RNA Biology最新文献_第7页

Mitochondrial RNA maturation. 线粒体 RNA 成熟。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-10-10 DOI: 10.1080/15476286.2024.2414157

Zofia M Chrzanowska-Lightowlers, Robert N Lightowlers

引用次数: 0

Multiple Oligo assisted RNA Pulldown via Hybridization followed by Mass Spectrometry (MORPH-MS) for exploring the RNA-Protein interactions. 通过杂交和质谱分析（MORPH-MS）的多重寡核苷酸辅助 RNA Pulldown，用于探索 RNA 与蛋白质之间的相互作用。

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2023-12-17 DOI: 10.1080/15476286.2023.2287302

Priyanka Pant, Regalla Kumarswamy

{"title":"Multiple Oligo assisted RNA Pulldown via Hybridization followed by Mass Spectrometry (MORPH-MS) for exploring the RNA-Protein interactions.","authors":"Priyanka Pant, Regalla Kumarswamy","doi":"10.1080/15476286.2023.2287302","DOIUrl":"10.1080/15476286.2023.2287302","url":null,"abstract":"Understanding RNA-protein interactions is crucial for deciphering the cellular functions and molecular mechanisms of regulatory RNAs. Consequently, there is a constant need to develop innovative and cost-effective methods to uncover such interactions. We developed a simple and cost-effective technique called Multiple Oligo assisted RNA Pulldown via Hybridization (MORPH) to identify proteins interacting with a specific RNA. MORPH employs a tiling array of antisense oligos (ASOs) to efficiently capture the RNA of interest along with proteins associated with it. Unlike existing techniques that rely on multiple individually biotinylated oligos spanning the entire RNA length, MORPH stands out by utilizing a single biotinylated oligo to capture all the ASOs. To evaluate MORPH's efficacy, we applied this technique combined with mass spectrometry to identify proteins interacting with lncRNA NEAT1, which has previously been studied using various methods. Our results demonstrate that despite being a simple and inexpensive procedure, MORPH performs on par with existing methods.Abbreviations: ASO, Antisense oligo; lncRNA, long non-coding RNA; MORPH, Multiple Oligo assisted RNA Pulldown via Hybridization.","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/PMC10730167/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138809126","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

Urea supplementation improves mRNA in vitro transcription by decreasing both shorter and longer RNA byproducts. 补充尿素可减少较短和较长的 RNA 副产物，从而改善 mRNA 的体外转录。

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-02-27 DOI: 10.1080/15476286.2024.2321764

Combes Francis, Pettersson Frida J, Bui Thanh-Huong, Molska Alicja, Komissarov Artem, Parot Jérémie, Borgos Sven Even

引用次数: 0

Translational impacts of enzymes that modify ribosomal RNA around the peptidyl transferase centre. 围绕肽基转移酶中心修改核糖体 RNA 的酶对转录的影响。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-07-01 DOI: 10.1080/15476286.2024.2368305

Letian Bao, Josefine Liljeruhm, Rubén Crespo Blanco, Gerrit Brandis, Jaanus Remme, Anthony C Forster

{"title":"Translational impacts of enzymes that modify ribosomal RNA around the peptidyl transferase centre.","authors":"Letian Bao, Josefine Liljeruhm, Rubén Crespo Blanco, Gerrit Brandis, Jaanus Remme, Anthony C Forster","doi":"10.1080/15476286.2024.2368305","DOIUrl":"10.1080/15476286.2024.2368305","url":null,"abstract":"Large ribosomal RNAs (rRNAs) are modified heavily post-transcriptionally in functionally important regions but, paradoxically, individual knockouts (KOs) of the modification enzymes have minimal impact on Escherichia coli growth. Furthermore, we recently constructed a strain with combined KOs of five modification enzymes (RluC, RlmKL, RlmN, RlmM and RluE) of the 'critical region' of the peptidyl transferase centre (PTC) in 23S rRNA that exhibited only a minor growth defect at 37°C (although major at 20°C). However, our combined KO of modification enzymes RluC and RlmE (not RluE) resulted in conditional lethality (at 20°C). Although the growth rates for both multiple-KO strains were characterized, the molecular explanations for such deficits remain unclear. Here, we pinpoint biochemical defects in these strains. In vitro fast kinetics at 20°C and 37°C with ribosomes purified from both strains revealed, counterintuitively, the slowing of translocation, not peptide bond formation or peptidyl release. Elongation rates of protein synthesis in vivo, as judged by the kinetics of β-galactosidase induction, were also slowed. For the five-KO strain, the biggest deficit at 37°C was in 70S ribosome assembly, as judged by a dominant 50S peak in ribosome sucrose gradient profiles at 5 mM Mg2+. Reconstitution of this 50S subunit from purified five-KO rRNA and ribosomal proteins supported a direct role in ribosome biogenesis of the PTC region modifications per se, rather than of the modification enzymes. These results clarify the importance and roles of the enigmatic rRNA modifications.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11221467/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141477311","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

The RNA-DNA world and the emergence of DNA-encoded heritable traits. RNA-DNA 世界和 DNA 编码遗传性状的出现。

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-05-24 DOI: 10.1080/15476286.2024.2355391

Suvam Roy, Supratim Sengupta

{"title":"The RNA-DNA world and the emergence of DNA-encoded heritable traits.","authors":"Suvam Roy, Supratim Sengupta","doi":"10.1080/15476286.2024.2355391","DOIUrl":"10.1080/15476286.2024.2355391","url":null,"abstract":"The RNA world hypothesis confers a central role to RNA molecules in information encoding and catalysis. Even though evidence in support of this hypothesis has accumulated from both experiments and computational modelling, the transition from an RNA world to a world where heritable genetic information is encoded in DNA remains an open question. Recent experiments show that both RNA and DNA templates can extend complementary primers using free RNA/DNA nucleotides, either non-enzymatically or in the presence of a replicase ribozyme. Guided by these experiments, we analyse protocellular evolution with an expanded set of reaction pathways made possible through the presence of DNA nucleotides. By encapsulating these reactions inside three different types of protocellular compartments, each subject to distinct modes of selection, we show how protocells containing DNA-encoded replicases in low copy numbers and replicases in high copy numbers can dominate the population. This is facilitated by a reaction that leads to auto-catalytic synthesis of replicase ribozymes from DNA templates encoding the replicase after the chance emergence of a replicase through non-enzymatic reactions. Our work unveils a pathway for the transition from an RNA world to a mixed RNA-DNA world characterized by Darwinian evolution, where DNA sequences encode heritable phenotypes.","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/PMC11135857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141088658","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

Poly(G)₇ box: a functional element of mammalian 18S rRNA involved in translation. Poly(G)7 box：哺乳动物 18S rRNA 中参与翻译的一个功能元件。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-09-05 DOI: 10.1080/15476286.2024.2399310

Dahao Wei, Zhangyu Mai, Xinan Li, Tianli Yu, Jiangchao Li

引用次数: 0

Temperature-sensing riboceptors. 温度感应核糖受体

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-07-17 DOI: 10.1080/15476286.2024.2379118

Savani Anbalagan

引用次数: 0

The role of dsRNA A-to-I editing catalyzed by ADAR family enzymes in the pathogeneses. ADAR 家族酶催化的 dsRNA A 到 I 编辑在病原体中的作用。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-10-24 DOI: 10.1080/15476286.2024.2414156

Wanqing Liu, Yufan Wu, Tong Zhang, Xiaobo Sun, Dean Guo, Zizhao Yang

{"title":"The role of dsRNA A-to-I editing catalyzed by ADAR family enzymes in the pathogeneses.","authors":"Wanqing Liu, Yufan Wu, Tong Zhang, Xiaobo Sun, Dean Guo, Zizhao Yang","doi":"10.1080/15476286.2024.2414156","DOIUrl":"10.1080/15476286.2024.2414156","url":null,"abstract":"The process of adenosine deaminase (ADAR)-catalyzed double-stranded RNA (dsRNA) Adenosine-to-Inosine (A-to-I) editing is essential for the correction of pathogenic mutagenesis, as well as the regulation of gene expression and protein function in mammals. The significance of dsRNA A-to-I editing in disease development and occurrence is explored using inferential statistics and cluster analyses to investigate the enzymes involved in dsRNA editing that can catalyze editing sites across multiple biomarkers. This editing process, which occurs in coding or non-coding regions, has the potential to activate abnormal signalling pathways that contributes to disease pathogenesis. Notably, the ADAR family enzymes play a crucial role in initiating the editing process. ADAR1 is upregulated in most diseases as an oncogene during tumorigenesis, whereas ADAR2 typically acts as a tumour suppressor. Furthermore, this review also provides an overview of small molecular inhibitors that disrupt the expression of ADAR enzymes. These inhibitors not only counteract tumorigenicity but also alleviate autoimmune disorders, neurological neurodegenerative symptoms, and metabolic diseases associated with aberrant dsRNA A-to-I editing processes. In summary, this comprehensive review offers detailed insights into the involvement of dsRNA A-to-I editing in disease pathogenesis and highlights the potential therapeutic roles for related small molecular inhibitors. These scientific findings will undoubtedly contribute to the advancement of personalized medicine based on dsRNA A-to-I editing.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11520539/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142506997","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

ECT2 peptide sequences outside the YTH domain regulate its m⁶A-RNA binding. YTH 结构域外的 ECT2 肽序列可调节其与 m6A-RNA 的结合。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-09-12 DOI: 10.1080/15476286.2024.2399914

Daphné Seigneurin-Berny, Claire Karczewski, Elise Delaforge, Karen Yaacoub, Celso Gaspar Litholdo, Jean-Jacques Favory, Malene Ringkjøbing Jensen, Cécile Bousquet-Antonelli, André Verdel

{"title":"ECT2 peptide sequences outside the YTH domain regulate its m6A-RNA binding.","authors":"Daphné Seigneurin-Berny, Claire Karczewski, Elise Delaforge, Karen Yaacoub, Celso Gaspar Litholdo, Jean-Jacques Favory, Malene Ringkjøbing Jensen, Cécile Bousquet-Antonelli, André Verdel","doi":"10.1080/15476286.2024.2399914","DOIUrl":"10.1080/15476286.2024.2399914","url":null,"abstract":"The m6A epitranscriptomic mark is the most abundant and widespread internal RNA chemical modification, which through the control of RNA acts as an important factor of eukaryote reproduction, growth, morphogenesis and stress response. The main m6A readers constitute a super family of proteins with hundreds of members that share a so-called YTH RNA binding domain. The majority of YTH proteins carry no obvious additional domain except for an Intrinsically Disordered Region (IDR). In Arabidopsis thaliana IDRs are important for the functional specialization among the different YTH proteins, known as Evolutionarily Conserved C-Terminal region, ECT 1 to 12. Here by studying the ECT2 protein and using an in vitro biochemical characterization, we show that full-length ECT2 and its YTH domain alone have a distinct ability to bind m6A, conversely to previously characterized YTH readers. We identify peptide regions outside of ECT2 YTH domain, in the N-terminal IDR, that regulate its binding to m6A-methylated RNA. Furthermore, we show that the selectivity of ECT2 binding for m6A is enhanced by a high uridine content within its neighbouring sequence, where ECT2 N-terminal IDR is believed to contact the target RNA in vivo. Finally, we also identify small structural elements, located next to ECT2 YTH domain and conserved in a large set of YTH proteins, that enhance its binding to m6A-methylated RNA. We propose from these findings that some of these regulatory regions are not limited to ECT2 or YTH readers of flowering plants but may be widespread among eukaryotic YTH readers.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11404569/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142294344","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

m6A modification of RNA in cervical cancer: role and clinical perspectives. 宫颈癌中 RNA 的 m6A 修饰：作用和临床前景。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-09-30 DOI: 10.1080/15476286.2024.2408707

Yajuan Gao, Qi Guo, Liming Yu

{"title":"m6A modification of RNA in cervical cancer: role and clinical perspectives.","authors":"Yajuan Gao, Qi Guo, Liming Yu","doi":"10.1080/15476286.2024.2408707","DOIUrl":"10.1080/15476286.2024.2408707","url":null,"abstract":"N6-methyladenosine (m6A) is widely recognized as the predominant form of RNA modification in higher organisms, with the capability to finely regulate RNA metabolism, thereby influencing a series of crucial physiological and pathological processes. These processes include regulation of gene expression, cell proliferation, invasion and metastasis, cell cycle control, programmed cell death, interactions within the tumour microenvironment, energy metabolism, and immune regulation. With advancing research into the mechanisms of RNA methylation, the pivotal role of m6A modification in the pathophysiology of reproductive system tumours, particularly cervical cancer, has been progressively unveiled. This discovery has opened new research avenues and presented significant potential for the diagnosis, prognostic evaluation, and treatment of diseases. This review delves deeply into the biological functions of m6A modification and its mechanisms of action in the onset and progression of cervical cancer. Furthermore, it explores the prospects of m6A modification in the precision diagnosis and treatment of cervical cancer, aiming to provide new perspectives and a theoretical basis for innovative and advanced treatment strategies for cervical cancer.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11445900/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142353017","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