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The chromosome folding problem and how cells solve it 染色体折叠问题及细胞如何解决这一问题
IF 64.5 1区 化学 Q2 CHEMISTRY, PHYSICAL Pub Date : 2024-11-14 DOI: 10.1016/j.cell.2024.10.026
Job Dekker, Leonid A. Mirny
Every cell must solve the problem of how to fold its genome. We describe how the folded state of chromosomes is the result of the combined activity of multiple conserved mechanisms. Homotypic affinity-driven interactions lead to spatial partitioning of active and inactive loci. Molecular motors fold chromosomes through loop extrusion. Topological features such as supercoiling and entanglements contribute to chromosome folding and its dynamics, and tethering loci to sub-nuclear structures adds additional constraints. Dramatically diverse chromosome conformations observed throughout the cell cycle and across the tree of life can be explained through differential regulation and implementation of these basic mechanisms. We propose that the first functions of chromosome folding are to mediate genome replication, compaction, and segregation and that mechanisms of folding have subsequently been co-opted for other roles, including long-range gene regulation, in different conditions, cell types, and species.
每个细胞都必须解决如何折叠基因组的问题。我们描述了染色体的折叠状态是多种保守机制共同作用的结果。同型亲和力驱动的相互作用导致了活性和非活性基因座的空间分区。分子马达通过环挤压折叠染色体。超卷曲和缠结等拓扑特征有助于染色体的折叠及其动态变化,而将基因座拴系在亚核结构上则增加了额外的限制。在整个细胞周期和整个生命树中观察到的染色体构象的巨大差异,可以通过这些基本机制的不同调控和实施来解释。我们提出,染色体折叠的最初功能是介导基因组复制、压实和分离,折叠机制随后在不同条件、细胞类型和物种中被用于其他作用,包括长程基因调控。
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引用次数: 0
The cellular dogma 细胞教条
IF 64.5 1区 化学 Q2 CHEMISTRY, PHYSICAL Pub Date : 2024-11-14 DOI: 10.1016/j.cell.2024.10.029
Stephen R. Quake
In this essay, I will put forth what I see as a major conceptual challenge for biology in the next decade, one that is inspired by Crick’s Central Dogma: understanding information flow in the cell in the most general sense.
在这篇文章中,我将提出我认为未来十年生物学面临的一个重大概念挑战,这个挑战的灵感来自克里克的 "中心教条":从最一般的意义上理解细胞中的信息流。
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引用次数: 0
STK19 positions TFIIH for cell-free transcription-coupled DNA repair STK19 将 TFIIH 定位于无细胞转录耦合 DNA 修复
IF 64.5 1区 化学 Q2 CHEMISTRY, PHYSICAL Pub Date : 2024-11-14 DOI: 10.1016/j.cell.2024.10.020
Tycho E.T. Mevissen, Maximilian Kümmecke, Ernst W. Schmid, Lucas Farnung, Johannes C. Walter
In transcription-coupled nucleotide excision repair (TC-NER), stalled RNA polymerase II (RNA Pol II) binds CSB and CRL4CSA, which cooperate with UVSSA and ELOF1 to recruit TFIIH. To explore the mechanism of TC-NER, we recapitulated this reaction in vitro. When a plasmid containing a site-specific lesion is transcribed in frog egg extract, error-free repair is observed that depends on CSB, CRL4CSA, UVSSA, and ELOF1. Repair also requires STK19, a factor previously implicated in transcription recovery after UV exposure. A 1.9-Å cryo-electron microscopy structure shows that STK19 binds the TC-NER complex through CSA and the RPB1 subunit of RNA Pol II. Furthermore, AlphaFold predicts that STK19 interacts with the XPD subunit of TFIIH, and disrupting this interface impairs cell-free repair. Molecular modeling suggests that STK19 positions TFIIH ahead of RNA Pol II for lesion verification. Our analysis of cell-free TC-NER suggests that STK19 couples RNA Pol II stalling to downstream repair events.
在转录偶联核苷酸切割修复(TC-NER)中,停滞的 RNA 聚合酶 II(RNA Pol II)与 CSB 和 CRL4CSA 结合,它们与 UVSSA 和 ELOF1 合作招募 TFIIH。为了探索TC-NER的机制,我们在体外重现了这一反应。当含有位点特异性病变的质粒在蛙卵提取物中转录时,可以观察到依赖于 CSB、CRL4CSA、UVSSA 和 ELOF1 的无差错修复。修复还需要 STK19,这是一种以前与紫外线暴露后转录恢复有关的因子。1.9 埃的冷冻电镜结构显示,STK19 通过 CSA 和 RNA Pol II 的 RPB1 亚基与 TC-NER 复合物结合。此外,AlphaFold 预测 STK19 与 TFIIH 的 XPD 亚基相互作用,破坏这一界面会损害无细胞修复。分子建模表明,STK19 使 TFIIH 先于 RNA Pol II 进行病变验证。我们对无细胞 TC-NER 的分析表明,STK19 将 RNA Pol II 停顿与下游修复事件联系起来。
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引用次数: 0
From bacterial operons to gene therapy: 50 years of the journal Cell 从细菌操作子到基因治疗:《细胞》杂志创刊 50 周年
IF 64.5 1区 化学 Q2 CHEMISTRY, PHYSICAL Pub Date : 2024-11-14 DOI: 10.1016/j.cell.2024.10.037
Tom Maniatis
Recombinant DNA technology has profoundly advanced virtually every aspect of biological and medical sciences, from basic research to biotechnology. Here, I discuss conceptual connections linking fundamental discoveries that were enabled by the technology, advances in the understanding of gene regulation in both prokaryotes and eukaryotes, and the recent FDA-approved CRISPR-based gene therapy for sickle cell anemia and β-thalassemia based on transcriptional derepression.
从基础研究到生物技术,DNA 重组技术几乎推动了生物和医学科学的方方面面。在此,我将讨论该技术带来的基础性发现、对原核生物和真核生物基因调控认识的进步,以及最近美国食品与药物管理局批准的基于 CRISPR 技术的基因疗法(基于转录抑制)治疗镰状细胞性贫血和β地中海贫血症之间的概念联系。
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引用次数: 0
Relativistic Prolapse-Free Gaussian Basis Sets of Double- and Triple-ζ Quality for s- and p-Block Elements: (aug-)RPF-2Z and (aug-)RPF-3Z. s 块和 p 块元素的双ζ和三ζ质量的相对论无拖尾高斯基集:(aug-)RPF-2Z 和 (aug-)RPF-3Z.
IF 5.7 1区 化学 Q2 CHEMISTRY, PHYSICAL Pub Date : 2024-11-14 DOI: 10.1021/acs.jctc.4c01211
Julielson Dos Santos Sousa, Eriosvaldo Florentino Gusmão, Anne Kéllen de Nazaré Dos Reis Dias, Roberto Luiz Andrade Haiduke

This study presents two new relativistic Gaussian basis sets without variational prolapse of double- and triple-ζ quality, RPF-2Z and RPF-3Z, along with augmented versions including additional diffuse functions, aug-RPF-2Z and aug-RPF-3Z, which are available for all s and p block elements from Hydrogen to Oganesson. The exponents of the Correlation/Polarization (C/P) functions are obtained from a polynomial version of the generator coordinate Dirac-Fock method (p-GCDF). The choice of C/P functions was guided by multireference configuration interaction calculations with single and double excitations (MR-CISD) based on a valence active space. Finally, calculations of fundamental properties done for atomic and molecular systems (bond lengths, vibrational frequencies, dipole moments, and electron affinities) ensure the expected quality of these new basis sets, which may also exhibit some computational efficiency advantages. Additionally, the prolapse-free feature of these sets must provide a reliable description of properties more dependent on core electron distributions, as well.

本研究提出了两个新的相对论高斯基集,即 RPF-2Z 和 RPF-3Z,以及包括附加扩散函数的增强版本,即 aug-RPF-2Z 和 aug-RPF-3Z,这两个基集无变分增殖,具有双重和三重ζ质量,可用于从氢到奥加内松的所有 s 和 p 块元素。相关/极化(C/P)函数的指数是从生成器坐标狄拉克-福克方法(p-GCDF)的多项式版本中获得的。C/P 函数的选择以基于价活性空间的单激发和双激发的多参量构型相互作用计算(MR-CISD)为指导。最后,对原子和分子系统的基本性质(键长、振动频率、偶极矩和电子亲和力)进行的计算确保了这些新基集的预期质量,它们还可能表现出一定的计算效率优势。此外,这些基集的无脱垂特性也必须能可靠地描述更依赖于核心电子分布的性质。
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引用次数: 0
Determining the N-Representability of a Reduced Density Matrix via Unitary Evolution and Stochastic Sampling. 通过单元演化和随机抽样确定还原密度矩阵的 N 代表性
IF 5.7 1区 化学 Q2 CHEMISTRY, PHYSICAL Pub Date : 2024-11-14 DOI: 10.1021/acs.jctc.4c01166
Gustavo E Massaccesi, Ofelia B Oña, Pablo Capuzzi, Juan I Melo, Luis Lain, Alicia Torre, Juan E Peralta, Diego R Alcoba, Gustavo E Scuseria

The N-representability problem consists in determining whether, for a given p-body matrix, there exists at least one N-body density matrix from which the p-body matrix can be obtained by contraction, that is, if the given matrix is a p-body reduced density matrix (p-RDM). The knowledge of all necessary and sufficient conditions for a p-body matrix to be N-representable allows the constrained minimization of a many-body Hamiltonian expectation value with respect to the p-body density matrix and, thus, the determination of its exact ground state. However, the number of constraints that complete the N-representability conditions grows exponentially with system size, and hence, the procedure quickly becomes intractable for practical applications. This work introduces a hybrid quantum-stochastic algorithm to effectively replace the N-representability conditions. The algorithm consists of applying to an initial N-body density matrix a sequence of unitary evolution operators constructed from a stochastic process that successively approaches the reduced state of the density matrix on a p-body subsystem, represented by a p-RDM, to a target p-body matrix, potentially a p-RDM. The generators of the evolution operators follow the well-known adaptive derivative-assembled pseudo-Trotter method (ADAPT), while the stochastic component is implemented by using a simulated annealing process. The resulting algorithm is independent of any underlying Hamiltonian, and it can be used to decide whether a given p-body matrix is N-representable, establishing a criterion to determine its quality and correcting it. We apply the proposed hybrid ADAPT algorithm to alleged reduced density matrices from a quantum chemistry electronic Hamiltonian, from the reduced Bardeen-Cooper-Schrieffer model with constant pairing, and from the Heisenberg XXZ spin model. In all cases, the proposed method behaves as expected for 1-RDMs and 2-RDMs, evolving the initial matrices toward different targets.

N-可再现性问题包括确定对于给定的 p 体矩阵,是否存在至少一个 N 体密度矩阵,可以通过收缩得到 p 体矩阵,即给定矩阵是否是 p 体还原密度矩阵(p-RDM)。掌握了 p 体矩阵可 N 表示的所有必要条件和充分条件,就可以对相对于 p 体密度矩阵的多体哈密顿期望值进行约束最小化,从而确定其精确基态。然而,完成 N-可表示性条件的约束条件数量随系统规模呈指数增长,因此,该过程在实际应用中很快变得难以处理。这项工作引入了一种量子-随机混合算法,以有效取代 N-可再现性条件。该算法包括对初始 N 体密度矩阵应用一串由随机过程构建的单元演化算子,该随机过程将 p 体子系统上密度矩阵的还原状态(由 p-RDM 表示)连续逼近目标 p 体矩阵(可能是 p-RDM)。演化算子的生成遵循著名的自适应导数组装伪特罗特方法(ADAPT),而随机部分则通过使用模拟退火过程来实现。由此产生的算法与任何底层哈密顿无关,可用于判断给定的 p 体矩阵是否可 N 代表示,建立判断其质量的标准并对其进行修正。我们将提出的混合 ADAPT 算法应用于量子化学电子哈密顿、具有恒定配对的还原巴丁-库珀-施里弗模型以及海森堡 XXZ 自旋模型的据称还原密度矩阵。在所有情况下,拟议方法在 1-RDM 和 2-RDM 中的表现都符合预期,初始矩阵朝着不同的目标演化。
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引用次数: 0
STK19 facilitates the clearance of lesion-stalled RNAPII during transcription-coupled DNA repair STK19 在转录耦合 DNA 修复过程中促进清除病变停滞的 RNAPII
IF 64.5 1区 化学 Q2 CHEMISTRY, PHYSICAL Pub Date : 2024-11-14 DOI: 10.1016/j.cell.2024.10.018
Diana van den Heuvel, Marta Rodríguez-Martínez, Paula J. van der Meer, Nicolas Nieto Moreno, Jiyoung Park, Hyun-Suk Kim, Janne J.M. van Schie, Annelotte P. Wondergem, Areetha D’Souza, George Yakoub, Anna E. Herlihy, Krushanka Kashyap, Thierry Boissière, Jane Walker, Richard Mitter, Katja Apelt, Klaas de Lint, Idil Kirdök, Mats Ljungman, Rob M.F. Wolthuis, Martijn S. Luijsterburg
Transcription-coupled DNA repair (TCR) removes bulky DNA lesions impeding RNA polymerase II (RNAPII) transcription. Recent studies have outlined the stepwise assembly of TCR factors CSB, CSA, UVSSA, and transcription factor IIH (TFIIH) around lesion-stalled RNAPII. However, the mechanism and factors required for the transition to downstream repair steps, including RNAPII removal to provide repair proteins access to the DNA lesion, remain unclear. Here, we identify STK19 as a TCR factor facilitating this transition. Loss of STK19 does not impact initial TCR complex assembly or RNAPII ubiquitylation but delays lesion-stalled RNAPII clearance, thereby interfering with the downstream repair reaction. Cryoelectron microscopy (cryo-EM) and mutational analysis reveal that STK19 associates with the TCR complex, positioning itself between RNAPII, UVSSA, and CSA. The structural insights and molecular modeling suggest that STK19 positions the ATPase subunits of TFIIH onto DNA in front of RNAPII. Together, these findings provide new insights into the factors and mechanisms required for TCR.
转录耦合 DNA 修复(TCR)可清除阻碍 RNA 聚合酶 II(RNAPII)转录的大块 DNA 病变。最近的研究概述了 TCR 因子 CSB、CSA、UVSSA 和转录因子 IIH(TFIIH)围绕病变停滞的 RNAPII 逐步组装的过程。然而,过渡到下游修复步骤(包括移除 RNAPII 以提供修复蛋白进入 DNA 病变)所需的机制和因子仍不清楚。在这里,我们发现 STK19 是促进这一过渡的 TCR 因子。STK19 的缺失不会影响最初的 TCR 复合物组装或 RNAPII 泛素化,但会延迟病变停滞的 RNAPII 清除,从而干扰下游修复反应。低温电子显微镜(cryo-EM)和突变分析表明,STK19 与 TCR 复合物结合,位于 RNAPII、UVSSA 和 CSA 之间。结构洞察和分子建模表明,STK19 将 TFIIH 的 ATPase 亚基定位在 RNAPII 前面的 DNA 上。这些发现共同为 TCR 所需的因素和机制提供了新的见解。
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引用次数: 0
Small and long non-coding RNAs: Past, present, and future 小型和长型非编码 RNA:过去、现在和未来
IF 64.5 1区 化学 Q2 CHEMISTRY, PHYSICAL Pub Date : 2024-11-14 DOI: 10.1016/j.cell.2024.10.024
Ling-Ling Chen, V. Narry Kim
Since the introduction of the central dogma of molecular biology in 1958, various RNA species have been discovered. Messenger RNAs transmit genetic instructions from DNA to make proteins, a process facilitated by housekeeping non-coding RNAs (ncRNAs) such as small nuclear RNAs (snRNAs), ribosomal RNAs (rRNAs), and transfer RNAs (tRNAs). Over the past four decades, a wide array of regulatory ncRNAs have emerged as crucial players in gene regulation. In celebration of Cell’s 50th anniversary, this Review explores our current understanding of the most extensively studied regulatory ncRNAs—small RNAs and long non-coding RNAs (lncRNAs)—which have profoundly shaped the field of RNA biology and beyond. While small RNA pathways have been well documented with clearly defined mechanisms, lncRNAs exhibit a greater diversity of mechanisms, many of which remain unknown. This Review covers pivotal events in their discovery, biogenesis pathways, evolutionary traits, action mechanisms, functions, and crosstalks among ncRNAs. We also highlight their roles in pathophysiological contexts and propose future research directions to decipher the unknowns of lncRNAs by leveraging lessons from small RNAs.
自 1958 年提出分子生物学的核心教条以来,人们发现了各种 RNA 物种。信使核糖核酸(Messenger RNA)将 DNA 的遗传指令传递给蛋白质的制造者,而这一过程则由核小核糖核酸(snRNA)、核糖体核糖核酸(rRNA)和转运核糖核酸(tRNA)等看家非编码核糖核酸(ncRNA)来完成。在过去的四十年中,一系列调控性 ncRNA 已经成为基因调控的关键角色。为庆祝《细胞》杂志创刊 50 周年,本综述探讨了我们目前对研究最广泛的调控 ncRNA--小 RNA 和长非编码 RNA(lncRNA)--的理解,它们深刻地影响了 RNA 生物学及其他领域。小 RNA 通路的机制已被清楚地记录下来,而 lncRNA 则表现出更多样化的机制,其中许多机制仍不为人所知。本综述涵盖了发现它们的关键事件、生物发生途径、进化特征、作用机制、功能以及 ncRNA 之间的交叉关系。我们还强调了它们在病理生理环境中的作用,并提出了未来的研究方向,以利用小 RNA 的经验教训来破解 lncRNA 的未知问题。
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引用次数: 0
Discovery and significance of protein-protein interactions in health and disease 发现健康和疾病中蛋白质与蛋白质之间的相互作用及其意义
IF 64.5 1区 化学 Q2 CHEMISTRY, PHYSICAL Pub Date : 2024-11-14 DOI: 10.1016/j.cell.2024.10.038
Jack F. Greenblatt, Bruce M. Alberts, Nevan J. Krogan
The identification of individual protein-protein interactions (PPIs) began more than 40 years ago, using protein affinity chromatography and antibody co-immunoprecipitation. As new technologies emerged, analysis of PPIs increased to a genome-wide scale with the introduction of intracellular tagging methods, affinity purification (AP) followed by mass spectrometry (MS), and co-fractionation MS (CF-MS). Now, combining the resulting catalogs of interactions with complementary methods, including crosslinking MS (XL-MS) and cryogenic electron microscopy (cryo-EM), helps distinguish direct interactions from indirect ones within the same or between different protein complexes. These powerful approaches and the promise of artificial intelligence applications like AlphaFold herald a future where PPIs and protein complexes, including energy-driven protein machines, will be understood in exquisite detail, unlocking new insights in the contexts of both basic biology and disease.
单个蛋白质-蛋白质相互作用(PPIs)的鉴定始于 40 多年前,当时使用的是蛋白质亲和层析法和抗体共沉淀法。随着新技术的出现,细胞内标记方法、亲和纯化(AP)后质谱分析(MS)以及共沉淀质谱分析(CF-MS)的引入,PPIs 的分析扩展到了全基因组范围。现在,将由此产生的相互作用目录与交联质谱(XL-MS)和低温电子显微镜(cryo-EM)等补充方法相结合,有助于区分同一蛋白质复合物内部或不同蛋白质复合物之间的直接相互作用和间接相互作用。这些强大的方法以及人工智能应用(如 AlphaFold)的前景预示着,在未来,PPIs 和蛋白质复合物(包括能量驱动的蛋白质机器)将被详细了解,从而为基础生物学和疾病研究带来新的启示。
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引用次数: 0
The ribosome comes to life 核糖体焕发生机
IF 64.5 1区 化学 Q2 CHEMISTRY, PHYSICAL Pub Date : 2024-11-14 DOI: 10.1016/j.cell.2024.10.035
Harry F. Noller
The ribosome, together with its tRNA substrates, links genotype to phenotype by translating the genetic information carried by mRNA into protein. During the past half-century, the structure and mechanisms of action of the ribosome have emerged from mystery and confusion. It is now evident that the ribosome is an ancient RNA-based molecular machine of staggering structural complexity and that it is fundamentally similar in all living organisms. The three central functions of protein synthesis—decoding, catalysis of peptide bond formation, and translocation of mRNA and tRNA—are based on elegant mechanisms that evolved from the properties of RNA, the founding macromolecule of life. Moreover, all three of these functions (and even life itself) seem to proceed in defiance of entropy. Protein synthesis thus appears to exploit both the energy of GTP hydrolysis and peptide bond formation to constrain the directionality and accuracy of events taking place on the ribosome.
核糖体及其 tRNA 底物将 mRNA 所携带的遗传信息转化为蛋白质,从而将基因型与表型联系起来。在过去的半个世纪里,核糖体的结构和作用机理已经从神秘和混乱中走了出来。现在我们可以清楚地看到,核糖体是一种古老的以 RNA 为基础的分子机器,其结构的复杂程度令人吃惊,而且它在所有生物体中都基本相似。蛋白质合成的三大核心功能--解码、肽键形成催化以及 mRNA 和 tRNA 的转运--都是基于优雅的机制,这些机制是从生命的基础大分子 RNA 的特性中演化而来的。此外,所有这三种功能(甚至生命本身)似乎都是在熵的作用下进行的。因此,蛋白质合成似乎利用了 GTP 水解和肽键形成的能量来限制核糖体上发生的事件的方向性和准确性。
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引用次数: 0
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Journal of Chemical Theory and Computation
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