as it establishes the correct open reading frame for triplet decoding.</p><p><strong>Methods: </strong>We have gathered and curated all published TIS consensus context sequences. We also included the TIS consensus context from novel 538 fungal genomes available from NCBI's RefSeq database. To do so, we wrote ad hoc programs in PERL to find and extract the TIS for each annotated gene, plus ten bases upstream and three downstream. For each genome, the sequences around the TIS of each gene were obtained and the consensus was further calculated according to the Cavener rules and by the LOGOS algorithm.</p><p><strong>Results: </strong>We created AUGcontext DB, a portal with a comprehensive collection of TIS context sequences across eukaryotes in a range from -10 to + 6. The compilation covers species of 30 vertebrates, 17 invertebrates, 25 plants, 14 fungi, and 11 protists studied in silico; 23 experimental studies; data on biotechnology; and the discovery of 8 diseases associated with specific mutations. Additionally, TIS context sequences of cellular IRESs was included. AUGcontext DB belongs to the National Institute of Cancer (Instituto Nacional de Cancerología, INCan), Mexico, and is freely available at http://108.161.138.77:8096/.</p><p><strong>Discussion: </strong>Our catalogue allows to do comparative studies between species, may help improve the diagnosis of certain diseases, and will be key to maximize the production of recombinant proteins.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143399899","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
Analysis of somatic piRNAs in the malaria mosquito Anopheles coluzzii reveals atypical classes of genic small RNAs.
IF 3.6 3区 生物学
RNA Biology Pub Date : 2025-02-06 DOI: 10.1080/15476286.2025.2463812
Sergei Funikov, Alexander Rezvykh, Natalia Akulenko, Jiangtao Liang, Igor V Sharakhov, Alla Kalmykova
{"title":"Analysis of somatic piRNAs in the malaria mosquito <i>Anopheles coluzzii</i> reveals atypical classes of genic small RNAs.","authors":"Sergei Funikov, Alexander Rezvykh, Natalia Akulenko, Jiangtao Liang, Igor V Sharakhov, Alla Kalmykova","doi":"10.1080/15476286.2025.2463812","DOIUrl":"https://doi.org/10.1080/15476286.2025.2463812","url":null,"abstract":"<p><p>Piwi-interacting small RNAs (piRNA) play a key role in controlling the activity of transposable elements (TEs) in the animal germline. In diverse arthropod species, including the pathogen vectors mosquitoes, the piRNA pathway is also active in nongonadal somatic tissues, where its targets and functions are less clear. Here, we studied the features of small RNA production in head and thorax tissues of an uninfected laboratory strain of <i>Anopheles coluzzii</i> focusing on the 24-32-nt-long RNAs. Small RNAs derived from repetitive elements constitute a minor fraction while most small RNAs process from long noncoding RNAs (lncRNAs) and protein-coding gene mRNAs. The majority of small RNAs derived from repetitive elements and lncRNAs exhibited typical piRNAs features. By contrast, majority of protein-coding gene-derived 24-32 nt small RNAs lack the hallmarks of piRNAs and have signatures of nontemplated 3' end tailing. Most of the atypical small RNAs exhibit female-biased expression and originate from mitochondrial and nuclear genes involved in energy metabolism. We also identified atypical genic small RNAs in <i>Anopheles gambiae</i> somatic tissues, which further validates the noncanonical mechanism of their production. We discuss a novel mechanism of small RNA production in mosquito somatic tissues and the possible functional significance of genic small RNAs.</p>","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143365764","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
An orthology-based methodology as a complementary approach to retrieve evolutionarily conserved A-to-I RNA editing sites. 基于同源物的方法是检索进化保守的 A 到 I RNA 编辑位点的补充方法。
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":"22 1","pages":"29-45"},"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":"77 1","pages":"1-16"},"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
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信