RNA Biology最新文献_第9页

Alternative splicing events driven by altered levels of GEMIN5 undergo translation. 由 GEMIN5 翻译水平改变所驱动的替代剪接事件。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-08-28 DOI: 10.1080/15476286.2024.2394755

Rosario Francisco-Velilla, Salvador Abellan, Juan Antonio Garcia-Martin, Juan Carlos Oliveros, Encarnacion Martinez-Salas

{"title":"Alternative splicing events driven by altered levels of GEMIN5 undergo translation.","authors":"Rosario Francisco-Velilla, Salvador Abellan, Juan Antonio Garcia-Martin, Juan Carlos Oliveros, Encarnacion Martinez-Salas","doi":"10.1080/15476286.2024.2394755","DOIUrl":"10.1080/15476286.2024.2394755","url":null,"abstract":"GEMIN5 is a multifunctional protein involved in various aspects of RNA biology, including biogenesis of snRNPs and translation control. Reduced levels of GEMIN5 confer a differential translation to selective groups of mRNAs, and biallelic variants reducing protein stability or inducing structural conformational changes are associated with neurological disorders. Here, we show that upregulation of GEMIN5 can be detrimental as it modifies the steady state of mRNAs and enhances alternative splicing (AS) events of genes involved in a broad range of cellular processes. RNA-Seq identification of the mRNAs associated with polysomes in cells with high levels of GEMIN5 revealed that a significant fraction of the differential AS events undergo translation. The association of mRNAs with polysomes was dependent on the type of AS event, being more frequent in the case of exon skipping. However, there were no major differences in the percentage of genes showing open-reading frame disruption. Importantly, differential AS events in mRNAs engaged in polysomes, eventually rendering non-functional proteins, encode factors controlling cell growth. The broad range of mRNAs comprising AS events engaged in polysomes upon GEMIN5 upregulation supports the notion that this multifunctional protein has evolved as a gene expression balancer, consistent with its dual role as a member of the SMN complex and as a modulator of protein synthesis, ultimately impinging on cell homoeostasis.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"23-34"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142081387","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

Correction. 更正。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-10-09 DOI: 10.1080/15476286.2024.2413227

引用次数: 0

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

Retrotransposon life cycle and its impacts on cellular responses. 逆转录转座子的生命周期及其对细胞反应的影响。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-10-13 DOI: 10.1080/15476286.2024.2409607

Ahmad Luqman-Fatah, Kei Nishimori, Shota Amano, Yukiko Fumoto, Tomoichiro Miyoshi

{"title":"Retrotransposon life cycle and its impacts on cellular responses.","authors":"Ahmad Luqman-Fatah, Kei Nishimori, Shota Amano, Yukiko Fumoto, Tomoichiro Miyoshi","doi":"10.1080/15476286.2024.2409607","DOIUrl":"10.1080/15476286.2024.2409607","url":null,"abstract":"Approximately 45% of the human genome is comprised of transposable elements (TEs), also known as mobile genetic elements. However, their biological function remains largely unknown. Among them, retrotransposons are particularly abundant, and some of the copies are still capable of mobilization within the genome through RNA intermediates. This review focuses on the life cycle of human retrotransposons and summarizes their regulatory mechanisms and impacts on cellular processes. Retrotransposons are generally epigenetically silenced in somatic cells, but are transcriptionally reactivated under certain conditions, such as tumorigenesis, development, stress, and ageing, potentially leading to genetic instability. We explored the dual nature of retrotransposons as genomic parasites and regulatory elements, focusing on their roles in genetic diversity and innate immunity. Furthermore, we discuss how host factors regulate retrotransposon RNA and cDNA intermediates through their binding, modification, and degradation. The interplay between retrotransposons and the host machinery provides insight into the complex regulation of retrotransposons and the potential for retrotransposon dysregulation to cause aberrant responses leading to inflammation and autoimmune diseases.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"11-27"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11485995/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142473696","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

Role of circular RNAs in DNA repair. 环状 RNA 在 DNA 修复中的作用。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-11-17 DOI: 10.1080/15476286.2024.2429945

Francisco Alejandro Lagunas-Rangel

{"title":"Role of circular RNAs in DNA repair.","authors":"Francisco Alejandro Lagunas-Rangel","doi":"10.1080/15476286.2024.2429945","DOIUrl":"10.1080/15476286.2024.2429945","url":null,"abstract":"Circular RNAs (circRNAs) exhibit a wide range of activities that allow them to participate in numerous cellular processes and make them relevant in a variety of diseases. In this regard, a key process in which circRNAs are involved, and which is the focus of this article, is DNA damage repair (DDR). This study aims to illustrate how circRNAs influence different DNA repair pathways, with particular emphasis on the underlying mechanisms. In addition, the potential medical applications of this knowledge are discussed, particularly in the diagnosis, prognosis and treatment of diseases. In this sense, circRNAs were found to play a crucial role in DNA repair processes by regulating the expression and activity of proteins involved in various DNA repair pathways. They influence the expression of DNA repair proteins by interacting with their mRNAs, sponging miRNAs that target these mRNAs, regulating transcription factors that bind to their promoters, modulating upstream signalling pathways, and affecting mRNA translation. Furthermore, circRNAs regulate the activity of DNA repair proteins by interacting directly with them, sequestering them in specific cellular compartments and controlling activation signalling or upstream DDR signalling.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"149-161"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11572198/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644755","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

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 3.6 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":"21 1","pages":"1-9"},"PeriodicalIF":3.6,"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 3.6 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

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 3.6 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":"21 1","pages":"1-9"},"PeriodicalIF":3.6,"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

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":"21 1","pages":"31-41"},"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