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A group 3 medulloblastoma stem cell program is maintained by OTX2-mediated alternative splicing 第3组髓母细胞瘤干细胞程序由OTX2介导的替代剪接维持。
IF 17.3 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-07-18 DOI: 10.1038/s41556-024-01460-5
Olivier Saulnier, Jamie Zagozewski, Lisa Liang, Liam D. Hendrikse, Paul Layug, Victor Gordon, Kimberly A. Aldinger, Parthiv Haldipur, Stephanie Borlase, Ludivine Coudière-Morrison, Ting Cai, Emma Martell, Naomi M. Gonzales, Gareth Palidwor, Christopher J. Porter, Stéphane Richard, Tanveer Sharif, Kathleen J. Millen, Brad W. Doble, Michael D. Taylor, Tamra E. Werbowetski-Ogilvie
OTX2 is a transcription factor and known driver in medulloblastoma (MB), where it is amplified in a subset of tumours and overexpressed in most cases of group 3 and group 4 MB. Here we demonstrate a noncanonical role for OTX2 in group 3 MB alternative splicing. OTX2 associates with the large assembly of splicing regulators complex through protein–protein interactions and regulates a stem cell splicing program. OTX2 can directly or indirectly bind RNA and this may be partially independent of its DNA regulatory functions. OTX2 controls a pro-tumorigenic splicing program that is mirrored in human cerebellar rhombic lip origins. Among the OTX2-regulated differentially spliced genes, PPHLN1 is expressed in the most primitive rhombic lip stem cells, and targeting PPHLN1 splicing reduces tumour growth and enhances survival in vivo. These findings identify OTX2-mediated alternative splicing as a major determinant of cell fate decisions that drive group 3 MB progression. Werbowetski-Ogilvie, Taylor and colleagues report a noncanonical role for OTX2 in regulating alternative splicing and controlling a stem cell and pro-tumorigenic splicing program in group 3 medulloblastoma.
OTX2 是一种转录因子,也是髓母细胞瘤(MB)的已知驱动因子,它在一部分肿瘤中扩增,并在第 3 组和第 4 组 MB 的大多数病例中过表达。在这里,我们证明了 OTX2 在第 3 组 MB 替代剪接中的非规范作用。OTX2 通过蛋白质与蛋白质之间的相互作用与剪接调节器大集合复合物结合,并调节干细胞剪接程序。OTX2 可直接或间接结合 RNA,这可能部分独立于其 DNA 调控功能。OTX2控制着一种促肿瘤性剪接程序,这种程序在人类小脑菱形唇起源中得到反映。在OTX2调控的不同剪接基因中,PPHLN1在最原始的菱形唇干细胞中表达,针对PPHLN1的剪接可减少肿瘤生长并提高体内存活率。这些研究结果表明,OTX2 介导的替代剪接是细胞命运决定的主要决定因素,而细胞命运决定是第 3 组 MB 进展的驱动力。
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引用次数: 0
Zeb1 mediates EMT/plasticity-associated ferroptosis sensitivity in cancer cells by regulating lipogenic enzyme expression and phospholipid composition Zeb1 通过调控生脂酶的表达和磷脂组成,介导癌细胞对 EMT/可塑性相关铁中毒的敏感性
IF 17.3 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-07-15 DOI: 10.1038/s41556-024-01464-1
Annemarie Schwab, Zhigang Rao, Jie Zhang, André Gollowitzer, Katharina Siebenkäs, Nino Bindel, Elisabetta D’Avanzo, Ruthger van Roey, Yussuf Hajjaj, Ece Özel, Isabell Armstark, Leonhard Bereuter, Fengting Su, Julia Grander, Ehsan Bonyadi Rad, Arwin Groenewoud, Felix B. Engel, George W. Bell, Whitney S. Henry, José Pedro Friedmann Angeli, Marc P. Stemmler, Simone Brabletz, Andreas Koeberle, Thomas Brabletz
Therapy resistance and metastasis, the most fatal steps in cancer, are often triggered by a (partial) activation of the epithelial–mesenchymal transition (EMT) programme. A mesenchymal phenotype predisposes to ferroptosis, a cell death pathway exerted by an iron and oxygen-radical-mediated peroxidation of phospholipids containing polyunsaturated fatty acids. We here show that various forms of EMT activation, including TGFβ stimulation and acquired therapy resistance, increase ferroptosis susceptibility in cancer cells, which depends on the EMT transcription factor Zeb1. We demonstrate that Zeb1 increases the ratio of phospholipids containing pro-ferroptotic polyunsaturated fatty acids over cyto-protective monounsaturated fatty acids by modulating the differential expression of the underlying crucial enzymes stearoyl-Co-A desaturase 1 (SCD), fatty acid synthase (FASN), fatty acid desaturase 2 (FADS2), elongation of very long-chain fatty acid 5 (ELOVL5) and long-chain acyl-CoA synthetase 4 (ACSL4). Pharmacological inhibition of selected lipogenic enzymes (SCD and FADS2) allows the manipulation of ferroptosis sensitivity preferentially in high-Zeb1-expressing cancer cells. Our data are of potential translational relevance and suggest a combination of ferroptosis activators and SCD inhibitors for the treatment of aggressive cancers expressing high Zeb1. Schwab, Rao et al. report that Zeb1 mediates enhanced ferroptosis sensitivity in cancer cells after EMT activation, associated with altered expression of selected lipogenic enzymes and an subsequent increase in the PUFA:MUFA ratio.
抗药性和转移是癌症中最致命的步骤,通常由(部分)激活上皮-间质转化(EMT)程序引发。间充质表型容易发生铁变态反应,铁变态反应是由铁和氧自由基介导的含有多不饱和脂肪酸的磷脂过氧化作用所产生的细胞死亡途径。我们在此表明,各种形式的 EMT 激活(包括 TGFβ 刺激和获得性耐药性)会增加癌细胞对铁中毒的易感性,而这种易感性取决于 EMT 转录因子 Zeb1。我们证明,Zeb1 通过调节基本关键酶硬脂酰-Co-A 去饱和酶 1(SCD)、脂肪酸合成酶(FASN)、脂肪酸去饱和酶 2(FADS2)、超长链脂肪酸伸长 5(ELOVL5)和长链酰基-CoA 合成酶 4(ACSL4)的差异表达,增加了含有促铁蛋白生成的多不饱和脂肪酸的磷脂比例,而非具有细胞保护作用的单不饱和脂肪酸。通过药理抑制选定的生脂酶(SCD 和 FADS2),可优先操纵高 Zeb1 表达癌细胞的铁突变敏感性。我们的数据具有潜在的转化意义,并建议结合使用铁蛋白沉积激活剂和 SCD 抑制剂来治疗高 Zeb1 表达的侵袭性癌症。
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引用次数: 0
The autophagy adaptor TRIAD3A promotes tau fibrillation by nested phase separation 自噬适配体TRIAD3A通过嵌套相分离促进tau纤维化
IF 17.3 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-07-15 DOI: 10.1038/s41556-024-01461-4
Jiechao Zhou, Yang ‘an Chuang, Javier Redding-Ochoa, Rongzhen Zhang, Alexander J. Platero, Alexander H. Barrett, Juan C. Troncoso, Paul F. Worley, Wenchi Zhang
Multiple neurodegenerative diseases are characterized by aberrant proteinaceous accumulations of tau. Here, we report a RING-in-between-RING-type E3 ligase, TRIAD3A, that functions as an autophagy adaptor for tau. TRIAD3A(RNF216) is an essential gene with mutations causing age-progressive neurodegeneration. Our studies reveal that TRIAD3A E3 ligase catalyses mixed K11/K63 polyubiquitin chains and self-assembles into liquid–liquid phase separated (LLPS) droplets. Tau is ubiquitinated and accumulates within TRIAD3A LLPS droplets and, via LC3 interacting regions, targets tau for autophagic degradation. Unexpectedly, tau sequestered within TRIAD3A droplets rapidly converts to fibrillar aggregates without the transitional liquid phase of tau. In vivo studies show that TRIAD3A decreases the accumulation of phosphorylated tau in a tauopathy mouse model, and a disease-associated mutation of TRIAD3A increases accumulation of phosphorylated tau, exacerbates gliosis and increases pathological tau spreading. In human Alzheimer disease brain, TRIAD3A co-localizes with tau amyloid in multiple histological forms, suggesting a role in tau proteostasis. TRIAD3A is an autophagic adaptor that utilizes E3 ligase and LLPS as a mechanism to capture cargo and appears especially relevant to neurodegenerative diseases. Zhou et al. show that the E3 ubiquitin ligase TRIAD3A assembles into liquid–liquid phase-separated droplets that contain tau and promote conversion to fibrillar aggregates and tau autophagic degradation.
多种神经退行性疾病的特征是 tau 蛋白质的异常积累。在这里,我们报告了一种 RING-in-between-RING 型 E3 连接酶 TRIAD3A,它可作为 tau 的自噬适配体发挥作用。TRIAD3A(RNF216)是一个重要基因,其突变可导致年龄进行性神经退行性变。我们的研究发现,TRIAD3A E3连接酶能催化混合的K11/K63多泛素链,并自组装成液相-液相分离(LLPS)液滴。Tau被泛素化并聚集在TRIAD3A LLPS液滴中,并通过LC3相互作用区将tau作为自噬降解的靶标。意想不到的是,螯合在TRIAD3A液滴中的tau会迅速转化为纤维状聚集体,而不会出现tau的过渡液相。体内研究表明,TRIAD3A 可减少磷酸化 tau 在一种 tauopathy 小鼠模型中的积累,而与疾病相关的 TRIAD3A 基因突变会增加磷酸化 tau 的积累,加剧胶质病变并增加病理 tau 的扩散。在人类阿尔茨海默病大脑中,TRIAD3A以多种组织学形式与tau淀粉样蛋白共定位,表明其在tau蛋白稳态中发挥作用。TRIAD3A是一种自噬适配体,利用E3连接酶和LLPS作为捕获货物的机制,似乎与神经退行性疾病特别相关。
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引用次数: 0
Pressure sensing of lysosomes enables control of TFEB responses in macrophages 溶酶体的压力感应可控制巨噬细胞中的 TFEB 反应
IF 17.3 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-07-12 DOI: 10.1038/s41556-024-01459-y
Ruiqi Cai, Ori Scott, Gang Ye, Trieu Le, Ekambir Saran, Whijin Kwon, Subothan Inpanathan, Blayne A. Sayed, Roberto J. Botelho, Amra Saric, Stefan Uderhardt, Spencer A. Freeman
Polymers are endocytosed and hydrolysed by lysosomal enzymes to generate transportable solutes. While the transport of diverse organic solutes across the plasma membrane is well studied, their necessary ongoing efflux from the endocytic fluid into the cytosol is poorly appreciated by comparison. Myeloid cells that employ specialized types of endocytosis, that is, phagocytosis and macropinocytosis, are highly dependent on such transport pathways to prevent the build-up of hydrostatic pressure that otherwise offsets lysosomal dynamics including vesiculation, tubulation and fission. Without undergoing rupture, we found that lysosomes incurring this pressure owing to defects in solute efflux, are unable to retain luminal Na+, which collapses its gradient with the cytosol. This cation ‘leak’ is mediated by pressure-sensitive channels resident to lysosomes and leads to the inhibition of mTORC1, which is normally activated by Na+-coupled amino acid transporters driven by the Na+ gradient. As a consequence, the transcription factors TFEB/TFE3 are made active in macrophages with distended lysosomes. In addition to their role in lysosomal biogenesis, TFEB/TFE3 activation causes the release of MCP-1/CCL2. In catabolically stressed tissues, defects in efflux of solutes from the endocytic pathway leads to increased monocyte recruitment. Here we propose that macrophages respond to a pressure-sensing pathway on lysosomes to orchestrate lysosomal biogenesis as well as myeloid cell recruitment. Cai et al. show that, in lysosomes under hydrostatic pressure in macrophages, lysosomal mechanosensitive channels cause a cation leak. This leads to the inhibition of mTORC1, activation of TFEB/TFE3 and release of monocyte chemoattractant proteins.
聚合物被内吞并被溶酶体酶水解,生成可运输的溶质。虽然对各种有机溶质通过质膜的运输进行了深入研究,但与之相比,对它们从内吞液持续流出到细胞质的必要性却知之甚少。采用特殊类型内吞作用(即吞噬和大蛋白内吞作用)的髓样细胞高度依赖这种转运途径来防止静水压的积累,否则就会抵消溶酶体的活力,包括囊泡化、管化和裂解。我们发现,溶酶体在不发生破裂的情况下,由于溶质外流缺陷而产生的这种压力无法保留管腔内的 Na+,从而使其与细胞质之间的梯度崩溃。这种阳离子 "泄漏 "是由常驻溶酶体的压力敏感通道介导的,并导致抑制 mTORC1,而 mTORC1 通常是由 Na+ 梯度驱动的 Na+ 偶联氨基酸转运体激活的。因此,转录因子 TFEB/TFE3 在溶酶体膨胀的巨噬细胞中变得活跃。除了在溶酶体生物生成过程中发挥作用外,TFEB/TFE3 的激活还会导致 MCP-1/CCL2 的释放。在受到代谢压力的组织中,内吞途径溶质外流缺陷会导致单核细胞招募增加。在这里,我们提出巨噬细胞对溶酶体上的压力传感途径做出反应,以协调溶酶体的生物生成以及髓系细胞的招募。
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引用次数: 0
Neutrophil-derived migrasomes are an essential part of the coagulation system 中性粒细胞衍生的迁移体是凝血系统的重要组成部分
IF 17.3 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-07-12 DOI: 10.1038/s41556-024-01440-9
Dong Jiang, Lin Jiao, Qing Li, Renxiang Xie, Haohao Jia, ShiHui Wang, Yining Chen, Siyuan Liu, Dandan Huang, Jiajia Zheng, Wenhao Song, Ying Li, JianFeng Chen, Jinsong Li, Binwu Ying, Li Yu
Migrasomes are organelles that are generated by migrating cells. Here we report the key role of neutrophil-derived migrasomes in haemostasis. We found that a large number of neutrophil-derived migrasomes exist in the blood of mice and humans. Compared with neutrophil cell bodies and platelets, these migrasomes adsorb and enrich coagulation factors on the surface. Moreover, they are highly enriched with adhesion molecules, which enable them to preferentially accumulate at sites of injury, where they trigger platelet activation and clot formation. Depletion of neutrophils, or genetic reduction of the number of these migrasomes, significantly decreases platelet plug formation and impairs coagulation. These defects can be rescued by intravenous injection of purified neutrophil-derived migrasomes. Our study reveals neutrophil-derived migrasomes as a previously unrecognized essential component of the haemostasis system, which may shed light on the cause of various coagulation disorders and open therapeutic possibilities. Jiang et al. document an abundance of neutrophil-derived migrasomes in the blood of mice and humans and show that migrasomes are enriched in coagulation factors, accumulate at sites of injury and trigger platelet activation and clot formation.
迁移体是由迁移细胞产生的细胞器。我们在此报告了中性粒细胞衍生的移行体在止血过程中的关键作用。我们发现,小鼠和人类血液中存在大量中性粒细胞衍生的移行体。与中性粒细胞体和血小板相比,这些移行体表面能吸附和富集凝血因子。此外,它们还高度富集了粘附分子,这使它们能够优先在损伤部位聚集,并在那里引发血小板活化和血凝块的形成。消耗中性粒细胞或通过基因减少这些移行体的数量,可显著减少血小板栓的形成并损害凝血功能。这些缺陷可以通过静脉注射纯化的中性粒细胞衍生的移行体来挽救。我们的研究揭示了嗜中性粒细胞衍生的移行体是止血系统中以前未被认识到的重要组成部分,这可能会揭示各种凝血障碍的原因,并为治疗提供可能性。
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引用次数: 0
Full-length GSDME mediates pyroptosis independent from cleavage 独立于裂解的全长 GSDME 介导了裂解热
IF 17.3 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-07-12 DOI: 10.1038/s41556-024-01463-2
Bo Zhou, Zhi-hong Jiang, Meng-ran Dai, Yuan-li Ai, Li Xiao, Chuan-qi Zhong, Liu-Zheng Wu, Qi-tao Chen, Hang-zi Chen, Qiao Wu
Gasdermin (GSDM) family proteins, known as the executors of pyroptosis, undergo protease-mediated cleavage before inducing pyroptosis. We here discovered a form of pyroptosis mediated by full-length (FL) GSDME without proteolytic cleavage. Intense ultraviolet-C irradiation-triggered DNA damage activates nuclear PARP1, leading to extensive formation of poly(ADP-ribose) (PAR) polymers. These PAR polymers are released to the cytoplasm, where they activate PARP5 to facilitate GSDME PARylation, resulting in a conformational change in GSDME that relieves autoinhibition. Moreover, ultraviolet-C irradiation promotes cytochrome c-catalysed cardiolipin peroxidation to elevate lipid reactive oxygen species, which is then sensed by PARylated GSDME, leading to oxidative oligomerization and plasma membrane targeting of FL-GSDME for perforation, eventually inducing pyroptosis. Reagents that concurrently stimulate PARylation and oxidation of FL-GSDME, synergistically promoting pyroptotic cell death. Overall, the present findings elucidate an unreported mechanism underlying the cleavage-independent function of GSDME in executing cell death, further enriching the paradigms and understanding of FL-GSDME-mediated pyroptosis. Zhou, Jiang, Dai et al report that upon ultraviolet-C radiation, full-length GSDME can induce pyroptosis without cleavage, likely due to conformational change and oxidative oligomerization after increased PARylation and mitochondrial lipid ROS levels.
Gasdermin (GSDM)家族蛋白被称为嗜热症的执行者,在诱导嗜热症之前会发生蛋白酶介导的裂解。我们在这里发现了一种由全长(FL)GSDME介导的无蛋白酶裂解的热昏迷形式。强烈的紫外线-C照射引发的DNA损伤激活了核PARP1,导致聚(ADP-核糖)(PAR)聚合物的广泛形成。这些 PAR 聚合物被释放到细胞质中,激活 PARP5,促进 GSDME PARyl 化,从而导致 GSDME 构象发生变化,解除自身抑制。此外,紫外线-C 照射会促进细胞色素 c 催化的心磷脂过氧化,使脂质活性氧升高,PAR 化的 GSDME 会感应到这一点,从而导致 FL-GSDME 氧化寡聚化和质膜靶向穿孔,最终诱发焦痂病。同时刺激 PARylation 和 FL-GSDME 氧化的试剂可协同促进细胞的热猝死。总之,本研究结果阐明了 GSDME 在执行细胞死亡过程中不依赖于裂解功能的一种未报道机制,进一步丰富了对 FL-GSDME 介导的热猝死的范式和理解。
{"title":"Full-length GSDME mediates pyroptosis independent from cleavage","authors":"Bo Zhou, Zhi-hong Jiang, Meng-ran Dai, Yuan-li Ai, Li Xiao, Chuan-qi Zhong, Liu-Zheng Wu, Qi-tao Chen, Hang-zi Chen, Qiao Wu","doi":"10.1038/s41556-024-01463-2","DOIUrl":"10.1038/s41556-024-01463-2","url":null,"abstract":"Gasdermin (GSDM) family proteins, known as the executors of pyroptosis, undergo protease-mediated cleavage before inducing pyroptosis. We here discovered a form of pyroptosis mediated by full-length (FL) GSDME without proteolytic cleavage. Intense ultraviolet-C irradiation-triggered DNA damage activates nuclear PARP1, leading to extensive formation of poly(ADP-ribose) (PAR) polymers. These PAR polymers are released to the cytoplasm, where they activate PARP5 to facilitate GSDME PARylation, resulting in a conformational change in GSDME that relieves autoinhibition. Moreover, ultraviolet-C irradiation promotes cytochrome c-catalysed cardiolipin peroxidation to elevate lipid reactive oxygen species, which is then sensed by PARylated GSDME, leading to oxidative oligomerization and plasma membrane targeting of FL-GSDME for perforation, eventually inducing pyroptosis. Reagents that concurrently stimulate PARylation and oxidation of FL-GSDME, synergistically promoting pyroptotic cell death. Overall, the present findings elucidate an unreported mechanism underlying the cleavage-independent function of GSDME in executing cell death, further enriching the paradigms and understanding of FL-GSDME-mediated pyroptosis. Zhou, Jiang, Dai et al report that upon ultraviolet-C radiation, full-length GSDME can induce pyroptosis without cleavage, likely due to conformational change and oxidative oligomerization after increased PARylation and mitochondrial lipid ROS levels.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":null,"pages":null},"PeriodicalIF":17.3,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141597638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
RNA glues it all 核糖核酸将一切连接起来
IF 17.3 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-07-11 DOI: 10.1038/s41556-024-01454-3
Fátima Gebauer
The role of RNA in preserving the integrity and dynamics of membrane-bound organelles remains largely unexplored. A study now identifies the Golgi-resident protein GM130 as an RNA-binding protein that scaffolds the Golgi ribbon in a polyadenylated-RNA-dependent manner.
RNA 在保持膜结合细胞器的完整性和动态性方面的作用在很大程度上仍未得到探索。现在的一项研究发现,高尔基驻留蛋白 GM130 是一种 RNA 结合蛋白,它以多聚腺苷酸 RNA 依赖性的方式支架高尔基体带。
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引用次数: 0
RNA scaffolds the Golgi ribbon by forming condensates with GM130 RNA 通过与 GM130 形成缩聚体来支撑高尔基体带
IF 17.3 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-07-11 DOI: 10.1038/s41556-024-01447-2
Yijun Zhang, Joachim Seemann
The mammalian Golgi is composed of stacks that are laterally connected into a continuous ribbon-like structure. The integrity and function of the ribbon is disrupted under stress conditions, but the molecular mechanisms remain unclear. Here we show that the ribbon is maintained by biomolecular condensates of RNA and the Golgi matrix protein GM130 (GOLGA2). We identify GM130 as a membrane-bound RNA-binding protein, which directly recruits RNA and associated RNA-binding proteins to the Golgi membrane. Acute degradation of RNA or GM130 in cells disrupts the ribbon. Under stress conditions, RNA dissociates from GM130 and the ribbon is disjointed, but after the cells recover from stress the ribbon is restored. When overexpressed in cells, GM130 forms RNA-dependent liquid-like condensates. GM130 contains an intrinsically disordered domain at its amino terminus, which binds RNA to induce liquid–liquid phase separation. These co-condensates are sufficient to link purified Golgi membranes, reconstructing lateral linking of stacks into a ribbon-like structure. Together, these studies show that RNA acts as a structural biopolymer that together with GM130 maintains the integrity of the Golgi ribbon. Zhang and Seemann show that GM130 forms a complex with RNA-binding proteins. RNA binding of GM130 induces liquid–liquid phase separation and these co-condensates function to link the Golgi ribbon.
哺乳动物的高尔基体由横向连接成连续带状结构的堆栈组成。在应激条件下,带状结构的完整性和功能会被破坏,但其分子机制仍不清楚。在这里,我们发现带状结构是由 RNA 和高尔基体基质蛋白 GM130(GOLGA2)的生物分子凝聚物维持的。我们发现 GM130 是一种膜结合 RNA 结合蛋白,可直接将 RNA 和相关 RNA 结合蛋白招募到高尔基体膜上。细胞中 RNA 或 GM130 的急性降解会破坏带状结构。在应激条件下,RNA 与 GM130 分离,带状结构脱节,但细胞从应激中恢复后,带状结构又会恢复。当 GM130 在细胞中过度表达时,会形成依赖于 RNA 的液态凝结物。GM130 的氨基末端含有一个固有紊乱结构域,该结构域与 RNA 结合,诱导液-液相分离。这些共凝结物足以连接纯化的高尔基体膜,将横向连接的膜堆重建为带状结构。这些研究共同表明,RNA 是一种结构性生物聚合物,它与 GM130 一起维持着高尔基体带状结构的完整性。
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引用次数: 0
Mapping the chromatin accessibility landscape of zebrafish embryogenesis at single-cell resolution by SPATAC-seq 通过 SPATAC-seq 以单细胞分辨率绘制斑马鱼胚胎发生的染色质可及性图谱
IF 17.3 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-07-08 DOI: 10.1038/s41556-024-01449-0
Keyong Sun, Xin Liu, Runda Xu, Chang Liu, Anming Meng, Xun Lan
Currently, the dynamic accessible elements that determine regulatory programs responsible for the unique identity and function of each cell type during zebrafish embryogenesis lack detailed study. Here we present SPATAC-seq: a split-pool ligation-based assay for transposase-accessible chromatin using sequencing. Using SPATAC-seq, we profiled chromatin accessibility in more than 800,000 individual nuclei across 20 developmental stages spanning the sphere stage to the early larval protruding mouth stage. Using this chromatin accessibility map, we identified 604 cell states and inferred their developmental relationships. We also identified 959,040 candidate cis-regulatory elements (cCREs) and delineated development-specific cCREs, as well as transcription factors defining diverse cell identities. Importantly, enhancer reporter assays confirmed that the majority of tested cCREs exhibited robust enhanced green fluorescent protein expression in restricted cell types or tissues. Finally, we explored gene regulatory programs that drive pigment and notochord cell differentiation. Our work provides a valuable open resource for exploring driver regulators of cell fate decisions in zebrafish embryogenesis. In two independent studies, Sun, Liu et al. and Sun et al. develop SPATAC-seq to map the chromatin accessibility landscape of zebrafish embryogenesis and mouse organogenesis, respectively, and identify transcription regulators that determine cell fate.
目前,对斑马鱼胚胎发育过程中决定每种细胞类型独特身份和功能的调控程序的动态可及元件缺乏详细研究。在这里,我们介绍 SPATAC-seq:一种基于分离池连接的检测方法,利用测序技术检测转座酶可及染色质。利用 SPATAC-seq,我们分析了从球体期到幼体突嘴期的 20 个发育阶段中 80 多万个细胞核的染色质可及性。利用染色质可及性图谱,我们确定了 604 种细胞状态,并推断出它们之间的发育关系。我们还确定了 959,040 个候选顺式调控元件(cCRE),并划分出发育特异性 cCRE 以及定义不同细胞特征的转录因子。重要的是,增强子报告实验证实,大多数测试过的 cCRE 在受限的细胞类型或组织中都表现出稳健的增强绿色荧光蛋白表达。最后,我们探索了驱动色素细胞和脊索细胞分化的基因调控程序。我们的工作为探索斑马鱼胚胎发生过程中细胞命运决定的驱动调控因子提供了宝贵的开放资源。
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引用次数: 0
A single-cell atlas of chromatin accessibility in mouse organogenesis 小鼠器官发生过程中染色质可及性的单细胞图谱
IF 17.3 1区 生物学 Q1 CELL BIOLOGY Pub Date : 2024-07-08 DOI: 10.1038/s41556-024-01435-6
Keyong Sun, Xin Liu, Xun Lan
Organogenesis is a highly complex and precisely regulated process. Here we profiled the chromatin accessibility in >350,000 cells derived from 13 mouse embryos at four developmental stages from embryonic day (E) 10.5 to E13.5 by SPATAC-seq in a single experiment. The resulting atlas revealed the status of 830,873 candidate cis-regulatory elements in 43 major cell types. By integrating the chromatin accessibility atlas with the previous transcriptomic dataset, we characterized cis-regulatory sequences and transcription factors associated with cell fate commitment, such as Nr5a2 in the development of gastrointestinal tract, which was preliminarily supported by the in vivo experiment in zebrafish. Finally, we integrated this atlas with the previous single-cell chromatin accessibility dataset from 13 adult mouse tissues to delineate the developmental stage-specific gene regulatory programmes within and across different cell types and identify potential molecular switches throughout lineage development. This comprehensive dataset provides a foundation for exploring transcriptional regulation in organogenesis. In two independent studies, Sun, Liu et al. and Sun et al. develop SPATAC-seq to map the chromatin accessibility landscape of zebrafish embryogenesis and mouse organogenesis, respectively, and identify transcription regulators that determine cell fate.
器官发生是一个高度复杂和精确调控的过程。在这里,我们在一次实验中通过 SPATAC-seq 分析了从胚胎 10.5 天到 13.5 天四个发育阶段的 13 个小鼠胚胎的 35 万个细胞的染色质可及性。结果图集揭示了 43 种主要细胞类型中 830,873 个候选顺式调控元件的状态。通过将染色质可及性图谱与之前的转录组数据集整合,我们确定了与细胞命运承诺相关的顺式调控序列和转录因子的特征,如 Nr5a2 在胃肠道发育中的作用,斑马鱼体内实验也初步证实了这一点。最后,我们将这一图集与之前来自 13 个成年小鼠组织的单细胞染色质可及性数据集整合在一起,以勾勒出不同细胞类型内部和跨细胞类型的发育阶段特异性基因调控方案,并识别整个品系发育过程中的潜在分子开关。这个全面的数据集为探索器官发生过程中的转录调控奠定了基础。
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引用次数: 0
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