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RNA polymerases reshape chromatin architecture and couple transcription on individual fibers. RNA 聚合酶重塑染色质结构,并将转录耦合到单个纤维上。
IF 14.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-05 Epub Date: 2024-08-26 DOI: 10.1016/j.molcel.2024.08.013
Thomas W Tullius, R Stefan Isaac, Danilo Dubocanin, Jane Ranchalis, L Stirling Churchman, Andrew B Stergachis

RNA polymerases must initiate and pause within a complex chromatin environment, surrounded by nucleosomes and other transcriptional machinery. This environment creates a spatial arrangement along individual chromatin fibers ripe for both competition and coordination, yet these relationships remain largely unknown owing to the inherent limitations of traditional structural and sequencing methodologies. To address this, we employed long-read chromatin fiber sequencing (Fiber-seq) in Drosophila to visualize RNA polymerase (Pol) within its native chromatin context with single-molecule precision along up to 30 kb fibers. We demonstrate that Fiber-seq enables the identification of individual Pol II, nucleosome, and transcription factor footprints, revealing Pol II pausing-driven destabilization of downstream nucleosomes. Furthermore, we demonstrate pervasive direct distance-dependent transcriptional coupling between nearby Pol II genes, Pol III genes, and transcribed enhancers, modulated by local chromatin architecture. Overall, transcription initiation reshapes surrounding nucleosome architecture and couples nearby transcriptional machinery along individual chromatin fibers.

RNA 聚合酶必须在复杂的染色质环境中启动和暂停,周围环绕着核糖体和其他转录机制。这种环境形成了沿染色质纤维的空间排列,竞争和协调的条件已经成熟,但由于传统结构和测序方法的固有局限性,这些关系在很大程度上仍不为人所知。为了解决这个问题,我们在果蝇中采用了长线程染色质纤维测序(Fiber-seq)技术,以单分子精度沿长达30 kb的纤维观察RNA聚合酶(Pol)在其原生染色质环境中的情况。我们证明了纤维-质谱能够识别单个 Pol II、核小体和转录因子的足迹,揭示了 Pol II 暂停驱动的下游核小体失稳。此外,我们还证明了附近的 Pol II 基因、Pol III 基因和转录增强子之间普遍存在直接的距离依赖性转录耦合,并受局部染色质结构的调节。总之,转录起始重塑了周围的核小体结构,并使附近的转录机制沿着单个染色质纤维耦合。
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引用次数: 0
Proteasomes safeguard the plant stress granule homeostasis 蛋白酶体保障植物应激颗粒的平衡
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-05 DOI: 10.1016/j.molcel.2024.08.011
Qi Chen, Xiaoxin Chen, Peiguo Yang

In this issue of Molecular Cell, Xie et al.1 revealed that the proteasome is a constitutive component of plant stress granules (SGs), and that enhanced proteolytic activity is essential for efficient SG disassembly and plant survival during the stress response.

在本期的《分子细胞》(Molecular Cell)杂志上,Xie 等人1揭示了蛋白酶体是植物胁迫颗粒(SGs)的组成成分,在胁迫响应期间,蛋白酶体活性的增强对 SG 的有效解体和植物的存活至关重要。
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引用次数: 0
Mechanisms controlling replication fork stalling and collapse at topoisomerase 1 cleavage complexes 控制拓扑异构酶 1 分裂复合物复制叉停滞和崩溃的机制
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-04 DOI: 10.1016/j.molcel.2024.08.004
Rose Westhorpe, Johann J. Roske, Joseph T.P. Yeeles

Topoisomerase 1 cleavage complexes (Top1-ccs) comprise a DNA-protein crosslink and a single-stranded DNA break that can significantly impact the DNA replication machinery (replisome). Consequently, inhibitors that trap Top1-ccs are used extensively in research and clinical settings to generate DNA replication stress, yet how the replisome responds upon collision with a Top1-cc remains obscure. By reconstituting collisions between budding yeast replisomes, assembled from purified proteins, and site-specific Top1-ccs, we have uncovered mechanisms underlying replication fork stalling and collapse. We find that stalled replication forks are surprisingly stable and that their stability is influenced by the template strand that Top1 is crosslinked to, the fork protection complex proteins Tof1-Csm3 (human TIMELESS-TIPIN), and the convergence of replication forks. Moreover, nascent-strand mapping and cryoelectron microscopy (cryo-EM) of stalled forks establishes replisome remodeling as a key factor in the initial response to Top1-ccs. These findings have important implications for the use of Top1 inhibitors in research and in the clinic.

拓扑异构酶 1 分裂复合物(Top1-ccs)由 DNA 蛋白交联和单链 DNA 断裂组成,可对 DNA 复制机制(复制体)产生重大影响。因此,捕获 Top1-ccs 的抑制剂被广泛用于研究和临床环境中,以产生 DNA 复制压力,但复制体在与 Top1-cc 碰撞时如何反应仍不清楚。通过重构由纯化蛋白组装而成的芽殖酵母复制体与特定位点的 Top1-cc 之间的碰撞,我们发现了复制叉停滞和崩溃的内在机制。我们发现,停滞的复制叉出奇地稳定,而且其稳定性受到 Top1 交联的模板链、叉保护复合体蛋白 Tof1-Csm3(人类 TIMELESS-TIPIN)以及复制叉汇聚的影响。此外,停滞叉的新生链图谱和低温电子显微镜(cryo-EM)证实,复制体重塑是对 Top1-ccs 最初反应的关键因素。这些发现对 Top1 抑制剂在研究和临床中的应用具有重要意义。
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引用次数: 0
The high-light-sensitivity mechanism and optogenetic properties of the bacteriorhodopsin-like channelrhodopsin GtCCR4 类细菌视紫红质通道视紫红质 GtCCR4 的高光敏机制和光遗传特性
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-03 DOI: 10.1016/j.molcel.2024.08.016
Tatsuki Tanaka, Shoko Hososhima, Yo Yamashita, Teppei Sugimoto, Toshiki Nakamura, Shunta Shigemura, Wataru Iida, Fumiya K. Sano, Kazumasa Oda, Takayuki Uchihashi, Kota Katayama, Yuji Furutani, Satoshi P. Tsunoda, Wataru Shihoya, Hideki Kandori, Osamu Nureki

Channelrhodopsins are microbial light-gated ion channels that can control the firing of neurons in response to light. Among several cation channelrhodopsins identified in Guillardia theta (GtCCRs), GtCCR4 has higher light sensitivity than typical channelrhodopsins. Furthermore, GtCCR4 shows superior properties as an optogenetic tool, such as minimal desensitization. Our structural analyses of GtCCR2 and GtCCR4 revealed that GtCCR4 has an outwardly bent transmembrane helix, resembling the conformation of activated G-protein-coupled receptors. Spectroscopic and electrophysiological comparisons suggested that this helix bend in GtCCR4 omits channel recovery time and contributes to high light sensitivity. An electrophysiological comparison of GtCCR4 and the well-characterized optogenetic tool ChRmine demonstrated that GtCCR4 has superior current continuity and action-potential spike generation with less invasiveness in neurons. We also identified highly active mutants of GtCCR4. These results shed light on the diverse structures and dynamics of microbial rhodopsins and demonstrate the strong optogenetic potential of GtCCR4.

通道闪烁蛋白是微生物的光门控离子通道,可以控制神经元对光的反应而发射。在Guillardia theta(GtCCRs)中发现的几种阳离子通道闪烁蛋白中,GtCCR4比典型的通道闪烁蛋白具有更高的光敏感性。此外,作为光遗传工具,GtCCR4 还显示出卓越的特性,如最小脱敏。我们对 GtCCR2 和 GtCCR4 的结构分析表明,GtCCR4 有一个向外弯曲的跨膜螺旋,类似于激活的 G 蛋白偶联受体的构象。光谱学和电生理学比较表明,GtCCR4 的这种螺旋弯曲省略了通道恢复时间,有助于提高光敏感性。对 GtCCR4 和特性良好的光遗传工具 ChRmine 的电生理学比较表明,GtCCR4 具有更优越的电流连续性和动作电位尖峰产生能力,对神经元的侵袭性更小。我们还发现了 GtCCR4 的高活性突变体。这些结果揭示了微生物视紫红质的不同结构和动力学,并证明了 GtCCR4 强大的光遗传潜力。
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引用次数: 0
Disorder-mediated interactions target proteins to specific condensates 无序介导的相互作用将蛋白质锁定在特定凝聚物上
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-03 DOI: 10.1016/j.molcel.2024.08.017
Nancy De La Cruz, Prashant Pradhan, Reshma T. Veettil, Brooke A. Conti, Mariano Oppikofer, Benjamin R. Sabari

Selective compartmentalization of cellular contents is fundamental to the regulation of biochemistry. Although membrane-bound organelles control composition by using a semi-permeable barrier, biomolecular condensates rely on interactions among constituents to determine composition. Condensates are formed by dynamic multivalent interactions, often involving intrinsically disordered regions (IDRs) of proteins, yet whether distinct compositions can arise from these dynamic interactions is not known. Here, by comparative analysis of proteins differentially partitioned by two different condensates, we find that distinct compositions arise through specific IDR-mediated interactions. The IDRs of differentially partitioned proteins are necessary and sufficient for selective partitioning. Distinct sequence features are required for IDRs to partition, and swapping these sequence features changes the specificity of partitioning. Swapping whole IDRs retargets proteins and their biochemical activity to different condensates. Our results demonstrate that IDR-mediated interactions can target proteins to specific condensates, enabling the spatial regulation of biochemistry within the cell.

细胞内容物的选择性分隔是调节生物化学的基础。虽然膜结合细胞器利用半透屏障控制成分,但生物分子凝聚体则依靠成分之间的相互作用来决定成分。凝结物是由动态多价相互作用形成的,通常涉及蛋白质的固有无序区(IDR),但这些动态相互作用是否会产生不同的成分尚不清楚。在这里,我们通过对两种不同凝聚物中不同分区的蛋白质进行比较分析,发现不同的组成是通过特定的 IDR 介导的相互作用产生的。不同分区蛋白质的 IDR 是选择性分区的必要条件和充分条件。IDR需要不同的序列特征才能分区,而交换这些序列特征会改变分区的特异性。交换整个 IDR 可将蛋白质及其生化活性重新定向到不同的凝聚物中。我们的研究结果表明,IDR 介导的相互作用可将蛋白质定向到特定的凝聚体,从而实现细胞内生化的空间调控。
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引用次数: 0
PICKLE-mediated nucleosome condensing drives H3K27me3 spreading for the inheritance of Polycomb memory during differentiation PICKLE介导的核小体缩聚驱动H3K27me3扩散,从而在分化过程中继承多角体记忆
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-03 DOI: 10.1016/j.molcel.2024.08.018
Zhenwei Liang, Tao Zhu, Yaoguang Yu, Caihong Wu, Yisui Huang, Yuanhao Hao, Xin Song, Wei Fu, Liangbing Yuan, Yuhai Cui, Shangzhi Huang, Chenlong Li

Spreading of H3K27me3 is crucial for the maintenance of mitotically inheritable Polycomb-mediated chromatin silencing in animals and plants. However, how Polycomb repressive complex 2 (PRC2) accesses unmodified nucleosomes in spreading regions for spreading H3K27me3 remains unclear. Here, we show in Arabidopsis thaliana that the chromatin remodeler PICKLE (PKL) plays a specialized role in H3K27me3 spreading to safeguard cell identity during differentiation. PKL specifically localizes to H3K27me3 spreading regions but not to nucleation sites and physically associates with PRC2. Loss of PKL disrupts the occupancy of the PRC2 catalytic subunit CLF in spreading regions and leads to aberrant dedifferentiation. Nucleosome density increase endowed by the ATPase function of PKL ensures that unmodified nucleosomes are accessible to PRC2 catalytic activity for H3K27me3 spreading. Our findings demonstrate that PKL-dependent nucleosome compaction is critical for PRC2-mediated H3K27me3 read-and-write function in H3K27me3 spreading, thus revealing a mechanism by which repressive chromatin domains are established and propagated.

在动物和植物中,H3K27me3的扩散对于维持有丝分裂可遗传的多角体介导的染色质沉默至关重要。然而,Polycomb抑制复合体2(PRC2)如何在扩散区域获得未修饰的核小体以扩散H3K27me3仍不清楚。在这里,我们在拟南芥中发现,染色质重塑因子 PICKLE(PKL)在 H3K27me3 扩增过程中发挥着特殊作用,以保护分化过程中的细胞特性。PKL特异性地定位在H3K27me3扩散区域,而不是成核位点,并与PRC2发生物理结合。PKL的缺失会破坏PRC2催化亚基CLF在扩增区域的占据,并导致异常的去分化。PKL的ATP酶功能提高了核小体密度,确保了PRC2催化活性可以获得未修饰的核小体,以进行H3K27me3扩增。我们的研究结果表明,依赖于PKL的核小体压实对于PRC2在H3K27me3扩散过程中介导的H3K27me3读写功能至关重要,从而揭示了抑制性染色质域的建立和传播机制。
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引用次数: 0
Stabilization of the hexasome intermediate during histone exchange by yeast SWR1 complex 酵母 SWR1 复合物在组蛋白交换过程中稳定六聚体中间体
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-09-02 DOI: 10.1016/j.molcel.2024.08.015
Adam S.B. Jalal, Paul Girvan, Eugene Y.D. Chua, Lexin Liu, Shijie Wang, Elizabeth A. McCormack, Michael T. Skehan, Carol L. Knight, David S. Rueda, Dale B. Wigley

The yeast SWR1 complex catalyzes the exchange of histone H2A/H2B dimers in nucleosomes with Htz1/H2B dimers. We use cryoelectron microscopy to determine the structure of an enzyme-bound hexasome intermediate in the reaction pathway of histone exchange, in which an H2A/H2B dimer has been extracted from a nucleosome prior to the insertion of a dimer comprising Htz1/H2B. The structure reveals a key role for the Swc5 subunit in stabilizing the unwrapping of DNA from the histone core of the hexasome. By engineering a crosslink between an Htz1/H2B dimer and its chaperone protein Chz1, we show that this blocks histone exchange by SWR1 but allows the incoming chaperone-dimer complex to insert into the hexasome. We use this reagent to trap an SWR1/hexasome complex with an incoming Htz1/H2B dimer that shows how the reaction progresses to the next step. Taken together the structures reveal insights into the mechanism of histone exchange by SWR1 complex.

酵母 SWR1 复合物催化核小体中组蛋白 H2A/H2B 二聚体与 Htz1/H2B 二聚体的交换。我们利用冷冻电子显微镜确定了组蛋白交换反应途径中酶结合六聚体中间体的结构,在该中间体中,H2A/H2B二聚体在插入由Htz1/H2B组成的二聚体之前已从核小体中提取出来。该结构揭示了 Swc5 亚基在稳定 DNA 从六聚体的组蛋白核心解开方面的关键作用。通过在 Htz1/H2B 二聚体和它的伴侣蛋白 Chz1 之间建立交联,我们发现这阻止了 SWR1 的组蛋白交换,但允许进入的伴侣蛋白二聚体复合物插入六聚体。我们用这种试剂捕获了一个带有进入的 Htz1/H2B 二聚体的 SWR1/六聚体复合物,展示了反应如何进行到下一步。总之,这些结构揭示了 SWR1 复合物交换组蛋白的机制。
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引用次数: 0
Genome access is transcription factor-specific and defined by nucleosome position 基因组访问是转录因子特异性的,由核小体位置决定
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-08-28 DOI: 10.1016/j.molcel.2024.08.009
Ralph Stefan Grand, Marco Pregnolato, Lisa Baumgartner, Leslie Hoerner, Lukas Burger, Dirk Schübeler

Mammalian gene expression is controlled by transcription factors (TFs) that engage sequence motifs in a chromatinized genome, where nucleosomes can restrict DNA access. Yet, how nucleosomes affect individual TFs remains unclear. Here, we measure the ability of over one hundred TF motifs to recruit TFs in a defined chromosomal locus in mouse embryonic stem cells. This identifies a set sufficient to enable the binding of TFs with diverse tissue specificities, functions, and DNA-binding domains. These chromatin-competent factors are further classified when challenged to engage motifs within a highly phased nucleosome. The pluripotency factors OCT4-SOX2 preferentially engage non-nucleosomal and entry-exit motifs, but not nucleosome-internal sites, a preference that also guides binding genome wide. By contrast, factors such as BANP, REST, or CTCF engage throughout, causing nucleosomal displacement. This supports that TFs vary widely in their sensitivity to nucleosomes and that genome access is TF specific and influenced by nucleosome position in the cell.

哺乳动物的基因表达受转录因子(TFs)的控制,TFs 与染色质化基因组中的序列基序结合,核小体可限制 DNA 的进入。然而,核小体如何影响单个转录因子仍不清楚。在这里,我们测量了小鼠胚胎干细胞中一百多个TF基序在一个确定的染色体位点上招募TF的能力。这确定了一组足以使具有不同组织特异性、功能和DNA结合域的TF结合的因子。这些染色质功能因子在与高度相位化的核小体中的基序结合时会被进一步分类。多能因子 OCT4-SOX2 优先与非核糖体和进入-退出基序结合,但不与核糖体内部位点结合,这种偏好也会引导基因组范围内的结合。与此相反,BANP、REST 或 CTCF 等因子则在整个基因组中参与,导致核糖体移位。这证明TF对核糖体的敏感性差异很大,基因组的进入是TF特异性的,并受核糖体在细胞中位置的影响。
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引用次数: 0
Histone chaperone HIRA, promyelocytic leukemia protein, and p62/SQSTM1 coordinate to regulate inflammation during cell senescence 组蛋白伴侣 HIRA、早幼粒细胞白血病蛋白和 p62/SQSTM1 协调调节细胞衰老过程中的炎症反应
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-08-22 DOI: 10.1016/j.molcel.2024.08.006
Nirmalya Dasgupta, Xue Lei, Christina Huan Shi, Rouven Arnold, Marcos G. Teneche, Karl N. Miller, Adarsh Rajesh, Andrew Davis, Valesca Anschau, Alexandre R. Campos, Rebecca Gilson, Aaron Havas, Shanshan Yin, Zong Ming Chua, Tianhui Liu, Jessica Proulx, Michael Alcaraz, Mohammed Iqbal Rather, Josue Baeza, David C. Schultz, Peter D. Adams

Cellular senescence, a stress-induced stable proliferation arrest associated with an inflammatory senescence-associated secretory phenotype (SASP), is a cause of aging. In senescent cells, cytoplasmic chromatin fragments (CCFs) activate SASP via the anti-viral cGAS/STING pathway. Promyelocytic leukemia (PML) protein organizes PML nuclear bodies (NBs), which are also involved in senescence and anti-viral immunity. The HIRA histone H3.3 chaperone localizes to PML NBs in senescent cells. Here, we show that HIRA and PML are essential for SASP expression, tightly linked to HIRA’s localization to PML NBs. Inactivation of HIRA does not directly block expression of nuclear factor κB (NF-κB) target genes. Instead, an H3.3-independent HIRA function activates SASP through a CCF-cGAS-STING-TBK1-NF-κB pathway. HIRA physically interacts with p62/SQSTM1, an autophagy regulator and negative SASP regulator. HIRA and p62 co-localize in PML NBs, linked to their antagonistic regulation of SASP, with PML NBs controlling their spatial configuration. These results outline a role for HIRA and PML in the regulation of SASP.

细胞衰老是一种压力诱导的稳定增殖停滞,与炎症性衰老相关分泌表型(SASP)有关,是衰老的原因之一。在衰老细胞中,细胞质染色质片段(CCF)通过抗病毒 cGAS/STING 途径激活 SASP。早幼粒细胞白血病(PML)蛋白组织 PML 核体(NBs),后者也参与衰老和抗病毒免疫。HIRA组蛋白H3.3伴侣蛋白定位于衰老细胞中的PML核体。在这里,我们发现 HIRA 和 PML 对于 SASP 的表达至关重要,这与 HIRA 定位于 PML NB 紧密相关。HIRA的失活不会直接阻断核因子κB(NF-κB)靶基因的表达。相反,独立于 H3.3 的 HIRA 功能通过 CCF-cGAS-STING-TBK1-NF-κB 途径激活 SASP。HIRA 与自噬调节因子和 SASP 负调节因子 p62/SQSTM1 存在物理相互作用。HIRA 和 p62 共同定位在 PML NB 中,这与它们对 SASP 的拮抗调控有关,PML NB 控制着它们的空间配置。这些结果概述了HIRA和PML在SASP调控中的作用。
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引用次数: 0
An intrinsically disordered region in MED13 turns Mediator on/off on cue MED13 中的一个内在无序区根据提示开启/关闭 Mediator
IF 16 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-08-22 DOI: 10.1016/j.molcel.2024.07.027
Vincent Villeret, Didier Monté, Alexis Verger

Complementary studies by Zhao et al.1 and Chen et al.2 reveal how an intrinsically disordered region in MED13 controls mutually exclusive binding of RNA Polymerase II and CDK8 kinase module to Mediator, switching Mediator and transcription activation on and off.

Zhao 等人1 和 Chen 等人2 的互补研究揭示了 MED13 中的一个固有紊乱区如何控制 RNA 聚合酶 II 和 CDK8 激酶模块与 Mediator 的互斥结合,从而开关 Mediator 和转录激活。
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引用次数: 0
期刊
Molecular Cell
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