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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 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-01-01 Epub Date: 2024-09-30 DOI: 10.1080/15476286.2024.2408707
Yajuan Gao, Qi Guo, Liming Yu

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.

人们普遍认为,N6-甲基腺苷(m6A)是高等生物体内主要的 RNA 修饰形式,能够精细调节 RNA 代谢,从而影响一系列关键的生理和病理过程。这些过程包括基因表达调控、细胞增殖、侵袭和转移、细胞周期控制、细胞程序性死亡、肿瘤微环境中的相互作用、能量代谢和免疫调节。随着对 RNA 甲基化机制研究的不断深入,m6A 修饰在生殖系统肿瘤(尤其是宫颈癌)病理生理学中的关键作用已逐渐被揭示出来。这一发现开辟了新的研究途径,为疾病的诊断、预后评估和治疗提供了巨大的潜力。本综述深入探讨了 m6A 修饰的生物学功能及其在宫颈癌发病和进展过程中的作用机制。此外,它还探讨了 m6A 修饰在宫颈癌精准诊断和治疗中的应用前景,旨在为宫颈癌的创新和先进治疗策略提供新的视角和理论依据。
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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 Q2 BIOCHEMISTRY & MOLECULAR 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

The current letter to the editor describes the presence of RNA byproducts in small-scale in vitro transcription (IVT) reactions as evaluated by capillary gel electrophoresis, asymmetric flow field flow fractionation, immunoblotting, cell-free translation assays, and in IFN reporter cells. We compare standard T7 RNA polymerase (RNAP) based IVT reactions to two recently described protocols employing either urea supplementation or using the VSW3 RNAP. Our results indicate that urea supplementation yields considerably less RNA byproducts and positively affects the overall number of full-length transcripts. In contrast, VSW3 IVT reactions demonstrated a low yield and generated a higher fraction of truncated transcripts. Lastly, both urea mRNA and VSW3 mRNA elicited considerably less IFN responses after transfection in mouse macrophages.

这封致编辑的信描述了通过毛细管凝胶电泳、非对称流场流动分馏、免疫印迹、无细胞翻译检测以及在 IFN 报告细胞中评估的小规模体外转录(IVT)反应中 RNA 副产物的存在情况。我们将基于标准 T7 RNA 聚合酶(RNAP)的 IVT 反应与最近描述的采用尿素补充或使用 VSW3 RNAP 的两种方案进行了比较。结果表明,补充尿素可大大减少 RNA 副产物的产生,并对全长转录本的总体数量产生积极影响。相比之下,VSW3 IVT 反应的产量较低,产生的截短转录本比例较高。最后,尿素 mRNA 和 VSW3 mRNA 转染小鼠巨噬细胞后引起的 IFN 反应都要少得多。
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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 Q2 BIOCHEMISTRY & MOLECULAR 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

In eukaryotes, the ribosomal small subunit (40S) is composed of 18S rRNA and 33 ribosomal proteins. 18S rRNA has a special secondary structure and is an indispensable part of the translation process. Herein, a special sequence located in mammalian 18S rRNA named Poly(G)7box, which is composed of seven guanines, was found. Poly(G)7 can form a special and stable secondary structure by binding to the translation elongation factor subunit eEF1D and the ribosomal protein RPL32. Poly(G)7box was transfected into cells, and the translation efficiency of cells was inhibited. We believe that Poly(G)7box is an important translation-related functional element located on mammalian 18S rRNA, meanwhile the Poly(G)7 located on mRNA 5' and 3' box does not affect mRNA translation.

在真核生物中,核糖体小亚基(40S)由 18S rRNA 和 33 种核糖体蛋白组成。18S rRNA 具有特殊的二级结构,是翻译过程中不可或缺的一部分。在这里,我们发现了哺乳动物 18S rRNA 中的一个特殊序列,名为 Poly(G)7box ,由 7 个鸟嘌呤组成。Poly(G)7 能与翻译延伸因子亚基 eEF1D 和核糖体蛋白 RPL32 结合,形成特殊而稳定的二级结构。将 Poly(G)7box 转染细胞后,细胞的翻译效率受到抑制。我们认为Poly(G)7box是位于哺乳动物18S rRNA上的一个重要的翻译相关功能元件,而位于mRNA 5'和3'框上的Poly(G)7并不影响mRNA的翻译。
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引用次数: 0
The role of SRP9/SRP14 in regulating Alu RNA. SRP9/SRP14在调控Alu RNA中的作用
IF 3.6 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-01-01 Epub Date: 2024-11-19 DOI: 10.1080/15476286.2024.2430817
Daniel Gussakovsky, Nicole A Black, Evan P Booy, Sean A McKenna

SRP9/SRP14 is a protein heterodimer that plays a critical role in the signal recognition particle through its interaction with the scaffolding signal recognition particle RNA (7SL). SRP9/SRP14 binding to 7SL is mediated through a conserved structural motif that is shared with the primate-specific Alu RNA. Alu RNA are transcription products of Alu elements, a retroelement that comprises ~10% of the human genome. Alu RNA are involved in myriad biological processes and are dysregulated in several human disease states. This review focuses on the roles SRP9/SRP14 has in regulating Alu RNA diversification, maturation, and function. The diverse mechanisms through which SRP9/SRP14 regulates Alu RNA exemplify the breadth of protein-mediated regulation of non-coding RNA.

SRP9/SRP14是一种蛋白质异源二聚体,通过与支架信号识别颗粒RNA(7SL)相互作用,在信号识别颗粒中发挥着关键作用。SRP9/SRP14 与 7SL 的结合是通过与灵长类特异性 Alu RNA 共享的保守结构基序介导的。Alu RNA是Alu元件的转录产物,Alu元件是一种逆转录元件,约占人类基因组的10%。Alu RNA 参与了无数的生物过程,并在多种人类疾病中出现失调。本综述重点探讨 SRP9/SRP14 在调节 Alu RNA 多样化、成熟和功能方面的作用。SRP9/SRP14调控Alu RNA的机制多种多样,体现了蛋白质介导的非编码RNA调控的广泛性。
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引用次数: 0
Endogenous ZAP affects Zika virus RNA interactome. 内源性 ZAP 影响寨卡病毒 RNA 交互组。
IF 3.6 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-01-01 Epub Date: 2024-08-25 DOI: 10.1080/15476286.2024.2388911
Ahmad Jawad Sabir, Nguyen Phuong Khanh Le, Prince Pal Singh, Uladzimir Karniychuk

One of the most recent advances in the analysis of viral RNA-cellular protein interactions is the Comprehensive Identification of RNA-binding Proteins by Mass Spectrometry (ChIRP-MS). Here, we used ChIRP-MS in mock-infected and Zika-infected wild-type cells and cells knockout for the zinc finger CCCH-type antiviral protein 1 (ZAP). We characterized 'ZAP-independent' and 'ZAP-dependent' cellular protein interactomes associated with flavivirus RNA and found that ZAP affects cellular proteins associated with Zika virus RNA. The ZAP-dependent interactome identified with ChIRP-MS provides potential ZAP co-factors for antiviral activity against Zika virus and possibly other viruses. Identifying the full spectrum of ZAP co-factors and mechanisms of how they act will be critical to understanding the ZAP antiviral system and may contribute to the development of antivirals.

在分析病毒 RNA 与细胞蛋白相互作用方面的最新进展之一是利用质谱法(ChIRP-MS)全面鉴定 RNA 结合蛋白。在这里,我们在模拟感染和 Zika 感染的野生型细胞以及锌指 CCCH 型抗病毒蛋白 1 (ZAP) 基因敲除细胞中使用了 ChIRP-MS。我们鉴定了与黄病毒 RNA 相关的 "ZAP 依赖性 "和 "ZAP 非依赖性 "细胞蛋白相互作用组,发现 ZAP 会影响与寨卡病毒 RNA 相关的细胞蛋白。利用 ChIRP-MS 鉴定出的 ZAP 依赖性相互作用组提供了潜在的 ZAP 辅助因子,可用于抗击寨卡病毒和其他可能的病毒。全面鉴定 ZAP 辅助因子及其作用机制对了解 ZAP 抗病毒系统至关重要,并可能有助于开发抗病毒药物。
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引用次数: 0
Small molecule inhibition of RNA binding proteins in haematologic cancer. 小分子抑制血液肿瘤中的 RNA 结合蛋白。
IF 4.1 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-01-01 Epub Date: 2024-02-08 DOI: 10.1080/15476286.2024.2303558
Amit K Jaiswal, Michelle L Thaxton, Georgia M Scherer, Jacob P Sorrentino, Neil K Garg, Dinesh S Rao

In recent years, advances in biomedicine have revealed an important role for post-transcriptional mechanisms of gene expression regulation in pathologic conditions. In cancer in general and leukaemia specifically, RNA binding proteins have emerged as important regulator of RNA homoeostasis that are often dysregulated in the disease state. Having established the importance of these pathogenetic mechanisms, there have been a number of efforts to target RNA binding proteins using oligonucleotide-based strategies, as well as with small organic molecules. The field is at an exciting inflection point with the convergence of biomedical knowledge, small molecule screening strategies and improved chemical methods for synthesis and construction of sophisticated small molecules. Here, we review the mechanisms of post-transcriptional gene regulation, specifically in leukaemia, current small-molecule based efforts to target RNA binding proteins, and future prospects.

近年来,生物医学的进步揭示了转录后基因表达调控机制在病理状态下的重要作用。在癌症,特别是白血病中,RNA 结合蛋白已成为 RNA 平衡的重要调节因子,在疾病状态下往往会出现失调。在确定了这些致病机制的重要性之后,人们已经做出了许多努力,利用基于寡核苷酸的策略以及有机小分子来靶向 RNA 结合蛋白。随着生物医学知识、小分子筛选策略以及用于合成和构建复杂小分子的化学方法的改进,该领域正处于一个令人兴奋的拐点。在此,我们将回顾转录后基因调控(尤其是白血病)的机制、目前基于小分子靶向 RNA 结合蛋白的研究工作以及未来前景。
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引用次数: 0
Assessment of different enrichment methods revealed the optimal approach to identify bovine circRnas. 对不同富集方法的评估揭示了识别牛 circRnas 的最佳方法。
IF 4.1 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-01-01 Epub Date: 2024-05-26 DOI: 10.1080/15476286.2024.2356334
Yixin Wang, Jian Wang, Robert J Gruninger, Tim A McAllister, Mingzhou Li, Le Luo Guan

Although circular RNAs (circRNAs) play important roles in regulating gene expression, the understanding of circRNAs in livestock animals is scarce due to the significant challenge to characterize them from a biological sample. In this study, we assessed the outcomes of bovine circRNA identification using six enrichment approaches with the combination of ribosomal RNAs removal (Ribo); linear RNAs degradation (R); linear RNAs and RNAs with structured 3' ends degradation (RTP); ribosomal RNAs coupled with linear RNAs elimination (Ribo-R); ribosomal RNA, linear RNAs and RNAs with poly (A) tailing elimination (Ribo-RP); and ribosomal RNA, linear RNAs and RNAs with structured 3' ends elimination (Ribo-RTP), respectively. RNA-sequencing analysis revealed that different approaches led to varied ratio of uniquely mapped reads, false-positive rate of identifying circRNAs, and the number of circRNAs per million clean reads (Padj <0.05). Out of 2,285 and 2,939 highly confident circRNAs identified in liver and rumen tissues, respectively, 308 and 260 were commonly identified from five methods, with Ribo-RTP method identified the highest number of circRNAs. Besides, 507 of 4,051 identified bovine highly confident circRNAs had shared splicing sites with human circRNAs. The findings from this work provide optimized methods to identify bovine circRNAs from cattle tissues for downstream research of their biological roles in cattle.

尽管环状 RNA(circRNA)在调控基因表达方面发挥着重要作用,但由于从生物样本中鉴定环状 RNA 所面临的巨大挑战,人们对家畜体内环状 RNA 的了解还很少。在这项研究中,我们使用六种富集方法,结合核糖体 RNAs 去除(Ribo)、线性 RNAs 降解(R)、线性 RNAs 和具有结构化 3' 末端的 RNAs 降解(RTP),评估了牛 circRNA 鉴定的结果;核糖体 RNA 与线性 RNAs 结合消除(Ribo-R);核糖体 RNA、线性 RNAs 和 RNAs 与聚(A)尾消除(Ribo-RP);核糖体 RNA、线性 RNAs 和 RNAs 与结构化 3'末端消除(Ribo-RTP)。RNA 测序分析表明,不同的方法会导致不同的唯一映射读数比率、识别 circRNA 的假阳性率以及每百万清晰读数的 circRNA 数量(Padj)。
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引用次数: 0
The catalytic activity of methyltransferase METTL15 is dispensable for its role in mitochondrial ribosome biogenesis. 甲基转移酶 METTL15 在线粒体核糖体生物发生过程中的作用离不开其催化活性。
IF 3.6 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-01-01 Epub Date: 2024-06-24 DOI: 10.1080/15476286.2024.2369374
Christian D Mutti, Lindsey Van Haute, Michal Minczuk

Ribosomes are large macromolecular complexes composed of both proteins and RNA, that require a plethora of factors and post-transcriptional modifications for their biogenesis. In human mitochondria, the ribosomal RNA is post-transcriptionally modified at ten sites. The N4-methylcytidine (m4C) methyltransferase, METTL15, modifies the 12S rRNA of the small subunit at position C1486. The enzyme is essential for mitochondrial protein synthesis and assembly of the mitoribosome small subunit, as shown here and by previous studies. Here, we demonstrate that the m4C modification is not required for small subunit biogenesis, indicating that the chaperone-like activity of the METTL15 protein itself is an essential component for mitoribosome biogenesis.

核糖体是由蛋白质和 RNA 组成的大分子复合体,其生物生成需要大量的因子和转录后修饰。在人类线粒体中,核糖体 RNA 经过十个位点的转录后修饰。N4-甲基胞嘧啶(m4C)甲基转移酶 METTL15 在 C1486 位修饰小亚基的 12S rRNA。如本文和之前的研究所示,该酶对线粒体蛋白质合成和 mitoribosome 小亚基的组装至关重要。在这里,我们证明了小亚基的生物发生不需要 m4C 修饰,这表明 METTL15 蛋白本身的类似伴侣的活性是 mitoribosome 生物发生的重要组成部分。
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引用次数: 0
An optimized workflow of full-length transcriptome sequencing for accurate fusion transcript identification. 优化全长转录组测序工作流程,准确识别融合转录本。
IF 3.6 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-01-01 Epub Date: 2024-11-14 DOI: 10.1080/15476286.2024.2425527
Liang Zong, Yabing Zhu, Yuan Jiang, Ying Xia, Qun Liu, Jing Wang, Song Gao, Bei Luo, Yongxian Yuan, Jingjiao Zhou, Sanjie Jiang

Next-generation sequencing has revolutionized cancer genomics by enabling high-throughput mutation screening yet detecting fusion genes reliably remains challenging. Long-read sequencing offers potential for accurate fusion transcript identification, though challenges persist. In this study, we present an optimized workflow using nanopore sequencing technology to precisely identify fusion transcripts. Our approach encompasses a tailored library preparation protocol, data processing, and fusion gene analysis pipeline. We evaluated the performance using Universal Human Reference RNA and human adenocarcinoma cell lines. Our optimized nanopore sequencing workflow generated high-quality full-length transcriptome data characterized by an extended length distribution and comprehensive transcript coverage. Validation experiments confirmed novel fusion events with potential clinical relevance. Our protocol aims to mitigate biases and enhance accuracy, facilitating increased adoption in clinical diagnostics. Continued advancements in long-read sequencing promise deeper insights into fusion gene biology and improved cancer diagnostics.

下一代测序技术实现了高通量突变筛选,从而彻底改变了癌症基因组学,但可靠地检测融合基因仍是一项挑战。长读测序为准确鉴定融合转录本提供了潜力,但挑战依然存在。在本研究中,我们介绍了一种利用纳米孔测序技术精确鉴定融合转录本的优化工作流程。我们的方法包括量身定制的文库制备方案、数据处理和融合基因分析流水线。我们使用通用人类参考 RNA 和人类腺癌细胞系对其性能进行了评估。我们优化的纳米孔测序工作流程生成了高质量的全长转录组数据,其特点是长度分布更广、转录本覆盖更全面。验证实验证实了具有潜在临床意义的新型融合事件。我们的方案旨在减少偏差并提高准确性,从而促进临床诊断中更多地采用这种方法。长读数测序技术的不断进步有望加深人们对融合基因生物学的认识并改进癌症诊断。
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引用次数: 0
Origin of ribonucleotide recognition motifs through ligand mimicry at early earth. 核糖核苷酸识别图案的起源是早期地球上的配体模仿。
IF 3.6 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-01-01 Epub Date: 2024-11-11 DOI: 10.1080/15476286.2024.2423149
Deepto Mozumdar, Raktim N Roy

In an RNA world, the emergence of template-specific self-replication and catalysis necessitated the presence of motifs facilitating reliable recognition between RNA molecules. What did these motifs entail, and how did they evolve into the proteinaceous RNA recognition entities observed today? Direct observation of these primordial entities is hindered by rapid degradation over geological time scales. To overcome this challenge, researchers employ diverse approaches, including scrutiny of conserved sequences and structural motifs across extant organisms and employing directed evolution experiments to generate RNA molecules with specific catalytic abilities. In this review, we delve into the theme of ribonucleotide recognition across key periods of early Earth's evolution. We explore scenarios of RNA interacting with small molecules and examine hypotheses regarding the role of minerals and metal ions in enabling structured ribonucleotide recognition and catalysis. Additionally, we highlight instances of RNA-protein mimicry in interactions with other RNA molecules. We propose a hypothesis where RNA initially recognizes small molecules and metal ions/minerals, with subsequent mimicry by proteins leading to the emergence of proteinaceous RNA binding domains.

在 RNA 世界中,由于出现了特定模板的自我复制和催化反应,因此必须存在一些促进 RNA 分子之间可靠识别的图案。这些图案是什么,它们又是如何进化成今天观察到的蛋白质 RNA 识别实体的呢?对这些原始实体的直接观察受到地质时间尺度上快速退化的阻碍。为了克服这一难题,研究人员采用了多种方法,包括仔细研究现存生物的保守序列和结构基调,以及利用定向进化实验生成具有特定催化能力的 RNA 分子。在本综述中,我们将深入探讨地球早期进化关键时期的核糖核苷酸识别主题。我们探讨了 RNA 与小分子相互作用的情景,并研究了有关矿物质和金属离子在实现结构化核糖核苷酸识别和催化方面作用的假设。此外,我们还强调了 RNA 与其他 RNA 分子相互作用时的 RNA 蛋白拟态实例。我们提出了一种假说,即 RNA 最初识别小分子和金属离子/矿物质,随后蛋白质进行模仿,从而出现了蛋白质 RNA 结合域。
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引用次数: 0
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RNA Biology
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