RNA Biology最新文献_第4页

RNA-binding proteins as therapeutic targets in cancer. rna结合蛋白作为癌症治疗靶点。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-02-27 DOI: 10.1080/15476286.2025.2470511

Jennifer Jungfleisch, Fátima Gebauer

引用次数: 0

Release and degradation of dissolved environmental RNAs from zebrafish cells. 斑马鱼细胞中溶解的环境 RNA 的释放和降解。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-04-01 DOI: 10.1080/15476286.2025.2486281

Zhongneng Xu, Shuichi Asakawa

{"title":"Release and degradation of dissolved environmental RNAs from zebrafish cells.","authors":"Zhongneng Xu, Shuichi Asakawa","doi":"10.1080/15476286.2025.2486281","DOIUrl":"https://doi.org/10.1080/15476286.2025.2486281","url":null,"abstract":"The sources and degradation profiles of dissolved environmental RNAs from fish in water remain unknown. In this study, laboratory experiments and mathematical modelling were conducted to investigate the permeability of RNA extracted from zebrafish cells through filters, the release of dissolved environmental RNAs from live and dying zebrafish cells, and the degradation of RNA extracted from zebrafish cells in a non-sterile aqueous environment. This research aimed to provide biological and ecological insights into fish RNAs dissolved in water. The results showed that most of the RNA extracted from zebrafish cells was detected in the filtrates after passage through 0.45 µm filters. Over the course of the 6-day experiment, dynamic levels of the RNAs in the liquid environment containing live or dying zebrafish cells were determined. The release and degradation rates of dissolved environmental RNA from zebrafish cells were calculated using mathematical modelling. RNA extracted from zebrafish cells degraded in non-sterile water in the tubes, and after 2 months, more than 15% of the RNAs in the water remained detectable. The half-life of the RNA in the tubes was approximately 20 ~ 43 days. The modelling results suggest that the levels of the dissolved environmental fish RNAs in natural waters or aquariums could be so low that it would be difficult to detect them using current techniques. The results obtained in this study will help develop new methods for measuring the dynamics of dissolved environmental fish RNAs in water and determining their significance.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143754369","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

S-1 pRNA 9-mers are a prominent length species during outgrowth of Bacillus subtilis cells from extended stationary phase. S-1 pRNA 9-mers是枯草芽孢杆菌延长固定期生长过程中的一个突出的长度物种。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-03-25 DOI: 10.1080/15476286.2025.2484519

Katrin Damm, Paul Klemm, Marcus Lechner, Dominik Helmecke, Roland K Hartmann

{"title":"S-1 pRNA 9-mers are a prominent length species during outgrowth of Bacillus subtilis cells from extended stationary phase.","authors":"Katrin Damm, Paul Klemm, Marcus Lechner, Dominik Helmecke, Roland K Hartmann","doi":"10.1080/15476286.2025.2484519","DOIUrl":"https://doi.org/10.1080/15476286.2025.2484519","url":null,"abstract":"Bacterial RNA polymerases (RNAP) utilize 6S RNAs as templates to synthesize ultrashort transcripts (up to ~ 14 nt), termed product RNAs (pRNAs), that play a key role in reversing the blockage of RNAP by 6S RNA. Here we resolved the pRNA length profile of 6 S-1 RNA from Bacillus subtilis, a major model system for the study of 6S RNA biology, during outgrowth of cells from extended stationary phase. 9-mers were found to be a particularly abundant pRNA length species, followed by 8/10/11-mers and 13/14-mers. Consistent with in vitro data from the Escherichia coli system, these findings support the mechanistic model according to which the housekeeping sigma factor (σ70 or σA) dissociates from 6S RNA:RNAP complexes upon synthesis of pRNA 9-mers, followed by final dissociation of 6S RNA and RNAP upon synthesis of longer pRNAs (13/14-mers). Methodologically, the identification of such ultrashort RNAs in total cellular extracts by RNA-Seq is inefficient with standard protocols using adapter ligation to RNA 3'-ends for reverse transcription and PCR-based cDNA sequencing. Here, we demonstrate that ultrashort RNAs can instead be incorporated into RNA-Seq libraries by polyA, polyC and potentially also polyU tailing of their 3'-ends. At positions where a non-tailing nucleotide is followed by one or more tailing nucleotides, an algorithm that integrates RNA-Seq results from at least two different 3'-end tailings allows one to approximate the fraction of read counts at such ambiguous positions. Finally, methodological biases and potential applications of our approach to other short RNAs are discussed.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710720","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

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