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Retrotransposon addiction promotes centromere function via epigenetically activated small RNAs 逆转录转座子成瘾通过表观遗传激活的小RNA促进中心粒功能
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-09-02 DOI: 10.1038/s41477-024-01773-1
Atsushi Shimada, Jonathan Cahn, Evan Ernst, Jason Lynn, Daniel Grimanelli, Ian Henderson, Tetsuji Kakutani, Robert A. Martienssen
Retrotransposons have invaded eukaryotic centromeres in cycles of repeat expansion and purging, but the function of centromeric retrotransposons has remained unclear. In Arabidopsis, centromeric ATHILA retrotransposons give rise to epigenetically activated short interfering RNAs in mutants in DECREASE IN DNA METHYLATION1 (DDM1). Here we show that mutants that lose both DDM1 and RNA-dependent RNA polymerase have pleiotropic developmental defects and mis-segregate chromosome 5 during mitosis. Fertility and segregation defects are epigenetically inherited with centromere 5, and can be rescued by directing artificial small RNAs to ATHILA5 retrotransposons that interrupt tandem satellite repeats. Epigenetically activated short interfering RNAs promote pericentromeric condensation, chromosome cohesion and chromosome segregation in mitosis. We propose that insertion of ATHILA silences centromeric transcription, while simultaneously making centromere function dependent on retrotransposon small RNAs in the absence of DDM1. Parallels are made with the fission yeast Schizosaccharomyces pombe, where chromosome cohesion depends on RNA interference, and with humans, where chromosome segregation depends on both RNA interference and HELLSDDM1. Centromeric satellite repeats on Arabidopsis chromosome 5 are interrupted by ATHILA5 retrotransposons, and cohesion is compromised in ddm1 chromatin remodelling mutants that have also lost RNAi. Mis-segregation is epigenetically inherited but can be rescued by ATHILA5 small RNA.
逆转座子在重复扩增和清除的循环中侵入了真核生物的中心粒,但中心粒逆转座子的功能仍不清楚。在拟南芥中,中心粒ATHILA逆转座子在DNA甲基化减少1(DDM1)突变体中产生表观遗传激活的短干扰RNA。在这里,我们发现同时失去 DDM1 和 RNA 依赖性 RNA 聚合酶的突变体具有多向发育缺陷,并在有丝分裂过程中出现 5 号染色体的错误分离。生育力和分离缺陷与中心粒5具有表观遗传性,可以通过将人工小RNA引导至ATHILA5逆转录载体来挽救,ATHILA5逆转录载体会中断串联卫星重复序列。表观遗传激活的短干扰 RNA 可促进有丝分裂中的中心粒周围凝聚、染色体内聚和染色体分离。我们认为 ATHILA 的插入会抑制中心粒的转录,同时在缺乏 DDM1 的情况下,使中心粒的功能依赖于逆转座小 RNA。这与裂殖酵母(Schizosaccharomyces pombe)和人类的情况相似,前者的染色体内聚依赖于 RNA 干扰,后者的染色体分离依赖于 RNA 干扰和 HELLSDDM1。
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引用次数: 0
A chemical approach to extend flower longevity of Japanese morning glory via inhibition of master senescence regulator EPHEMERAL1 通过抑制衰老主调节因子 EPHEMERAL1 延长日本牵牛花花期的化学方法
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-08-29 DOI: 10.1038/s41477-024-01767-z
Kenichi Shibuya, Akira Nozawa, Chikako Takahashi, Tatsuya Sawasaki
Petal senescence in flowering plants is a type of programmed cell death with highly regulated onset and progression. A NAM/ATAF1,2/CUC2 transcription factor, EPHEMERAL1 (EPH1), has been identified as a key regulator of petal senescence in Japanese morning glory (Ipomoea nil). Here we used a novel chemical approach to delay petal senescence in Japanese morning glory by inhibiting the DNA-binding activity of EPH1. A cell-free high-throughput screening system and subsequent bioassays found two tetrafluorophthalimide-based compounds, Everlastin1 and Everlastin2, that inhibited the EPH1–DNA interaction and delayed petal senescence. The inhibitory mechanism was due to the suppression of EPH1 dimerization. RNA-sequencing analysis revealed that the chemical treatment strongly suppressed the expression of programmed cell death- and autophagy-related genes. These results suggest that a chemical approach targeting a transcription factor can regulate petal senescence. Transcription factors are regarded as desirable targets for drug discovery. Here novel chemical compounds that delay flower petal aging were identified by a cell-free high-throughput screening system targeting EPHEMERAL1, a NAC transcription factor.
开花植物的花瓣衰老是一种程序性细胞死亡,其发生和发展受到高度调控。一种 NAM/ATAF1,2/CUC2 转录因子 EPHEMERAL1(EPH1)已被确定为日本牵牛花(Ipomoea nil)花瓣衰老的关键调节因子。在这里,我们采用了一种新的化学方法,通过抑制 EPH1 的 DNA 结合活性来延缓日本牵牛花的花瓣衰老。通过无细胞高通量筛选系统和随后的生物测定,我们发现了两种基于四氟邻苯二甲酰亚胺的化合物 Everlastin1 和 Everlastin2,它们能抑制 EPH1 与 DNA 的相互作用并延缓花瓣衰老。其抑制机制是由于抑制了 EPH1 的二聚化。RNA 序列分析表明,化学处理强烈抑制了程序性细胞死亡和自噬相关基因的表达。这些结果表明,针对转录因子的化学方法可以调节花瓣的衰老。
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引用次数: 0
An RdDM-independent function of Pol V transcripts in gene regulation and plant defence Pol V 转录本在基因调控和植物防御中的功能与 RdDM 无关。
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-08-26 DOI: 10.1038/s41477-024-01774-0
Yuxiang Yuan, Yujie Liu, Lu Han, Yan Li, Yijun Qi
RNA polymerase V (Pol V) and Pol IV are known to be specialized for RNA-directed DNA methylation (RdDM). Here we report that Pol V, but not Pol IV, regulates hundreds of genes including jasmonic acid-responsive genes and confers plant defence to Botrytis cinerea and Spodoptera exigua. About half of the Pol V-regulated genes are associated with Pol V transcripts (PVTs). We thus hypothesized that some PVTs could regulate gene expression in an RdDM-independent manner. To test this hypothesis, we studied three PVTs, PVT-ERF5a/b and PVT-ERF6, as models. PVT-ERF5a/b and PVT-ERF6 are transcribed from the upstream regions of ERF5 and ERF6 and positively regulate their transcription, thereby regulating plant defence. Such regulation involves PVT-dependent H3K4me3 deposition and requires the DRD1-DMS3-RDM1 complex that mediates Pol V recruitment to the target loci. These findings highlight an unprecedented role for PVTs in regulating gene transcription, apart from serving as scaffold RNAs to direct DNA methylation. Pol V transcripts are known to serve as scaffold RNAs to direct DNA methylation. This study shows that they can also regulate the transcription of neighbouring genes and confer plant defence, independently of RNA-directed DNA methylation.
已知 RNA 聚合酶 V(Pol V)和 Pol IV 专门从事 RNA 引导的 DNA 甲基化(RdDM)。在这里,我们报告了 Pol V(而非 Pol IV)调控数百个基因,包括茉莉酸响应基因,并使植物防御灰霉病和鞘翅目旋毛虫。大约一半的 Pol V 调节基因与 Pol V 转录本(PVTs)相关。因此,我们推测一些 PVTs 可能以不依赖 RdDM 的方式调控基因表达。为了验证这一假设,我们以 PVT-ERF5a/b 和 PVT-ERF6 这三种 PVT 为模型进行了研究。PVT-ERF5a/b 和 PVT-ERF6 从 ERF5 和 ERF6 的上游区域转录,并正向调节它们的转录,从而调节植物防御。这种调控涉及 PVT 依赖性 H3K4me3 沉积,需要 DRD1-DMS3-RDM1 复合物介导 Pol V 招募到目标基因座。这些发现凸显了 PVT 除了作为引导 DNA 甲基化的支架 RNA 外,还在调控基因转录方面发挥了前所未有的作用。
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引用次数: 0
aChIP is an efficient and sensitive ChIP-seq technique for economically important plant organs aChIP 是一种高效、灵敏的 ChIP-seq 技术,适用于具有重要经济价值的植物器官
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-08-23 DOI: 10.1038/s41477-024-01743-7
Qing Zhang, Wenying Zhong, Guangfeng Zhu, Lulu Cheng, Caijun Yin, Li Deng, Yang Yang, Zhengjing Zhang, Jinxiong Shen, Tingdong Fu, Jian-Kang Zhu, Lun Zhao
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is crucial for profiling histone modifications and transcription factor binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits and flowers is challenging due to their sturdy cell walls and complex constituents. Here we present advanced ChIP (aChIP), an optimized method that efficiently isolates chromatin from plant tissues while simultaneously removing cell walls and cellular constituents. aChIP precisely profiles histone modifications in all 14 tested EIPOs and identifies transcription factor and chromatin-modifying enzyme binding sites. In addition, aChIP enhances ChIP efficiency, revealing numerous novel modified sites compared with previous methods in vegetative tissues. aChIP reveals the histone modification landscape for rapeseed dry seeds, highlighting the intricate roles of chromatin dynamics during seed dormancy and germination. Altogether, aChIP is a powerful, efficient and sensitive approach for comprehensive chromatin profiling in virtually all plant tissues, especially in EIPOs. This study presents an advanced ChIP-seq method, provides a valuable epigenomics resource for 14 economically important plant organs and reveals histone modification landscape dynamics and functions during rapeseed seed dormancy and germination.
染色质免疫沉淀测序(ChIP-seq)对于分析整个基因组的组蛋白修饰和转录因子结合至关重要。然而,由于种子、果实和花朵等具有重要经济价值的植物器官(EIPOs)的细胞壁坚固、成分复杂,因此将其应用于这些器官具有挑战性。在这里,我们介绍了先进的 ChIP(aChIP),这是一种经过优化的方法,能从植物组织中有效分离染色质,同时去除细胞壁和细胞成分。aChIP 能精确分析所有 14 种受测 EIPO 的组蛋白修饰,并确定转录因子和染色质修饰酶的结合位点。此外,aChIP 还提高了 ChIP 的效率,与以前在无性组织中使用的方法相比,它揭示了许多新的修饰位点。aChIP 揭示了油菜籽干种子的组蛋白修饰情况,突出了种子休眠和萌发过程中染色质动态的复杂作用。总之,aChIP 是一种功能强大、高效灵敏的方法,可用于几乎所有植物组织,尤其是 EIPO 的染色质全面分析。
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引用次数: 0
aChIP for comprehensive chromatin profiling in economically important plant organs aChIP 用于对具有重要经济价值的植物器官进行染色质综合分析
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-08-23 DOI: 10.1038/s41477-024-01744-6
We developed aChIP, an advanced chromatin immunoprecipitation followed by sequencing (ChIP–seq) method for economically important plant organs (EIPOs). aChIP provides a valuable epigenomics resource that comprises 14 representative EIPOs, and reveals the dynamics and functions of histone modification landscapes during rapeseed seed dormancy and germination.
我们针对具有重要经济价值的植物器官(EIPOs)开发了一种先进的染色质免疫共沉淀-测序(ChIP-seq)方法--aChIP。aChIP提供了宝贵的表观基因组学资源,包括14个具有代表性的EIPOs,揭示了油菜籽休眠和萌发过程中组蛋白修饰景观的动态和功能。
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引用次数: 0
Discovery of a component of the chloroplast-associated protein degradation system 发现叶绿体相关蛋白质降解系统的一个组成部分。
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-08-21 DOI: 10.1038/s41477-024-01770-4
Regulation of chloroplast protein import by chloroplast-associated protein degradation (CHLORAD) is crucial for chloroplast biogenesis and plant development. This study identifies PUX10 as a CHLORAD component that functions as a membrane-bound scaffold to recruit cytosolic Cdc48 to the chloroplast surface and bring it into proximity with CHLORAD substrates.
叶绿体相关蛋白降解(CHLORAD)对叶绿体蛋白导入的调控对叶绿体生物发生和植物发育至关重要。本研究发现,PUX10 是一种 CHLORAD 成分,其功能是作为膜结合支架将细胞质 Cdc48 募集到叶绿体表面,并使其接近 CHLORAD 底物。
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引用次数: 0
Pretty privilege 很有特权
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-08-21 DOI: 10.1038/s41477-024-01785-x
Botanically inclined scientists are well acquainted with ‘plant blindness’, the common tendency to overlook flora and concentrate on fauna. But we are similarly afflicted by aesthetic opinions with serious consequences for conservation.
喜欢植物的科学家都知道 "植物盲症",即忽视植物而专注于动物的普遍倾向。但我们也同样受到审美观点的影响,这对保护工作造成了严重后果。
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引用次数: 0
Recruitment of Cdc48 to chloroplasts by a UBX-domain protein in chloroplast-associated protein degradation 在叶绿体相关蛋白降解过程中,UBX 域蛋白将 Cdc48 招募到叶绿体中
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-08-19 DOI: 10.1038/s41477-024-01769-x
Na Li, R. Paul Jarvis
The translocon at the outer chloroplast membrane (TOC) is the gateway for chloroplast protein import and so is vital for photosynthetic establishment and plant growth. Chloroplast-associated protein degradation (CHLORAD) is a ubiquitin-dependent proteolytic system that regulates TOC. In CHLORAD, cytosolic Cdc48 provides motive force for the retrotranslocation of ubiquitinated TOC proteins to the cytosol but how Cdc48 is recruited is unknown. Here, we identify plant UBX-domain protein PUX10 as a component of the CHLORAD machinery. We show that PUX10 is an integral chloroplast outer membrane protein that projects UBX and ubiquitin-associated domains into the cytosol. It interacts with Cdc48 via its UBX domain, bringing it to the chloroplast surface, and with ubiquitinated TOC proteins via its ubiquitin-associated domain. Genetic analyses in Arabidopsis revealed a requirement for PUX10 during CHLORAD-mediated regulation of TOC function and plant development. Thus, PUX10 coordinates ubiquitination and retrotranslocation activities of CHLORAD to enable efficient TOC turnover. Extraction of ubiquitinated proteins from chloroplasts in CHLORAD is driven by the cytosolic ATPase Cdc48. The UBX-domain protein PUX10 is shown to be a CHLORAD component that recruits Cdc48 to the chloroplast surface.
叶绿体外膜上的转化子(TOC)是叶绿体蛋白质输入的门户,因此对光合作用的建立和植物生长至关重要。叶绿体相关蛋白降解(CHLORAD)是一种依赖于泛素的蛋白水解系统,可调节 TOC。在 CHLORAD 中,细胞质 Cdc48 为泛素化 TOC 蛋白向细胞质逆转位提供动力,但 Cdc48 是如何被招募的尚不清楚。在这里,我们发现植物 UBX 域蛋白 PUX10 是 CHLORAD 机制的一个组成部分。我们发现,PUX10 是一种完整的叶绿体外膜蛋白,能将 UBX 和泛素相关结构域投射到细胞质中。它通过其 UBX 结构域与 Cdc48 相互作用,将其带到叶绿体表面,并通过其泛素相关结构域与泛素化的 TOC 蛋白相互作用。拟南芥的遗传分析表明,在 CHLORAD 介导的 TOC 功能调控和植物发育过程中需要 PUX10。因此,PUX10 可协调 CHLORAD 的泛素化和逆转位活动,从而实现高效的 TOC 转化。
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引用次数: 0
Keeping D6PK polar 保持 D6PK 极地
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-08-14 DOI: 10.1038/s41477-024-01766-0
Katarina Kurtović, Vojtěch Schmidt, Jan Petrášek
The PIN-FORMED (PIN) auxin efflux carriers in the plasma membrane are activated by the D6 serine/threonine protein kinase (D6PK). A recent study reveals how D6PK is anchored to membranes and trafficked between the plasma membrane and transport vesicles.
质膜上的 PIN-FORMED(PIN)辅助素外流载体是由 D6 丝氨酸/苏氨酸蛋白激酶(D6PK)激活的。最近的一项研究揭示了 D6PK 如何锚定在膜上并在质膜和运输囊泡之间运输。
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引用次数: 0
Share the meat 分享肉类
IF 15.8 1区 生物学 Q1 PLANT SCIENCES Pub Date : 2024-08-14 DOI: 10.1038/s41477-024-01784-y
Guillaume Tena
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引用次数: 0
期刊
Nature Plants
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