Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation.
Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation.
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DOI：
10.7554/elife.00808
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发表时间：
2013-06-18
期刊：
影响因子：
7.7
通讯作者：
Meyer BJ
中科院分区：
文献类型：
--
作者：
Kruesi WS;Core LJ;Waters CT;Lis JT;Meyer BJ
称为剂量补偿的 X 染色体基因调控过程可确保男性 (1X) 和女性 (2X) 表达相同水平的 X 染色体转录本。由于转录起始位点 (TSS) 注释不正确，秀丽隐杆线虫的机制一直难以捉摸。在这里，我们定义了野生型和剂量补偿缺陷动物中 TSS 和转录参与 RNA 聚合酶 II (Pol II) 在全基因组范围内的分布，以剖析这种调节机制。我们的 TSS 作图策略将跟踪新生转录的 GRO-seq 与该方法的一种新衍生物（称为 GRO-cap）相结合，该方法在通过共转录处理去除 5' 帽之前恢复带有 5' 帽的新生 RNA。我们的分析表明，与其他后生动物不同，启动子近端暂停很少见，而且启动子出人意料地位于成熟 mRNA 5' 端的上游。我们发现，线虫通过使用染色体重组凝缩蛋白复合物减少雌雄同体 X 连锁基因启动子的 Pol II 募集，从而使两性之间的 X 染色体表达均衡到与常染色体相当的水平。 DOI：http://dx.doi.org/10.7554/eLife.00808.001 在包括人类在内的许多物种中，女性有两条 X 染色体，而男性只有一条。为了确保雌性最终不会获得双倍剂量的由 X 染色体上的基因编码的蛋白质，动物采用一种称为剂量补偿的策略来控制 X 连锁基因的表达。剂量补偿的机制因物种而异，但它们通常涉及一种调节复合物，该复合物与一种性别的 X 染色体结合以改变基因表达。线虫秀丽隐杆线虫由雌雄同体 (XX) 和雄性 (XO) 组成，这种调节复合物称为剂量补偿复合物 (DCC)，与 XX 个体的两条 X 染色体结合，使每个个体的基因表达降低 50%。 DCC 与一种称为凝缩蛋白的蛋白质复合物共享许多亚基，该蛋白质复合物可调节染色体的结构以实现适当的染色体分离。然而，目前尚不清楚 DCC 到底如何控制 X 连锁基因的表达。对于要表达的基因，一种称为 RNA 聚合酶 II 的酶必须与基因的启动子（基因蛋白质编码部分上游的一段 DNA）结合，以便它可以开始将 DNA 转录为 RNA。在线虫中的启动子很难定义，但 Kruesi 等人。设计了一种策略来绘制整个蠕虫基因组的转录起始位点以及启动子。该策略整合了两种方法的结果：一种测量每个基因转录区域的范围和方向，另一种定位标记新制备的 RNA 的真正 5' 末端的独特帽结构。利用这一新的启动子信息，再加上对野生型和剂量补偿缺陷动物新合成转录物水平的全基因组测量，他们表明秀丽隐杆线虫通过减少RNA聚合酶II向XX个体中X连锁基因启动子的募集来实现剂量补偿。克鲁西等人。还发现了第二种调节机制，该机制在两性中都起作用，以增加 X 染色体上基因的转录水平。这确保了剂量补偿后，X 染色体上的基因的表达水平与常染色体（除 X 和 Y 之外的所有染色体）上的基因相似。 Kruesi 等人的研究不仅揭示了秀丽隐杆线虫发生剂量补偿的机制。提供了关于蠕虫转录起始位点的有价值的数据集，并提出了可用于绘制其他物种中这些位点的通用策略。 DOI：http://dx.doi.org/10.7554/eLife.00808.002
The X-chromosome gene regulatory process called dosage compensation ensures that males (1X) and females (2X) express equal levels of X-chromosome transcripts. The mechanism in Caenorhabditis elegans has been elusive due to improperly annotated transcription start sites (TSSs). Here we define TSSs and the distribution of transcriptionally engaged RNA polymerase II (Pol II) genome-wide in wild-type and dosage-compensation-defective animals to dissect this regulatory mechanism. Our TSS-mapping strategy integrates GRO-seq, which tracks nascent transcription, with a new derivative of this method, called GRO-cap, which recovers nascent RNAs with 5′ caps prior to their removal by co-transcriptional processing. Our analyses reveal that promoter-proximal pausing is rare, unlike in other metazoans, and promoters are unexpectedly far upstream from the 5′ ends of mature mRNAs. We find that C. elegans equalizes X-chromosome expression between the sexes, to a level equivalent to autosomes, by reducing Pol II recruitment to promoters of hermaphrodite X-linked genes using a chromosome-restructuring condensin complex. DOI: http://dx.doi.org/10.7554/eLife.00808.001 In many species, including humans, females have two X chromosomes whereas males have only one. To ensure that females do not end up with a double dose of the proteins encoded by genes on the X chromosome, animals employ a strategy called dosage compensation to control the expression of X-linked genes. The mechanisms underlying dosage compensation vary between species, but they typically involve a regulatory complex that binds to the X chromosomes of one sex to modify gene expression. In the nematode worm Caenorhabditis elegans—which consists of hermaphrodites (XX) and males (XO)—this regulatory complex, called the dosage compensation complex (DCC), binds to both X chromosomes of XX individuals, reducing gene expression from each by 50%. DCC shares many subunits with a protein complex called condensin, which regulates the structure of chromosomes to achieve proper chromosome segregation. However, it is unclear exactly how the DCC controls the expression of X-linked genes. For a gene to be expressed, an enzyme called RNA polymerase II must bind to the gene’s promoter—a stretch of DNA upstream of the protein-coding part of the gene—so that it can begin transcribing the DNA into RNA. Promoters have been difficult to define in C. elegans, but Kruesi et al. devised a strategy to map transcription start sites, and hence promoters, throughout the worm genome. The strategy integrates the results of two methods: One measures the extent and orientation of each gene’s transcribed region, and the other locates the distinctive cap structures that mark the true 5′ ends of newly made RNAs. Using this new promoter information, coupled with genome-wide measurements of the levels of newly synthesized transcripts from wild-type and dosage-compensation-defective animals, they showed that C. elegans achieves dosage compensation by reducing the recruitment of RNA polymerase II to the promoters of X-linked genes in XX individuals. Kruesi et al. also identified a second regulatory mechanism that acts in both sexes to increase the level of transcription of genes on the X chromosome. This ensures that after dosage compensation, genes on the X chromosome are expressed at a similar level to those on the autosomes (all chromosomes other than X and Y). As well as shedding light on the mechanism by which dosage compensation occurs in C. elegans, the study by Kruesi et al. provides a valuable data set on transcription start sites in the worm, and puts forward a general strategy that could be used to map these sites in other species. DOI: http://dx.doi.org/10.7554/eLife.00808.002