RUVBL1

引言组蛋白变体H2A.Z在启动子上发现并调节转录。ATP依赖性染色质重塑器SRCAP复合体(SRCAP-C)促进标准组蛋白H2A.Z-H2B二聚体被H2A–H2B取代。2024年2月8日，复旦大学徐彦辉及Wang Li共同通讯在Cell Discovery（IF 33.5）在线发表题为“Structural insights into histone exchange by human SRCAP complex”的研究论文，该研究确定了人类SRCAP-C与含H2A的核小体结合的结构。在真核细胞中，基因组DNA包裹在组蛋白八聚体周围，在基因组上产生排列的核小体。典型核小体包含四个组蛋白H2A、H2B、H3和H4的两个拷贝。为了实现功能调节，ATP依赖性染色质重塑复合体(重塑复合体)改变核小体的组成和沿DNA的位置。染色质重塑复合物根据其催化ATP酶的异同可分为4个家族：模仿开关(ISWI)、染色质结构域解旋酶DNA结合(CHD)、开关/sucrose不可发酵(SWI/ SNF)和肌醇营养不良80 (INO80)。其中两种重塑蛋白由单个亚基(CHD家族)或几个亚基(ISWI家族)组成。相比之下，SWI/SNF和INO80家族是多亚基复合物，除了超家族II解旋酶样运动亚基外，还含有肌动蛋白和肌动蛋白相关蛋白(ARPs)以及其他具有不同功能的重塑蛋白特异性亚基。人类染色质重塑子SNF2相关CPB激活蛋白(SRCAP)复合物(SRCAP-C)及其酵母对应物SWR1复合物(SWR-C)属于INO80染色质重塑子家族。SRCAP-C和SWR-C可以用H2A.Z-H2B二聚体以ATP依赖的方式取代H2A-H2B二聚体，这一过程可能需要组蛋白伴侣。生成的H2A.Z含核小体富集于几乎所有常染色质基因的启动子区域，并参与转录和其他过程的调控，如DNA复制、DNA修复和染色体分离。在真核细胞中，H2A.Z主要存在于它位于启动子的远端，在RNAPII的起始和延伸中起关键作用。H2A.Z在复制起点也广泛富集，并通过调节早期复制起点的起始和复制时间与DNA复制直接相关。此外，研究表明，协调H2A.Z双链断裂(DSBs)中的动力学对DNA修复至关重要。H2A.Z在染色体分离过程中也起着至关重要的作用，以维持基因组处于稳定状态。与其他染色质重塑子不同，SWR-C与核小体结合并诱导DNA展开和重新包裹，但不产生净DNA易位，表现出一种典型特征。核小体结合的SRCAP-C的整体结构（Credit: Cell Discovery）人SRCAP-C是一种~1-MDa复合物，由SRCAP、YL1、RUVBL1、RUVBL2、ARP6、ZNHIT1、DMAP1、ACTL6A、ACTB和YEATS4等10个亚基组成，酵母SRCAP-C由10个相同的亚基组成，分别为Swr1、Swc2、RvB1、RvB2、ARP6、Swc6、Swc4、Arp4、Actin、Yaf9和另外4个酵母特异性亚基Swc3、Swc5、Swc7和Bdf1。先前的研究已经揭示了酵母SWR-C、人SRCAP-C和核小体结合酵母SWR-C在ATP类似物ADP-BeFx存在下的结构。SWR-C含有RuvBL蛋白的异六聚体，Swr1中的插入物通过RuvBL六聚体延伸。Swr1的ATP酶结构域在超螺旋位置(SHL) 2上抓住DNA，导致DNA在ADP-BeFx结合状态下移位1bp。此外，进入DNA部分被解开，组蛋白核心“弯曲”。与酵母SWR-C相比，SRCAP-C采用了大致相似的结构，包含一个带有两个独立臂的环状“头”。该研究测定了核小体结合的SRCAP-C在不同核苷酸结合状态下的结构，并进行了结构引导染色质免疫沉淀测序(ChIP-seq)分析，以测试ZNHIT1对H2A.Z在体内掺入的影响。SRCAP-C介导的Z交换。SRCAP亚基集成了一个6亚基肌动蛋白相关蛋白(ARP)模块和一个含ATP酶的马达模块。ATP酶相关的ARP模块沿DNA包围核小体的一半，并可能抑制净DNA易位，这是SRCAP-C的独特特征。motor模块在载脂蛋白(无核苷酸)、ADP结合和ADP-BeFx结合状态下采用不同的核小体结合模式，表明ATP酶驱动的运动通过解开进入DNA的包裹使H2A-H2B不稳定，并通过ZNHIT1亚基将H2A-H2B拉出核小体。结构导向的染色质免疫沉淀测序分析证实了H2A接触ZNHIT1维持H2A.Z基因组上占用率的必要性。该研究为SRCAP-C介导的H2A-H2A.Z交换机制提供了结构性的见解。原文链接https://www.nature.com/articles/s41421-023-00640-1责编|探索君排版|探索君文章来源|“iNature”End往期精选围观一文读透细胞死亡(Cell Death) | 24年Cell重磅综述（长文收藏版）热文Science最新发布：全世界最前沿的125个科学问题热文Nature | 2024年值得关注的七项技术热文Nature | 自身免疫性疾病能被治愈吗？科学家们终于看到了希望热文Nature | 癌症与神经系统的致命舞蹈

如今，胰腺癌依然是全球人群面临的最致命性的恶性肿瘤之一，由于胰腺导管腺癌（PDAC）患者的5年生存率仅为3%左右，因此在全球范围内PDAC都很难利用外科手术进行治疗，为了开发出新型疗法策略，研究人员就需要在分子水平上更好地理解PDAC的生物学特征。近日，一篇发表在国际杂志Cancer Science上题为“Identification of a novel target of SETD1A histone methyltransferase and the clinical significance in pancreatic cancer”的研究报告中，来自东京医牙大学等机构的科学家们通过研究识别出了一种新型靶向性基因，其或许对于PDAC病例有着很强的临床意义。此前研究结果表明，癌细胞能表达一种由SETD1A基因所编码的高水平的特殊酶类—组蛋白H3K4甲基转移酶（histone H3K4 methyltransferase），该酶能通过甲基化化学基团添加到特定靶向性基因的组蛋白（染色质必要的结构组分）上，这一过程就称之为甲基化过程，然而，诱发该酶类过表达以及其对癌细胞效应的分子机制，目前研究人员并不清楚。当组蛋白发生甲基化后，靶向性基因就会被激活，如果SETD1A的靶向性基因能支持癌症的发育和进展，这一点就特别具有意义，因此，研究人员非常感兴趣理解SETD1A的过表达在PDAC中所扮演的关键角色。研究者Takeshi Ishii说道，尽管此前研究结果表明，SETD1A在多种癌症中处于过表达装填，比如胃癌和肺癌等，但我们并不清楚其在PDAC中的特定分子事件，PDAC中SETD1A的靶向性基因目前尚未被确定或识别。科学家识别出抵御人类胰腺癌的关键分子靶点。图片来源：Cancer Science (2022). DOI:10.1111/cas.15615这项研究中，研究人员在其所分析的51.4%的人类PDAC样本中观察到了高水平SETD1A的表达，他们还确定了SETD1A或许是患者无疾病生存的独立预后因素，这就意味着，当患者机体的肿瘤被切除后，携带高水平SETD1A的患者相比低水平SETD1A的患者而言无疾病状态的持续时间就会变短，相关研究结果也证明了在PDAC中SETD1A表达的临床重要性。随后，研究人员利用人工培育的PDAC细胞来分析改变SETD1A的表达如何影响机体细胞的行为，当其过表达了SETD1A的水平时，细胞的生长和迁移的能力都会增加；在另外一组PDAC细胞中，研究人员利用分子技术来干扰SETD1A的表达，随后分析了因此而受到影响的其它基因；利用名为RNA测序的特殊技术，研究人员分析了敲低SETD1A的表达后总体的基因表达状况，结果发现，另外一个名为RUVBL1的基因的表达水平也较低。进一步研究结果表明，SETD1A能使得RUVBL1基因附近的组蛋白甲基化并激活其基因表达，敲低PDAC细胞中RUVBL1的表达或许会产生与之前对SETD1A进行干扰所观察到的相类似的生物学效应，对生存率的分析结果表明，携带高水平SETD1A和RUVBL1的PDAC患者的总体生存率较低，这就表明，其共同表达是指示这种癌症的重要预后生物标志物。综上，本文研究结果提供了对PDAC中SETD1A和RUVBL1表达意义更为深入的理解，同时还提供了关键的细节来帮助临床医生对经历严重疾病的患者制定关键的临床治疗决策。原始出处：Takeshi Ishii,Yoshimitsu Akiyama,Shu Shimada, et al. Identification of a novel target of SETD1A histone methyltransferase and the clinical significance in pancreatic cancer, Cancer Science (2022). DOI: 10.1111/cas.15615

Molecular motors are complex devices composed of many different parts that consume energy to perform various cellular activities. In short, molecular machines transform energy into useful work. Understanding the mechanistical aspects underlying these motors begins with generating a detailed description of their overall architecture and atomic organization. However, to uncover the core mechanisms energizing these motors it is essential to decode all of the molecular dynamics in atomic detail. Now, researchers reveal the architecture, complete functional cycle and the mechanism of such a molecular motor. Molecular motors are complex devices composed of many different parts that consume energy to perform various cellular activities. In short, molecular machines transform energy into useful work. Understanding the mechanistical aspects underlying these motors begins with generating a detailed description of their overall architecture and atomic organisation. However, to uncover the core mechanisms energizing these motors it is essential to decode all of the molecular dynamics in atomic detail. Now, the research team of Thomas C. Marlovits from the Centre for Structural Systems Biology CSSB at DESY and the University Medical Center Hamburg-Eppendorf (UKE) in Hamburg reveals the architecture, complete functional cycle and the mechanism of such a molecular motor: They report in the journal Nature, how a 'RuvAB branch migration complex' converts chemical energy into mechanical work to perform recombination and repair of DNA. DNA recombination is one of the most fundamental biological processes in living organisms. It is the process by which chromosomes "swap" DNA either to generate genetic diversity, by creating new offspring, or to maintain genetic integrity, by repairing breaks in existing chromosomes. During DNA recombination, four DNA arms separate from their double-helix formations and join together at an intersection known as a Holliday junction. Here the DNA arms exchange strands in a process called active branch migration. The essential energy needed for this branch migration to occur comes from a molecular machinery that scientists have tagged as the RuvAB branch migration complex. This complex assembles around the Holliday junction and is made of two motors labelled RuvB AAA+ ATPases, that fuel the reaction, and a RuvA stator. The research team has now provided an intricate blueprint that explains how the RuvB AAA+ motors work under the regulation of the RuvA protein to perform synchronized DNA movement. The active branch migrations energized by the RuvB AAA+ motor molecule are very fast and highly dynamic. To determine the individual steps of this process, the scientists used time-resolved cryo electron microscopy to observe the motor's machinery in slow motion. "We basically provided the RuvB AAA+ motor with a slower burning fuel which allowed us to capture the biochemical reactions as they occur," explains Marlovits. The scientist captured over ten million images of the motor machinery interacting with the Holliday junction. Jiri Wald (CSSB, UKE and part of the Vienna BioCenter PhD Program), the paper's first author, combed through the immense amount of data and carefully classified the subtle changes occurring in each image. Using the high-performance computing facility at DESY, the scientists were then able to put all the puzzle pieces together to generate a high-resolution movie detailing how the RuvAB complex functions on the molecular scale. "We were able to visualize seven distinct states of the motor and demonstrate how the interconnected elements work together in a cyclical manner," explains Wald. "We also demonstrated that the RuvB motor converts energy into a lever motion which generates the force that drives branch migration. We were amazed by the discovery that the motors use a basic lever mechanism to move the DNA substrate. Overall, the sequential mechanism, coordination and force generation manner of the RuvAB motor share conceptual similarities with combustion engines." AAA+ motors are often used in other biological systems, such as protein transport, therefore this detailed model of the RuvB AAA+ motor can be used as a blueprint for similar molecular motors. "We understand how the motor works and now we can put this motor into another system with some minor adaptations," explains Marlovits. "We are essentially presenting core principles for AAA+ motors." The Marlovits group's future work will explore ways to interfere with the function of AAA+ motors. This could provide the basis for the development of a new generation of drugs, which would disrupt the mechanisms of such a motor in pathogens and thus halt the spread of infection. "We are excited to explore the possibilities that exist now that we have a blueprint of the RuvB AAA+ motor," notes Wald. Scientists from CSSB, UKE, the Institute of Molecular Biotechnology, the Research Institute of Molecular Pathology, both in Vienna, Austria, and DESY contributed to this research. CSSB is a joint initiative of ten research partners from Northern Germany, including three universities and six research institutes that devotes itself to infection biology research. DESY is one of the world's leading particle accelerator centres and investigates the structure and function of matter -- from the interaction of tiny elementary particles and the behaviour of novel nanomaterials and vital biomolecules to the great mysteries of the universe. The particle accelerators and detectors that DESY develops and builds at its locations in Hamburg and Zeuthen are unique research tools. They generate the most intense X-ray radiation in the world, accelerate particles to record energies and open up new windows onto the universe. DESY is a member of the Helmholtz Association, Germany's largest scientific association, and receives its funding from the German Federal Ministry of Education and Research (BMBF) (90 per cent) and the German federal states of Hamburg and Brandenburg (10 per cent).