RNA聚合酶动态及染色质结构调控拟南芥基因转录的机制研究

  真核生物中大部分蛋白质编码基因的转录过程由RNA聚合酶（Pol II）介导，转录本身是一个Pol II沿染色质移动的高度动态的过程，受到染色质结构等因素的精细调控。以Pol II为核心的转录机器在染色质开放区域识别并结合基因的启动子，起始转录，经过延伸和终止，并伴随RNA的加工产生成熟的mRNA。转录过程中，RNA聚合酶需要打开染色质结构，移除核小体障碍，才能进行转录起始和延伸，而核小体的移除和组装常常需要通过组蛋白分子伴侣来实现。此外，转录时Pol II的构象也在动态变化，且转录的不同阶段间、转录及不同的RNA加工过程间均存在协同作用，以保证转录的有序进行。因此，Pol II的动态和染色质结构是调控基因转录过程的两个重要因素。植物中关于转录调控的研究滞后于动物和酵母，并且由于演化上分歧久远，基于动物和酵母的知识常不能直接套用在植物里。因此，在植物中真正揭示转录调控的基本机制对于理解植物的生命过程十分重要。以此为出发点，本论文从Pol II的转录动态以及组蛋白分子伴侣介导的染色质结构调控两个方面综合探究了模式植物拟南芥基因转录调控的分子机制。

首先，本论文探究了拟南芥Pol II在基因上的动态分布规律及其调控机制。通过pNET-seq结合其它几种组学数据，本论文发现Pol II在基因3' 端的停顿是拟南芥基因转录的一个重要特征，而且Pol II在基因3' 端停顿的位置而非强度与转录终止效率相关，表明虽然Pol II在基因3' 端的停顿与转录终止密切偶联，但仍有其他因素决定3' 端停顿的强度。与此相符，在转录终止缺陷的xrn3及fca fpa突变体中，Pol II在基因3' 端停顿的水平没有受到强烈的影响。经过进一步分析，发现基因的内含子数目以及内含子整体的共转录剪接效率与Pol II在基因3' 端停顿的水平呈紧密的正相关，暗示内含子的共转录剪接可能是影响3' 端停顿水平的重要因素。利用剪接抑制剂GEX1A处理植物，抑制剪接复合体的组装进而抑制剪接，发现Pol II在基因3' 端停顿的水平剧烈降低，且基因的内含子数目和3' 端停顿水平间的相关性被打破；基因的内含子数目越多，其3' 端Pol II的停顿水平降低越多。因此，基因内含子数目与内含子的共转录剪接偶联并决定了Pol II在基因3' 端停顿的水平，剪接复合体的有效组装是Pol II在3' 端停顿的必要条件，而Pol II在3' 端停顿可能为多内含子基因高效的共转录剪接提供保障。综上，本论文明确了植物Pol II在基因3' 端停顿的意义及调控规律。

  此外，本论文进一步探究了染色质结构对基因转录的调控规律，通过文献调研选取了一类与基因转录密切关联的组蛋白分子伴侣DEK进行深入研究。DEK在染色质上丰度很高，但其分子功能尚不清晰。通过在体外和体内的相互作用分析，发现DEK和H3.3及H3.1都存在互作；并且DEK的C端结构域上存在多个和游离组蛋白结合所必需的氨基酸。利用CRISPR/Cas9技术对拟南芥中四个DEK同源基因进行突变，产生了多个dek单突变体和多突变体。表型分析发现DEK通过调控FLC和FT基因的表达参与调控开花，且四个DEK存在功能冗余。此外，dek1234 flc比flc开花更早，FT的表达水平也进一步升高，表明DEK对FT表达的调控不完全依赖FLC。经过进一步探究，将DEK蛋白上负责和组蛋白结合的C端结构域突变，再回补至dek1234四突变体中，发现C端结构域突变的DEK和完整的DEK都能回补dek1234的早花表型。因此，在调控植物开花过程中，DEK不依赖其C端结构域介导的结合组蛋白的功能，提示DEK可能具有除组蛋白分子伴侣以外的其他功能。

本论文进一步利用质谱分析了DEK的蛋白质互作网络，结合免疫共沉淀实验，发现DEK和已知的参与FT转录抑制的H3K27me3阅读器蛋白EBS/SHL存在体内互作。通过遗传分析，在ebs和ebs shl的背景下分别进一步突变DEK，发现dek1234 ebs和dek1234 ebs shl开花更早，且表现出了更严重的生长缺陷，比如花器官发育紊乱，表明DEK和EBS/SHL存在重要的协同作用参与植物生长发育。同时，转录组数据显示在进一步突变DEK之后，dek1234 ebs和dek1234 ebs shl的基因表达变化程度也更剧烈，包括很多已知的H3K27me3的靶基因。而H3K27me3的ChIP-seq数据也显示在ebs shl背景下DEK的缺失会引起H3K27me3水平进一步降低。因此，综合以上结果，DEK在拟南芥中协同H3K27me3的阅读器蛋白EBS/SHL对H3K27me3的维持及基因转录发挥重要调控作用。

  综上所述，本论文从Pol II的动态和组蛋白分子伴侣介导的染色质结构调控两个方面探究了植物中基因转录调控的机制，为Pol II的转录终止调控提供了新的线索，也为共转录剪接和转录终止调控之间的联系提供了新的证据；阐明了拟南芥中组蛋白分子伴侣DEK调控开花的遗传学路径，揭示了其通过调控染色质上组蛋白H3K27me3修饰从而对植物基因表达及生长发育发挥的重要作用。

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