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PKM2-G-quadruplex interactions conspire to regulate the cancer transcriptome PKM2-G-四叠体相互作用共同调控癌症转录组
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-03 DOI: 10.1016/j.molcel.2024.09.013
Prakash Kharel, Pavel Ivanov
In this issue of Molecular Cell, Anastasakis et al. describe a novel function of the metabolic enzyme PKM2 as an RNA G-quadruplex binding protein, which could contribute to cancer biology.
在本期《分子细胞》(Molecular Cell)杂志上,Anastasakis 等人描述了代谢酶 PKM2 作为 RNA G-quadruplex 结合蛋白的一种新功能,它可能有助于癌症生物学。
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引用次数: 0
50 years in the making: acp3U, an amino-acid-containing nucleoside, links N-glycans and RNA in glycoRNA 50 年历程:含氨基酸的核苷 acp3U 在糖核糖核酸中将 N-糖和核糖核酸连接起来
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-03 DOI: 10.1016/j.molcel.2024.09.014
Kfir B. Steinbuch, Yitzhak Tor
In a recent publication in Cell, Xie et al.1 report a sensitive and scalable method for the detection and characterization of native glycoRNAs and identify acp3U, an abundant modified nucleoside discovered 50 years ago in tRNAPhe, as one of the primary attachment sites for N-glycans.
在最近发表于《细胞》(Cell)的一篇文章中,Xie 等人1 报道了一种灵敏且可扩展的方法,用于检测和表征原生的糖核糖核酸,并将 50 年前在 tRNAPhe 中发现的一种丰富的修饰核苷--acp3U 确定为 N-糖的主要附着位点之一。
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引用次数: 0
Dual regulation of IP3 receptors by IP3 and PIP2 controls the transition from local to global Ca2+ signals IP3 和 PIP2 对 IP3 受体的双重调控控制着 Ca2+ 信号从局部向全局的过渡
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-03 DOI: 10.1016/j.molcel.2024.09.009
Adelina Ivanova, Peace Atakpa-Adaji, Shanlin Rao, Maria Marti-Solano, Colin W. Taylor
The spatial organization of inositol 1,4,5-trisphosphate (IP3)-evoked Ca2+ signals underlies their versatility. Low stimulus intensities evoke Ca2+ puffs, localized Ca2+ signals arising from a few IP3 receptors (IP3Rs) within a cluster tethered beneath the plasma membrane. More intense stimulation evokes global Ca2+ signals. Ca2+ signals propagate regeneratively as the Ca2+ released stimulates more IP3Rs. How is this potentially explosive mechanism constrained to allow local Ca2+ signaling? We developed methods that allow IP3 produced after G-protein coupled receptor (GPCR) activation to be intercepted and replaced by flash photolysis of a caged analog of IP3. We find that phosphatidylinositol 4,5-bisphosphate (PIP2) primes IP3Rs to respond by partially occupying their IP3-binding sites. As GPCRs stimulate IP3 formation, they also deplete PIP2, relieving the priming stimulus. Loss of PIP2 resets IP3R sensitivity and delays the transition from local to global Ca2+ signals. Dual regulation of IP3Rs by PIP2 and IP3 through GPCRs controls the transition from local to global Ca2+ signals.
1,4,5-三磷酸肌醇(IP3)诱发的 Ca2+ 信号的空间组织是其多功能性的基础。低刺激强度会唤起 Ca2+ 浮肿,这是局部的 Ca2+ 信号,由系在质膜下的一个簇内的少数 IP3 受体(IP3R)产生。更强烈的刺激会唤起整体 Ca2+ 信号。当释放的 Ca2+ 刺激更多 IP3Rs 时,Ca2+ 信号会再生传播。这种潜在的爆炸性机制是如何限制局部 Ca2+ 信号的呢?我们开发出了一些方法,可以拦截 G 蛋白偶联受体(GPCR)激活后产生的 IP3,并通过闪光光解 IP3 的笼状类似物来取代 IP3。我们发现,磷脂酰肌醇 4,5-二磷酸(PIP2)通过部分占据 IP3R 的 IP3 结合位点,促使 IP3R 作出反应。当 GPCR 刺激 IP3 形成时,它们也会耗尽 PIP2,从而缓解启动刺激。PIP2 的缺失会重置 IP3R 的敏感性,并延迟从局部到全局 Ca2+ 信号的过渡。PIP2 和 IP3 通过 GPCR 对 IP3R 的双重调控控制着从局部到全局 Ca2+ 信号的过渡。
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引用次数: 0
PRC2-RNA interactions: Viewpoint from YongWoo Lee and Jeannie T. Lee PRC2-RNA 相互作用:李容宇和李贞妮的观点
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-03 DOI: 10.1016/j.molcel.2024.09.006
YongWoo Lee, Jeannie T. Lee
Here, we expound on the view that Xist RNA directly controls Polycomb repressive complex 2 (PRC2) recruitment, off-loading to chromatin, catalytic activity, and eviction from chromatin. RNA-PRC2 interactions also control RNA polymerase II transcription pausing. Dynamic RNA folding determines PRC2 activity. Disparate studies and interpretations abound but can be reconciled.
在这里,我们阐述了 Xist RNA 直接控制多聚核酸抑制复合体 2(PRC2)的招募、卸载到染色质、催化活性以及从染色质中驱逐的观点。RNA-PRC2 的相互作用还控制着 RNA 聚合酶 II 的转录暂停。RNA 的动态折叠决定了 PRC2 的活性。不同的研究和解释比比皆是,但都是可以调和的。
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引用次数: 0
Nuclear sorting of short RNA polymerase II transcripts 短 RNA 聚合酶 II 转录本的核分选
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-03 DOI: 10.1016/j.molcel.2024.08.024
William Garland, Torben Heick Jensen
Mammalian genomes produce an abundance of short RNA. This is, to a large extent, due to the genome-wide and spurious activity of RNA polymerase II (RNAPII). However, it is also because the vast majority of initiating RNAPII, regardless of the transcribed DNA unit, terminates within a ∼3-kb early “pausing zone.” Given that the resultant RNAs constitute both functional and non-functional species, their proper sorting is critical. One way to think about such quality control (QC) is that transcripts, from their first emergence, are relentlessly targeted by decay factors, which may only be avoided by engaging protective processing pathways. In a molecular materialization of this concept, recent progress has found that both “destructive” and “productive” RNA effectors assemble at the 5′ end of capped RNA, orchestrated by the essential arsenite resistance protein 2 (ARS2) protein. Based on this principle, we here discuss early QC mechanisms and how these might sort short RNAs to their final fates.
哺乳动物基因组产生大量短 RNA。这在很大程度上是由于 RNA 聚合酶 II(RNAPII)在全基因组范围内的虚假活性。不过,这也是因为绝大多数启动的 RNAPII,无论转录的 DNA 单元是什么,都会在∼3 kb 的早期 "暂停区 "内终止。鉴于由此产生的 RNA 既有功能性的,也有非功能性的,因此对它们进行适当的分类至关重要。对这种质量控制(QC)的一种看法是,转录本从一开始出现就被衰变因子无情地锁定,只有通过保护性处理途径才能避免衰变。在这一概念的分子具体化过程中,最新研究进展发现,"破坏性 "和 "生产性 "RNA效应因子都会在封端RNA的5′末端聚集,并由重要的亚砷酸盐抗性蛋白2(ARS2)蛋白协调。基于这一原理,我们在此讨论早期 QC 机制,以及这些机制如何将短 RNA 分类到它们的最终命运。
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引用次数: 0
Exploring the expanding universe of host-virus interactions mediated by viral RNA 探索病毒 RNA 介导的宿主-病毒相互作用的不断扩展的宇宙
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-03 DOI: 10.1016/j.molcel.2024.08.027
Alfredo Castello, Lucía Álvarez, Wael Kamel, Louisa Iselin, Janosch Hennig
RNA is a central molecule in RNA virus biology; however, the interactions that it establishes with the host cell are only starting to be elucidated. In recent years, a methodology revolution has dramatically expanded the scope of host-virus interactions involving the viral RNA (vRNA). A second wave of method development has enabled the precise study of these protein-vRNA interactions in a life cycle stage-dependent manner, as well as providing insights into the interactome of specific vRNA species. This review discusses these technical advances and describes the new regulatory mechanisms that have been identified through their use. Among these, we discuss the importance of vRNA in regulating protein function through a process known as riboregulation. We envision that the elucidation of vRNA interactomes will open new avenues of research, including pathways to the discovery of host factors with therapeutic potential against viruses.
RNA 是 RNA 病毒生物学的核心分子;然而,它与宿主细胞之间的相互作用才刚刚开始被阐明。近年来,一场方法革命极大地扩展了涉及病毒 RNA(vRNA)的宿主-病毒相互作用的范围。第二波方法开发浪潮使人们能够以生命周期阶段依赖的方式精确研究这些蛋白质-vRNA 相互作用,并深入了解特定 vRNA 种类的相互作用组。这篇综述讨论了这些技术进展,并介绍了通过使用这些技术所发现的新调控机制。其中,我们讨论了 vRNA 通过一种称为核糖核酸调控的过程调控蛋白质功能的重要性。我们认为,阐明 vRNA 相互作用组将开辟新的研究途径,包括发现具有抗病毒治疗潜力的宿主因子的途径。
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引用次数: 0
Epitranscriptome in action: RNA modifications in the DNA damage response Epitranscriptome in action:DNA 损伤反应中的 RNA 修饰
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-03 DOI: 10.1016/j.molcel.2024.09.003
Blerta Xhemalçe, Kyle M. Miller, Natalia Gromak
Complex pathways involving the DNA damage response (DDR) contend with cell-intrinsic and -extrinsic sources of DNA damage. DDR mis-regulation results in genome instability that can contribute to aging and diseases including cancer and neurodegeneration. Recent studies have highlighted key roles for several RNA species in the DDR, including short RNAs and RNA/DNA hybrids (R-loops) at DNA break sites, all contributing to efficient DNA repair. RNAs can undergo more than 170 distinct chemical modifications. These RNA modifications have emerged as key orchestrators of the DDR. Here, we highlight the function of enzyme- and non-enzyme-induced RNA modifications in the DDR, with particular emphasis on m6A, m5C, and RNA editing. We also discuss stress-induced RNA damage, including RNA alkylation/oxidation, RNA-protein crosslinks, and UV-induced RNA damage. Uncovering molecular mechanisms that underpin the contribution of RNA modifications to DDR and genome stability will have direct application to disease and approaches for therapeutic intervention.
涉及 DNA 损伤应答(DDR)的复杂通路要与细胞内在和外在的 DNA 损伤源进行抗争。DDR 失调会导致基因组不稳定,从而引起衰老以及癌症和神经变性等疾病。最近的研究强调了几种 RNA 在 DDR 中的关键作用,包括 DNA 断裂位点的短 RNA 和 RNA/DNA 杂交(R-环),它们都有助于高效的 DNA 修复。RNA 可进行 170 多种不同的化学修饰。这些 RNA 修饰已成为 DDR 的关键协调者。在此,我们将重点介绍酶和非酶诱导的 RNA 修饰在 DDR 中的功能,特别强调 m6A、m5C 和 RNA 编辑。我们还讨论了应激诱导的 RNA 损伤,包括 RNA 烷基化/氧化、RNA 蛋白交联和紫外线诱导的 RNA 损伤。揭示 RNA 修饰对 DDR 和基因组稳定性所起作用的分子机制将直接应用于疾病和治疗干预方法。
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引用次数: 0
PRC2-RNA interactions: Viewpoint from Jimmy K. Guo, Mario R. Blanco, and Mitchell Guttman PRC2-RNA 相互作用:Jimmy K. Guo、Mario R. Blanco 和 Mitchell Guttman 的观点
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-03 DOI: 10.1016/j.molcel.2024.09.007
Jimmy K. Guo, Mario R. Blanco, Mitchell Guttman
Many reported PRC2-RNA interactions have been shown to be functionally dispensable, raising questions about whether they occur in vivo. Here, we lay out technical issues with existing evidence for direct binding and argue that there is currently a lack of biochemical or functional evidence for direct PRC2-RNA binding in vivo.
许多报道的 PRC2-RNA 相互作用已被证明在功能上是可有可无的,从而引发了关于它们是否在体内发生的疑问。在这里,我们阐述了现有直接结合证据的技术问题,并认为目前缺乏 PRC2-RNA 在体内直接结合的生化或功能证据。
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引用次数: 0
Emerging and re-emerging themes in co-transcriptional pre-mRNA splicing 共转录前 mRNA 剪接中新出现和再次出现的主题
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-03 DOI: 10.1016/j.molcel.2024.08.036
Tucker J. Carrocci, Karla M. Neugebauer
Proper gene expression requires the collaborative effort of multiple macromolecular machines to produce functional messenger RNA. As RNA polymerase II (RNA Pol II) transcribes DNA, the nascent pre-messenger RNA is heavily modified by other complexes such as 5′ capping enzymes, the spliceosome, the cleavage, and polyadenylation machinery as well as RNA-modifying/editing enzymes. Recent evidence has demonstrated that pre-mRNA splicing and 3′ end cleavage can occur on similar timescales as transcription and significantly cross-regulate. In this review, we discuss recent advances in co-transcriptional processing and how it contributes to gene regulation. We highlight how emerging areas—including coordinated splicing events, physical interactions between the RNA synthesis and modifying machinery, rapid and delayed splicing, and nuclear organization—impact mRNA isoforms. Coordination among RNA-processing choices yields radically different mRNA and protein products, foreshadowing the likely regulatory importance of co-transcriptional RNA folding and co-transcriptional modifications that have yet to be characterized in detail.
基因的正常表达需要多种大分子机器的协同努力,才能产生功能性信使 RNA。当 RNA 聚合酶 II(RNA Pol II)转录 DNA 时,新生的前信使 RNA 会被其他复合体(如 5′封端酶、剪接体、裂解和多聚腺苷化机制以及 RNA 修饰/编辑酶)大量修饰。最近的证据表明,前 mRNA 剪接和 3′末端裂解可与转录发生在相似的时间尺度上,并具有显著的交叉调节作用。在这篇综述中,我们将讨论共转录处理的最新进展及其如何促进基因调控。我们强调了新出现的领域--包括协调剪接事件、RNA 合成和修饰机制之间的物理相互作用、快速和延迟剪接以及核组织--是如何影响 mRNA 同工型的。RNA加工选择之间的协调产生了截然不同的mRNA和蛋白质产物,这预示着共转录RNA折叠和共转录修饰可能具有重要的调控作用,而这些作用尚有待详细描述。
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引用次数: 0
Understanding nuclear mRNA export: Survival under stress 了解核 mRNA 的输出:压力下的生存
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-10-03 DOI: 10.1016/j.molcel.2024.08.028
Johanna Franziska Seidler, Katja Sträßer
Nuclear messenger RNA (mRNA) export is vital for cell survival under both physiological and stress conditions. To cope with stress, cells block bulk mRNA export while selectively exporting stress-specific mRNAs. Under physiological conditions, nuclear adaptor proteins recruit the mRNA exporter to the mRNA for export. By contrast, during stress conditions, the mRNA exporter is likely directly recruited to stress-specific mRNAs at their transcription sites to facilitate selective mRNA export. In this review, we summarize our current understanding of nuclear mRNA export. Importantly, we explore insights into the mechanisms that block bulk mRNA export and facilitate transcript-specific mRNA export under stress, highlighting the gaps that still need to be filled.
核信使核糖核酸(mRNA)的输出对于细胞在生理和应激条件下的生存至关重要。为了应对应激,细胞会阻止大量 mRNA 的输出,同时选择性地输出应激特异性 mRNA。在生理条件下,核适配蛋白会将 mRNA 导出器吸引到 mRNA 上进行导出。相比之下,在应激条件下,mRNA导出器很可能直接被招募到应激特异性mRNA的转录位点,以促进mRNA的选择性导出。在这篇综述中,我们总结了目前对核 mRNA 导出的理解。重要的是,我们探讨了应激状态下阻止大量 mRNA 导出和促进转录本特异性 mRNA 导出的机制,并强调了仍需填补的空白。
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引用次数: 0
期刊
Molecular Cell
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