RNA Biology最新文献_第10页

The potential regulatory role of RNA methylation in ovarian cancer. RNA甲基化在卵巢癌中的潜在调节作用。

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-01-01 DOI: 10.1080/15476286.2023.2213915

Shijie Zhao, Mengxue Zhang, Xiaolan Zhu, Jie Xing, Jiaming Zhou, Xinming Yin

{"title":"The potential regulatory role of RNA methylation in ovarian cancer.","authors":"Shijie Zhao, Mengxue Zhang, Xiaolan Zhu, Jie Xing, Jiaming Zhou, Xinming Yin","doi":"10.1080/15476286.2023.2213915","DOIUrl":"https://doi.org/10.1080/15476286.2023.2213915","url":null,"abstract":"Updates in whole genome sequencing technologies have revealed various RNA modifications in cancer, among which RNA methylation is a frequent posttranscriptional modification. RNA methylation is essential for regulating biological processes such as RNA transcription, splicing, structure, stability, and translation. Its dysfunction is strongly associated with the development of human malignancies. Research advances with respect to the regulatory role of RNA modifications in ovarian cancer include N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), and N7-methylguanosine (m7G). Numerous studies have demonstrated that epigenetic modifications of RNA can influence the progression and metastasis of ovarian cancer and may provide excellent targets for cancer therapy. This review highlights advances in research on RNA methylation modifications and ovarian cancer prognosis, carcinogenesis, and resistance, which could provide a theoretical foundation for designing therapeutic strategies for ovarian cancer based on RNA methylation modifications.","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/PMC10193916/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9575417","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: 1

Serine-arginine splicing factor 2 promotes oesophageal cancer progression by regulating alternative splicing of interferon regulatory factor 3. 丝氨酸-精氨酸剪接因子2通过调节干扰素调节因子3的选择性剪接促进食管癌的进展。

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-01-01 DOI: 10.1080/15476286.2023.2223939

Ziqing Wei, Yuyao Wang, Wenyuan Ma, Wenqing Xing, Peng Lu, Zhijie Shang, Feng Li, Huiyu Li, Yuxuan Wang

{"title":"Serine-arginine splicing factor 2 promotes oesophageal cancer progression by regulating alternative splicing of interferon regulatory factor 3.","authors":"Ziqing Wei, Yuyao Wang, Wenyuan Ma, Wenqing Xing, Peng Lu, Zhijie Shang, Feng Li, Huiyu Li, Yuxuan Wang","doi":"10.1080/15476286.2023.2223939","DOIUrl":"https://doi.org/10.1080/15476286.2023.2223939","url":null,"abstract":"Objective: Often, alternative splicing is used by cancer cells to produce or increase proteins that promote growth and survival through alternative splicing. Although RNA-binding proteins are known to regulate alternative splicing events associated with tumorigenesis, their role in oesophageal cancer (EC) has rarely been explored.Methods: We analysed the expression pattern of several relatively well characterized splicing regulators on 183 samples from TCGA cohort of oesophageal cancer; the effectiveness of the knockdown of SRSF2 was subsequently verified by immunoblotting; we measured the ability of cells treated with lenti-sh-SRSF2/lenti-sh2-SRSF2 to invade through an extracellular matrix coating by transwell invasion assay; using RNA-seq data to identify its potential target genes; we performed qRT-PCR to detect the changes of exon 2 usage in lenti-sh-SRSF2 transduced KYSE30 cells to determine the possible effect of SRSF2 on splicing regulation of IRF3; RNA Electrophoretic mobility shift assay (RNA-EMSA) was performed by the incubation of purified SRSF2 protein and biotinylated RNA probes; we performed luciferase assay to confirm the effect of SRSF2 on IFN1 promoter activity.Results: We found upregulation of SRSF2 is correlated with the development of EC; Knock-down of SRSF2 inhibits EC cell proliferation, migration, and invasion; SRSF2 regulates the splicing pattern of IRF3 in EC cells; SRSF2 interacts with exon 2 of IRF3 to regulate its exclusion; SRSF2 inhibits the transcription of IFN1 in EC cells.Conclusion: This study identified a novel regulatory axis involved in EC from the various aspects of splicing regulation.","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/f3/ea/KRNB_20_2223939.PMC10281462.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9708086","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

Identification of circular RNAs hosted by the RPGR ORF15 genomic locus. 由RPGR ORF15基因组位点承载的环状rna的鉴定。

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-01-01 DOI: 10.1080/15476286.2022.2159165

Tatyana Appelbaum, Gustavo D Aguirre, William A Beltran

{"title":"Identification of circular RNAs hosted by the RPGR ORF15 genomic locus.","authors":"Tatyana Appelbaum, Gustavo D Aguirre, William A Beltran","doi":"10.1080/15476286.2022.2159165","DOIUrl":"https://doi.org/10.1080/15476286.2022.2159165","url":null,"abstract":"Mutations in the retina-specific isoform of the gene encoding retinitis pigmentosa GTPase regulator (RPGRorf15) cause X-linked retinitis pigmentosa, a severe and early onset inherited retinal degeneration. The underlying pathogenic mechanisms and variability in disease severity remain to be fully elucidated. The present study examines structural features of the ORF15 exonic region to provide new insights into the disease pathogenesis. Using canine and human RNA samples, we identified several novel RPGR ORF15-like linear RNA transcripts containing cryptic introns (exitrons) within the annotated exon ORF15. Furthermore, using outward-facing primers designed inside exitrons in the ORF15 exonic region, we found many of previously unidentified circular RNAs (circRNAs) that formed via back fusion of linear parts of the RPGRorf15 pre-mRNAs. These circRNAs (resistant to RNAse R treatment) were found in all studied cells and tissues. Notably, some circRNAs were present in cytoplasmic and polysomal RNA fractions. Although certain RPGR circRNAs may be cell type specific, we found some of the same circRNAs expressed in different cell types, suggesting similarities in their biogenesis and functions. Sequence analysis of RPGR circRNAs revealed several remarkable features, including identification of N6-methyladenosine (m6A) consensus sequence motifs and high prevalence of predictive microRNA binding sites pointing to the functional roles of these circRNAs. Our findings also illustrate the presence of non-canonical RPGR circRNA biogenesis pathways independent of the known back splicing mechanism. The obtained data on novel RPGR circRNAs further underline structural complexity of the RPGR ORF15 region and provide a potential molecular basis for the disease phenotypic heterogeneity.","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/13/c5/KRNB_20_2159165.PMC9817113.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10009010","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

Ageing-associated small RNA cargo of extracellular vesicles. 衰老相关的细胞外囊泡小RNA货物。

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-01-01 DOI: 10.1080/15476286.2023.2234713

Fabian Kern, Thomas Kuhn, Nicole Ludwig, Martin Simon, Laura Gröger, Natalie Fabis, Ernesto Aparicio-Puerta, Abdulrahman Salhab, Tobias Fehlmann, Oliver Hahn, Annika Engel, Viktoria Wagner, Marcus Koch, Katarzyna Winek, Hermona Soreq, Irina Nazarenko, Gregor Fuhrmann, Tony Wyss-Coray, Eckart Meese, Verena Keller, Matthias W Laschke, Andreas Keller

{"title":"Ageing-associated small RNA cargo of extracellular vesicles.","authors":"Fabian Kern, Thomas Kuhn, Nicole Ludwig, Martin Simon, Laura Gröger, Natalie Fabis, Ernesto Aparicio-Puerta, Abdulrahman Salhab, Tobias Fehlmann, Oliver Hahn, Annika Engel, Viktoria Wagner, Marcus Koch, Katarzyna Winek, Hermona Soreq, Irina Nazarenko, Gregor Fuhrmann, Tony Wyss-Coray, Eckart Meese, Verena Keller, Matthias W Laschke, Andreas Keller","doi":"10.1080/15476286.2023.2234713","DOIUrl":"https://doi.org/10.1080/15476286.2023.2234713","url":null,"abstract":"Previous work on murine models and humans demonstrated global as well as tissue-specific molecular ageing trajectories of RNAs. Extracellular vesicles (EVs) are membrane vesicles mediating the horizontal transfer of genetic information between different tissues. We sequenced small regulatory RNAs (sncRNAs) in two mouse plasma fractions at five time points across the lifespan from 2-18 months: (1) sncRNAs that are free-circulating (fc-RNA) and (2) sncRNAs bound outside or inside EVs (EV-RNA). Different sncRNA classes exhibit unique ageing patterns that vary between the fcRNA and EV-RNA fractions. While tRNAs showed the highest correlation with ageing in both fractions, rRNAs exhibited inverse correlation trajectories between the EV- and fc-fractions. For miRNAs, the EV-RNA fraction was exceptionally strongly associated with ageing, especially the miR-29 family in adipose tissues. Sequencing of sncRNAs and coding genes in fat tissue of an independent cohort of aged mice up to 27 months highlighted the pivotal role of miR-29a-3p and miR-29b-3p in ageing-related gene regulation that we validated in a third cohort by RT-qPCR.","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/PMC10376918/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9883908","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

Comprehensive identification of diverse ribosomal RNA modifications by targeted nanopore direct RNA sequencing and JACUSA2. 利用靶向纳米孔直接RNA测序和JACUSA2综合鉴定多种核糖体RNA修饰。

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-01-01 DOI: 10.1080/15476286.2023.2248752

Isabel S Naarmann-de Vries, Christiane Zorbas, Amina Lemsara, Michael Piechotta, Felix G M Ernst, Ludivine Wacheul, Denis L J Lafontaine, Christoph Dieterich

{"title":"Comprehensive identification of diverse ribosomal RNA modifications by targeted nanopore direct RNA sequencing and JACUSA2.","authors":"Isabel S Naarmann-de Vries, Christiane Zorbas, Amina Lemsara, Michael Piechotta, Felix G M Ernst, Ludivine Wacheul, Denis L J Lafontaine, Christoph Dieterich","doi":"10.1080/15476286.2023.2248752","DOIUrl":"https://doi.org/10.1080/15476286.2023.2248752","url":null,"abstract":"Ribosomal RNAs are decorated by numerous post-transcriptional modifications whose exact roles in ribosome biogenesis, function, and human pathophysiology remain largely unknown. Here, we report a targeted direct rRNA sequencing approach involving a substrate selection step and demonstrate its suitability to identify differential modification sites in combination with the JACUSA2 software. We compared JACUSA2 to other tools designed for RNA modification detection and show that JACUSA2 outperforms other software with regard to detection of base modifications such as methylation, acetylation and aminocarboxypropylation. To illustrate its widespread usability, we applied our method to a collection of CRISPR-Cas9 engineered colon carcinoma cells lacking specific enzymatic activities responsible for particular rRNA modifications and systematically compared them to isogenic wild-type RNAs. Besides the numerous 2'-O methylated riboses and pseudouridylated residues, our approach was suitable to reliably identify differential base methylation and acetylation events. Importantly, our method does not require any prior knowledge of modification sites or the need to train complex models. We further report for the first time detection of human rRNA modifications by direct RNA-sequencing on Flongle flow cells, the smallest-scale nanopore flow cell available to date. The use of these smaller flow cells reduces RNA input requirements, making our workflow suitable for the analysis of samples with limited availability and clinical work.","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/PMC10464549/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10264729","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: 1

MiR-2b-2-5p regulates lipid metabolism and reproduction by targeting CREB in Bactrocera dorsalis. MiR-2b-2-5p通过靶向CREB调控背小实蝇的脂质代谢和繁殖。

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-01-01 DOI: 10.1080/15476286.2023.2204579

Shengfeng Zhang, Junfei Xie, Rengang Luo, Hongyu Zhang, Weiwei Zheng

{"title":"MiR-2b-2-5p regulates lipid metabolism and reproduction by targeting CREB in Bactrocera dorsalis.","authors":"Shengfeng Zhang, Junfei Xie, Rengang Luo, Hongyu Zhang, Weiwei Zheng","doi":"10.1080/15476286.2023.2204579","DOIUrl":"https://doi.org/10.1080/15476286.2023.2204579","url":null,"abstract":"In female animals, metabolic homoeostasis and reproductive fitness are critical to population expansion. The trade-off between lipid storage and reproduction inevitably occurs. However, most studies have focused on the complex network of relationships between reproductive and metabolic physiology at the transcriptional level. In this study, we identified a microRNA, miR-2b-2-5p, in a highly invasive quarantine pest, Bactrocera dorsalis. Knockdown of miR-2b-2-5p by antagomiR microinjection impaired ovarian development, reduced fecundity, and decreased triglyceride (TAG) storage in the fat body, whereas overexpression of miR-2b-2-5p by injection of its mimic caused reproductive defects similar to knockdown but increased TAG. Bioinformatics analysis and dual luciferase assay indicated that cyclic AMP response element (CRE)-binding protein (CREB) was the target gene of miR-2b-2-5p. RNAi-mediated knockdown of CREB led to excessive lipid storage and reproductive defects. Further starvation treatment revealed that miR-2b-2-5p functions by fine-tuning CREB expression in response to dietary stimuli. These results suggest that miR-2b-2-5p acts as a monitor to regulate CREB mRNA levels in the fat body, maintaining lipid homoeostasis and keeping the reproductive system on track. Thus, our study not only provides new insights into the interaction between metabolism and reproduction at the posttranscriptional level in B. dorsalis, but also providing a potential eco-friendly control strategy (RNAi-based biopesticides targeting essential miRNAs) for this notorious agricultural pest.","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/b3/bd/KRNB_20_2204579.PMC10128458.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9446344","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

Synthetic biology tools to promote the folding and function of RNA aptamers in mammalian cells. 在哺乳动物细胞中促进RNA适体折叠和功能的合成生物学工具。

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-01-01 DOI: 10.1080/15476286.2023.2206248

Qian Hou, Samie R Jaffrey

引用次数: 1

DMD antisense oligonucleotide mediated exon skipping efficiency correlates with flanking intron retention time and target position within the exon. DMD反义寡核苷酸介导的外显子跳跃效率与侧翼内含子保留时间和外显子内目标位置相关。

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-01-01 DOI: 10.1080/15476286.2023.2254041

Remko Goossens, Nisha Verwey, Yavuz Ariyurek, Fred Schnell, Annemieke Aartsma-Rus

{"title":"DMD antisense oligonucleotide mediated exon skipping efficiency correlates with flanking intron retention time and target position within the exon.","authors":"Remko Goossens, Nisha Verwey, Yavuz Ariyurek, Fred Schnell, Annemieke Aartsma-Rus","doi":"10.1080/15476286.2023.2254041","DOIUrl":"https://doi.org/10.1080/15476286.2023.2254041","url":null,"abstract":"Mutations in the DMD gene are causative for Duchenne muscular dystrophy (DMD). Antisense oligonucleotide (AON) mediated exon skipping to restore disrupted dystrophin reading frame is a therapeutic approach that allows production of a shorter but functional protein. As DMD causing mutations can affect most of the 79 exons encoding dystrophin, a wide variety of AONs are needed to treat the patient population. Design of AONs is largely guided by trial-and-error, and it is yet unclear what defines the skippability of an exon. Here, we use a library of phosphorodiamidate morpholino oligomer (PMOs) AONs of similar physical properties to test the skippability of a large number of DMD exons. The DMD transcript is non-sequentially spliced, meaning that certain introns are retained longer in the transcript than downstream introns. We tested whether the relative intron retention time has a significant effect on AON efficiency, and found that targeting an out-of-frame exon flanked at its 5'-end by an intron that is retained in the transcript longer ('slow' intron) leads to overall higher exon skipping efficiency than when the 5'-end flanking intron is 'fast'. Regardless of splicing speed of flanking introns, we find that positioning an AON closer to the 5'-end of the target exon leads to higher exon skipping efficiency opposed to targeting an exons 3'-end. The data enclosed herein can be of use to guide future target selection and preferential AON binding sites for both DMD and other disease amenable by exon skipping therapies.","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/PMC10481881/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10211285","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

Shortened CRISPR-Cas9 arrays enable multiplexed gene targeting in bacteria from a smaller DNA footprint. 缩短的CRISPR-Cas9阵列可以从更小的DNA足迹中实现细菌中的多重基因靶向。

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-01-01 DOI: 10.1080/15476286.2023.2247247

Sandra Gawlitt, Chunyu Liao, Tatjana Achmedov, Chase L Beisel

{"title":"Shortened CRISPR-Cas9 arrays enable multiplexed gene targeting in bacteria from a smaller DNA footprint.","authors":"Sandra Gawlitt, Chunyu Liao, Tatjana Achmedov, Chase L Beisel","doi":"10.1080/15476286.2023.2247247","DOIUrl":"https://doi.org/10.1080/15476286.2023.2247247","url":null,"abstract":"CRISPR technologies comprising a Cas nuclease and a guide RNA (gRNA) can utilize multiple gRNAs to enact multi-site editing or regulation in the same cell. Nature devised a highly compact means of encoding gRNAs in the form of CRISPR arrays composed of conserved repeats separated by targeting spacers. However, the capacity to acquire new spacers keeps the arrays longer than necessary for CRISPR technologies. Here, we show that CRISPR arrays utilized by the Cas9 nuclease can be shortened without compromising and sometimes even enhancing targeting activity. Using multiplexed gene repression in E. coli, we found that each region could be systematically shortened to varying degrees before severely compromising targeting activity. Surprisingly, shortening some spacers yielded enhanced targeting activity, which was linked to folding of the transcribed array prior to processing. Overall, shortened CRISPR-Cas9 arrays can facilitate multiplexed editing and gene regulation from a smaller DNA footprint across many bacterial applications of CRISPR technologies.","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/61/1d/KRNB_20_2247247.PMC10478742.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10212798","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 modification-mediated translational control in immune cells. RNA修饰介导的免疫细胞翻译控制。

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-01-01 DOI: 10.1080/15476286.2023.2246256

Yujuan Zhang, Weiguo Hu, Hua-Bing Li

引用次数: 0