RNA Biology最新文献_第10页

TBP facilitates RNA Polymerase I transcription following mitosis. TBP 有助于有丝分裂后的 RNA 聚合酶 I 转录。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-07-03 DOI: 10.1080/15476286.2024.2375097

James Z J Kwan, Thomas F Nguyen, Sheila S Teves

{"title":"TBP facilitates RNA Polymerase I transcription following mitosis.","authors":"James Z J Kwan, Thomas F Nguyen, Sheila S Teves","doi":"10.1080/15476286.2024.2375097","DOIUrl":"10.1080/15476286.2024.2375097","url":null,"abstract":"The TATA-box binding protein (TBP) is the sole transcription factor common in the initiation complexes of the three major eukaryotic RNA Polymerases (Pol I, II and III). Although TBP is central to transcription by the three RNA Pols in various species, the emergence of TBP paralogs throughout evolution has expanded the complexity in transcription initiation. Furthermore, recent studies have emerged that questioned the centrality of TBP in mammalian cells, particularly in Pol II transcription, but the role of TBP and its paralogs in Pol I transcription remains to be re-evaluated. In this report, we show that in murine embryonic stem cells TBP localizes onto Pol I promoters, whereas the TBP paralog TRF2 only weakly associates to the Spacer Promoter of rDNA, suggesting that it may not be able to replace TBP for Pol I transcription. Importantly, acute TBP depletion does not fully disrupt Pol I occupancy or activity on ribosomal RNA genes, but TBP binding in mitosis leads to efficient Pol I reactivation following cell division. These findings provide a more nuanced role for TBP in Pol I transcription in murine embryonic stem cells.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"42-51"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11225926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141493161","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

HNRNPD regulates the biogenesis of circRNAs and the ratio of mRNAs to circRNAs for a set of genes. HNRNPD 可调节 circRNA 的生物生成以及一组基因的 mRNA 与 circRNA 的比例。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-08-24 DOI: 10.1080/15476286.2024.2386500

Shuhui Chang, Yucong Wang, Xiaolin Wang, Hanyuan Liu, Tao Zhang, Yangge Zheng, Xueren Wang, Ge Shan, Liang Chen

{"title":"HNRNPD regulates the biogenesis of circRNAs and the ratio of mRNAs to circRNAs for a set of genes.","authors":"Shuhui Chang, Yucong Wang, Xiaolin Wang, Hanyuan Liu, Tao Zhang, Yangge Zheng, Xueren Wang, Ge Shan, Liang Chen","doi":"10.1080/15476286.2024.2386500","DOIUrl":"10.1080/15476286.2024.2386500","url":null,"abstract":"Exonic circular RNAs (ecircRNAs) in animal cells are generated by backsplicing, and the biogenesis of ecircRNAs is regulated by an array of RNA binding proteins (RBPs). HNRNPD is a heterogeneous nuclear ribonucleoprotein family member with both cytoplasmic and nuclear roles, and whether HNRNPD regulates the biogenesis of circRNAs remains unknown. In this study, we examine the role of HNRNPD in the biogenesis of ecircRNAs. The levels of ecircRNAs are primarily increased upon depletion of HNRNPD. HNRNPD preferentially binds to motifs enriched with A and U nucleotides, and the flanking introns of ecircRNAs tend to have more numbers and higher intensity of HNRNPD binding sites. The levels of mRNAs are generally not significantly altered in HNRNPD knockout cells. For a small set of genes, the circRNA:mRNA ratio is substantially affected, and the mRNA levels of some of these genes demonstrate a significant decrease in HNRNPD knockout cells. CDK1 is identified as a key gene modulated by HNRNPD in the context of circRNA biogenesis. HNRNPD suppresses the biogenesis of circCDK1 and favours the generation of CDK1 mRNA, and the CDK1 protein is a critical regulator of the cell cycle and apoptosis. HNRNPD can participate in cellular physiology, including the cell cycle and apoptosis, and plays roles in clear cell renal cell carcinoma (ccRCC) by modulating circRNA biogenesis and the mRNA levels of key genes, such as CDK1.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"1-15"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11346550/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142047127","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

Regulation of magnesium ion transport in Escherichia coli: insights into the role of the 5' upstream region in corA expression. 大肠杆菌镁离子转运的调控：5' 上游区域在 corA 表达中的作用。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-11-08 DOI: 10.1080/15476286.2024.2421665

A-S Vézina Bédard, A Michaud, F Quenette, N Singh, F de Lemos Martins, J T Wade, M Guillier, D A Lafontaine

{"title":"Regulation of magnesium ion transport in Escherichia coli: insights into the role of the 5' upstream region in corA expression.","authors":"A-S Vézina Bédard, A Michaud, F Quenette, N Singh, F de Lemos Martins, J T Wade, M Guillier, D A Lafontaine","doi":"10.1080/15476286.2024.2421665","DOIUrl":"10.1080/15476286.2024.2421665","url":null,"abstract":"In Escherichia coli, transport of magnesium ions across the cellular membrane relies on MgtA and CorA transporters. While the expression of mgtA is controlled by the two-component system PhoQ/PhoP and 5' upstream region elements, corA expression is considered to be constitutive and not to depend on cellular factors. Importantly, the 5' upstream region of corA is predicted to fold into structures highly similar to the magnesium-sensing mgtA 5' upstream region. Here using biochemical and genetic assays, we show that the intracellular concentration of magnesium ions affects corA expression. Similarly to mgtA, we find that the effect of magnesium ions on corA expression is mediated by the 5' upstream region. We demonstrate that the RNA structure is important for regulation and that the Rho transcription factor is involved in the modulation of transcription termination. Consistent with previous studies, we find that translation of corL, a short ORF located within the 5' upstream region, is important for corA regulation. Our data indicate that the efficiency of corL translation is inversely proportional to corA expression, similar to what has been described for mgtA and corA in Salmonella enterica. Using a novel assay to control the import of magnesium ions, we show that while the expression of mgtA is regulated by both extra- and intracellular magnesium ions, corA is regulated by variations in intracellular magnesium ions. Our results support a model in which the expression of corA is regulated by the 5' upstream region that senses variations of intracellular magnesium ions.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"94-106"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11552253/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606044","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

Low dose ribosomal DNA P-loop mutation affects development and enforces autophagy in Arabidopsis 低剂量核糖体 DNA P 环突变影响拟南芥的生长发育并强化自噬作用

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-12-29 DOI: 10.1080/15476286.2023.2298532

Thiruvenkadam Shanmugam, Palak Chaturvedi, Deniz Streit, Arindam Ghatak, Thorsten Bergelt, Stefan Simm, Wolfram Weckwerth, Enrico Schleiff

引用次数: 0

Structural and computational studies of HIV-1 RNA HIV-1 RNA 的结构和计算研究

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-12-15 DOI: 10.1080/15476286.2023.2289709

Lev Levintov, Harish Vashisth

引用次数: 0

mRNA nuclear export: how mRNA identity features distinguish functional RNAs from junk transcripts mRNA 核输出：mRNA 身份特征如何区分功能 RNA 与垃圾转录本

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-12-13 DOI: 10.1080/15476286.2023.2293339

Alexander F. Palazzo, Yi Qiu, Yoon Mo Kang

引用次数: 0

Therapeutic potential of natural antisense transcripts and various mechanisms involved for clinical applications and disease prevention 天然反义转录本的治疗潜力以及临床应用和疾病预防所涉及的各种机制

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-12-13 DOI: 10.1080/15476286.2023.2293335

Ashiq Ali, Aisha Khatoon, Chenran Shao, Bilal Murtaza, Qaisar Tanveer, Zhongjing Su

引用次数: 0

Unraveling C-to-U RNA editing events from direct RNA sequencing 通过直接 RNA 测序揭示 C 到 U RNA 编辑事件

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-12-13 DOI: 10.1080/15476286.2023.2290843

Adriano Fonzino, Caterina Manzari, Paola Spadavecchia, Uday Munagala, Serena Torrini, Silvestro Conticello, Graziano Pesole, Ernesto Picardi

引用次数: 0

Correction. 校正

IF 4.1 3区生物学

RNA Biology Pub Date : 2023-09-30 DOI: 10.1080/15476286.2023.2264666

引用次数: 0

Presentation of Ocular Syphilis with Bilateral Optic Neuropathy. 眼部梅毒并发双侧视神经病变。

IF 0.8 3区生物学

RNA Biology Pub Date : 2023-07-05 eCollection Date: 2023-01-01 DOI: 10.1080/01658107.2023.2222800

Mustafa Kayabaşı, Seher Köksaldı, Ali Osman Saatci, Meltem Söylev Bajin

{"title":"Presentation of Ocular Syphilis with Bilateral Optic Neuropathy.","authors":"Mustafa Kayabaşı, Seher Köksaldı, Ali Osman Saatci, Meltem Söylev Bajin","doi":"10.1080/01658107.2023.2222800","DOIUrl":"10.1080/01658107.2023.2222800","url":null,"abstract":"A 60-year-old otherwise healthy male presented with a 1 year history of bilateral progressive visual loss. His best-corrected visual acuity was counting fingers at 2 m with his right eye and counting fingers at 0.5 m with his left eye. Visual field testing revealed bilateral near-total loss of visual fields. Slit-lamp examination was unremarkable, apart from bilateral grade two nuclear sclerotic cataracts. Both optic discs were pale-looking with some retinal pigment epithelial alterations at the left papillomacular region. Enhanced depth imaging optical coherence tomography depicted punctate hyperreflective dots at the inner choroidal level corresponding to the retinal pigment epithelial changes in the left eye. Fundus autofluorescence imaging revealed patchy hyper-autofluorescent and hypo-autofluorescent areas, and there was mild staining in the early and late phases of the fluorescein angiogram at the papillomacular region in the left eye. A diagnosis of bilateral optic neuropathy was made. A full systemic work-up was carried out, and serological tests pointed out the presence of syphilis with normal cranial magnetic resonance imaging. He was treated accordingly. Our case clearly demonstrates the importance of a high clinical suspicion for syphilis in cases of optic neuropathy.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"13 1","pages":"274-280"},"PeriodicalIF":0.8,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10732629/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82015129","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