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Exploring patterns in molecular biology 探索分子生物学的模式
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-16 DOI: 10.1016/j.molcel.2024.12.020
Demis Menolfi

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Patterns can be broadly defined as regular repetitions in contrast to random or casual arrangements. They are associated with order and are often governed by underlying rules. Close inspection of the natural world reveals pervasive patterns that are more common than one might think. For example, macroscopic patterns in the animal and plant kingdoms appear in the stripes of a zebra or the spiral arrangement of a pinecone’s scales. In the microscopic world, the internal organization of cells
章节片段正文模式可广义地定义为有规律的重复,而不是随机或随意的排列。它们与秩序相关联,通常受潜在规则的支配。仔细观察自然界就会发现,普遍存在的模式比人们想象的更为常见。例如,动物界和植物界的宏观模式表现为斑马的条纹或松果鳞片的螺旋排列。在微观世界中,细胞的内部组织
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引用次数: 0
Programming of synthetic regulatory DNA for cell-type targeting in humans 人类细胞类型靶向的合成调控DNA编程
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-16 DOI: 10.1016/j.molcel.2024.12.019
Leandro N. Ventimiglia, Aleksej Zelezniak
In a recent study in Nature, Gosai et al.1 introduce a framework to engineer and validate synthetic DNA regulatory elements showing cell-type-specific activity in human cell lines, closing the distance to the machine-driven design of functional regulatory sequences with therapeutic applications in humans.
在最近发表于《自然》(Nature)的一项研究中,Gosai 等人1 提出了一个框架,用于设计和验证在人类细胞系中显示出细胞类型特异性活性的合成 DNA 调控元件,从而拉近了机器驱动的功能性调控序列设计与人类治疗应用之间的距离。
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引用次数: 0
A tale of two strands: Decoding chromatin replication through strand-specific sequencing 两条链的故事:通过链特异性测序解码染色质复制
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-16 DOI: 10.1016/j.molcel.2024.10.035
Zhiming Li, Zhiguo Zhang
DNA replication, a fundamental process in all living organisms, proceeds with continuous synthesis of the leading strand by DNA polymerase ε (Pol ε) and discontinuous synthesis of the lagging strand by polymerase δ (Pol δ). This inherent asymmetry at each replication fork necessitates the development of methods to distinguish between these two nascent strands in vivo. Over the past decade, strand-specific sequencing strategies, such as enrichment and sequencing of protein-associated nascent DNA (eSPAN) and Okazaki fragment sequencing (OK-seq), have become essential tools for studying chromatin replication in eukaryotic cells. In this review, we outline the foundational principles underlying these methodologies and summarize key mechanistic insights into DNA replication, parental histone transfer, epigenetic inheritance, and beyond, gained through their applications. Finally, we discuss the limitations and challenges of current techniques, highlighting the need for further technological innovations to better understand the dynamics and regulation of chromatin replication in eukaryotic cells.
DNA复制是所有生物体的基本过程,DNA聚合酶ε (Pol ε)连续合成前导链,聚合酶δ (Pol δ)不连续合成后导链。这种内在的不对称在每个复制叉需要开发方法来区分这两个新生链在体内。在过去的十年中,链特异性测序策略,如蛋白质相关新生DNA的富集和测序(eSPAN)和Okazaki片段测序(OK-seq),已经成为研究真核细胞染色质复制的重要工具。在这篇综述中,我们概述了这些方法的基本原理,并总结了通过它们的应用获得的DNA复制、亲本组蛋白转移、表观遗传等方面的关键机制见解。最后,我们讨论了当前技术的局限性和挑战,强调需要进一步的技术创新,以更好地理解真核细胞中染色质复制的动力学和调控。
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引用次数: 0
Metabolism-driven chromatin dynamics: Molecular principles and technological advances 代谢驱动的染色质动力学:分子原理和技术进步
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-16 DOI: 10.1016/j.molcel.2024.12.012
Varun Sahu, Chao Lu
Cells integrate metabolic information into core molecular processes such as transcription to adapt to environmental changes. Chromatin, the physiological template of the eukaryotic genome, has emerged as a sensor and rheostat for fluctuating intracellular metabolites. In this review, we highlight the growing list of chromatin-associated metabolites that are derived from diverse sources. We discuss recent advances in our understanding of the mechanisms by which metabolic enzyme activities shape the chromatin structure and modifications, how specificity may emerge from their seemingly broad effects, and technologies that facilitate the study of epigenome-metabolome interplay. The recognition that metabolites are immanent components of the chromatin regulatory network has significant implications for the evolution, function, and therapeutic targeting of the epigenome.
细胞将代谢信息整合到转录等核心分子过程中,以适应环境变化。染色质作为真核生物基因组的生理模板,已成为细胞内代谢物波动的传感器和调节器。在这篇综述中,我们将重点介绍越来越多的染色质相关代谢物,这些代谢物的来源多种多样。我们讨论了在理解代谢酶活动塑造染色质结构和修饰的机制方面的最新进展、代谢酶看似广泛的作用如何产生特异性以及促进表观基因组-代谢组相互作用研究的技术。认识到代谢物是染色质调控网络的内在组成部分,对表观基因组的进化、功能和靶向治疗具有重要意义。
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引用次数: 0
USP4 Auto-Deubiquitylation Promotes Homologous Recombination USP4自去泛素化促进同源重组
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-15 DOI: 10.1016/j.molcel.2024.12.024
Paul Wijnhoven, Rebecca Konietzny, Andrew N. Blackford, Jonathan Travers, Benedikt M. Kessler, Ryotaro Nishi, Stephen P. Jackson
(Molecular Cell 60, 362–373; November 5, 2015)
(分子细胞》60期,362-373页;2015年11月5日)
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引用次数: 0
Deciphering functional tumor-immune crosstalk through highly multiplexed imaging and deep visual proteomics 通过高复用成像和深度视觉蛋白质组学解读功能性肿瘤免疫串扰
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-14 DOI: 10.1016/j.molcel.2024.12.023
Xiang Zheng, Andreas Mund, Matthias Mann
Deciphering the intricate tumor-immune interactions within the microenvironment is crucial for advancing cancer immunotherapy. Here, we introduce mipDVP, an advanced approach integrating highly multiplexed imaging, single-cell laser microdissection, and sensitive mass spectrometry to spatially profile the proteomes of distinct cell populations in a human colorectal and tonsil cancer with high sensitivity. In a colorectal tumor—a representative cold tumor—we uncovered spatial compartmentalization of an immunosuppressive macrophage barrier that potentially impedes T cell infiltration. Spatial proteomic analysis revealed distinct functional states of T cells in different tumor compartments. In a tonsil cancer sample—a hot tumor—we identified significant proteomic heterogeneity among cells influenced by proximity to cytotoxic T cell subtypes. T cells in the tumor parenchyma exhibit metabolic adaptations to hypoxic regions. Our spatially resolved, highly multiplexed strategy deciphers the complex cellular interplay within the tumor microenvironment, offering valuable insights for identifying immunotherapy targets and predictive signatures.
破译微环境中复杂的肿瘤免疫相互作用对于推进癌症免疫治疗至关重要。在这里,我们介绍了mipDVP,这是一种先进的方法,集成了高复用成像,单细胞激光显微解剖和敏感质谱,以高灵敏度空间描绘人类结直肠癌和扁桃体癌中不同细胞群的蛋白质组。在结直肠肿瘤中——一种典型的冷肿瘤——我们发现了免疫抑制巨噬细胞屏障的空间区隔化,该屏障可能阻碍T细胞的浸润。空间蛋白质组学分析揭示了T细胞在不同肿瘤区室中的不同功能状态。在扁桃体癌样本(一种热肿瘤)中,我们发现了受接近细胞毒性T细胞亚型影响的细胞之间显著的蛋白质组异质性。肿瘤实质中的T细胞表现出对缺氧区的代谢适应。我们的空间分辨率高,高度复用的策略破译了肿瘤微环境中复杂的细胞相互作用,为识别免疫治疗靶点和预测特征提供了有价值的见解。
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引用次数: 0
Structural basis of 5′ splice site recognition by the minor spliceosome 小剪接体识别 5′剪接位点的结构基础
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-14 DOI: 10.1016/j.molcel.2024.12.017
Jiangfeng Zhao, Daniel Peter, Irina Brandina, Xiangyang Liu, Wojciech P. Galej
The minor spliceosome catalyzes excision of U12-dependent introns from precursors of eukaryotic messenger RNAs (pre-mRNAs). This process is critical for many cellular functions, but the underlying molecular mechanisms remain elusive. Here, we report a cryoelectron microscopy (cryo-EM) reconstruction of the 13-subunit human U11 small nuclear ribonucleoprotein particle (snRNP) complex in apo and substrate-bound forms, revealing the architecture of the U11 small nuclear RNA (snRNA), five minor spliceosome-specific factors, and the mechanism of the U12-type 5′ splice site (5′SS) recognition. SNRNP25 and SNRNP35 specifically recognize U11 snRNA, while PDCD7 bridges SNRNP25 and SNRNP48, located at the distal ends of the particle. SNRNP48 and ZMAT5 are positioned near the 5′ end of U11 snRNA and stabilize binding of the incoming 5′SS. Recognition of the U12-type 5′SS is achieved through base-pairing to the 5′ end of the U11 snRNA and unexpected, non-canonical base-triple interactions with the U11 snRNA stem-loop 3. Our structures provide mechanistic insights into U12-dependent intron recognition and the evolution of the splicing machinery.
小剪接体催化真核信使rna (pre- mrna)前体中u12依赖性内含子的切除。这一过程对许多细胞功能至关重要,但其潜在的分子机制仍然难以捉摸。在这里,我们报告了一个低温电镜(cro - em)重建的13亚基人U11小核核糖核蛋白颗粒(snRNP)复合物的载子和底物结合形式,揭示了U11小核RNA (snRNA)的结构,五个次要剪接体特异性因子,以及u12型5 ‘剪接位点(5 ’ ss)识别的机制。SNRNP25和SNRNP35特异性识别U11 snRNA,而PDCD7连接SNRNP25和SNRNP48,位于颗粒的远端。SNRNP48和ZMAT5位于U11 snRNA的5 ‘端附近,稳定了传入的5 ’ ss的结合。对u12型5 ‘ ss的识别是通过与U11 snRNA 5 ’端的碱基配对以及与U11 snRNA茎环3的非标准碱基三元相互作用实现的。我们的结构提供了对u12依赖性内含子识别和剪接机制进化的机制见解。
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引用次数: 0
Centromere inactivation during aging can be rescued in human cells 人类细胞在衰老过程中可以挽救着丝粒失活
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-13 DOI: 10.1016/j.molcel.2024.12.018
Sweta Sikder, Songjoon Baek, Truman McNeil, Yamini Dalal
Aging involves a range of genetic, epigenetic, and physiological alterations. A key characteristic of aged cells is the loss of global heterochromatin, accompanied by a reduction in canonical histone levels. In this study, we track the fate of centromeres in aged human fibroblasts and tissues and in various cellular senescent models. Our findings reveal that the centromeric histone H3 variant CENP-A is downregulated in aged cells in a p53-dependent manner. We observe repression of centromeric noncoding transcription through an epigenetic mechanism via recruitment of a lysine-specific demethylase 1 (LSD1/KDM1A) to centromeres. This suppression results in defective de novo CENP-A loading at aging centromeres. By dual inhibition of p53 and LSD1/KDM1A in aged cells, we mitigate the reduction in centromeric proteins and centromeric transcripts, leading to the mitotic rejuvenation of these cells. These results offer insights into a unique mechanism for centromeric inactivation during aging and provide potential strategies to reactivate centromeres.
衰老包括一系列遗传、表观遗传和生理上的改变。衰老细胞的一个关键特征是整体异染色质的丧失,伴随着标准组蛋白水平的降低。在这项研究中,我们在衰老的人类成纤维细胞和组织以及各种细胞衰老模型中追踪着丝粒的命运。我们的研究结果表明,着丝粒组蛋白H3变体CENP-A在衰老细胞中以p53依赖的方式下调。我们观察到着丝粒非编码转录的抑制是通过表观遗传机制通过赖氨酸特异性去甲基酶1 (LSD1/KDM1A)募集到着丝粒。这种抑制导致老化着丝粒中有缺陷的新生CENP-A负载。通过在衰老细胞中双重抑制p53和LSD1/KDM1A,我们减轻了着丝粒蛋白和着丝粒转录物的减少,导致这些细胞的有丝分裂再生。这些结果提供了对衰老过程中着丝粒失活的独特机制的见解,并提供了重新激活着丝粒的潜在策略。
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引用次数: 0
RBBP6 anchors pre-mRNA 3′ end processing to nuclear speckles for efficient gene expression RBBP6将前mrna 3 '端加工锚定在核斑点上,以实现有效的基因表达
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-10 DOI: 10.1016/j.molcel.2024.12.016
Yoseop Yoon, Elodie Bournique, Lindsey V. Soles, Hong Yin, Hsu-Feng Chu, Christopher Yin, Yinyin Zhuang, Xiangyang Liu, Liang Liu, Joshua Jeong, Clinton Yu, Marielle Valdez, Lusong Tian, Lan Huang, Xiaoyu Shi, Georg Seelig, Fangyuan Ding, Liang Tong, Rémi Buisson, Yongsheng Shi
Pre-mRNA 3′ processing is an integral step in mRNA biogenesis. However, where this process occurs in the nucleus remains unknown. Here, we demonstrate that nuclear speckles (NSs), membraneless organelles enriched with splicing factors, are major sites for pre-mRNA 3′ processing in human cells. We show that the essential pre-mRNA 3′ processing factor retinoblastoma-binding protein 6 (RBBP6) associates strongly with NSs via its C-terminal intrinsically disordered region (IDR). Importantly, although the conserved N-terminal domain (NTD) of RBBP6 is sufficient for pre-mRNA 3′ processing in vitro, its IDR-mediated association with NSs is required for efficient pre-mRNA 3′ processing in cells. Through proximity labeling analyses, we provide evidence that pre-mRNA 3′ processing for over 50% of genes occurs near NSs. We propose that NSs serve as hubs for RNA polymerase II transcription, pre-mRNA splicing, and 3′ processing, thereby enhancing the efficiency and coordination of different gene expression steps.
前mRNA 3 '加工是mRNA生物发生的重要步骤。然而,这个过程发生在细胞核的什么地方仍然未知。在这里,我们证明了核斑点(NSs),即富含剪接因子的无膜细胞器,是人类细胞中pre-mRNA 3 '加工的主要位点。研究人员发现,视网膜母细胞瘤结合蛋白6 (RBBP6)通过其c端内在无序区(IDR)与NSs密切相关。重要的是,尽管RBBP6的保守n端结构域(NTD)足以在体外加工pre-mRNA 3 ‘,但idr介导的与NSs的关联是细胞中有效的pre-mRNA 3 ’加工所必需的。通过接近标记分析,我们提供的证据表明,超过50%的基因的前mrna 3 '加工发生在NSs附近。我们认为NSs是RNA聚合酶II转录、前mrna剪接和3 '加工的枢纽,从而提高了不同基因表达步骤的效率和协调性。
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引用次数: 0
Chromatin hubs drive key regulatory networks in leukemia 染色质中心驱动白血病的关键调控网络
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-02 DOI: 10.1016/j.molcel.2024.12.011
Alok Swaroop, Feng Yue
In this issue of Molecular Cell, Gambi, Boccalatte, Hernaez, et al.1 apply multiomics followed by genetic engineering to define then characterize epigenetic hubs that regulate processes crucial for T-ALL and use this insight to offer new avenues for therapeutic targeting.
在本期的《分子细胞》杂志上,Gambi、Boccalatte、Hernaez等人应用多组学和基因工程技术来定义和表征对T-ALL至关重要的调控过程的表观遗传中心,并利用这一见解为靶向治疗提供新的途径。
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引用次数: 0
期刊
Molecular Cell
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