Impact of nonsense-mediated mRNA decay on the global expression profile of budding yeast.
Impact of nonsense-mediated mRNA decay on the global expression profile of budding yeast.
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DOI：
10.1371/journal.pgen.0020203
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发表时间：
2006-11-24
期刊：
影响因子：
4.5
通讯作者：
Culbertson, Michael R.
中科院分区：
文献类型：
--
作者：
Guan, Qiaoning;Zheng, Wei;Tang, Shijie;Liu, Xiaosong;Zinkel, Robert A.;Tsui, Kam-Wah;Yandell, Brian S.;Culbertson, Michael R.
无义介导的mRNA衰变（NMD）是一种真核生物的RNA监视机制，它选择性地消除编码潜在有害蛋白质的异常转录本。NMD还在基因表达的正常库中起作用。在酿酒酵母中，数百种内源性RNA聚合酶II转录物达到依赖于NMD的稳态水平。对于某些情况，衰减率直接受NMD（直接目标）的影响。对于其他人来说，丰度是NMD敏感的，但对衰变率没有任何影响（间接目标）。为了区分直接和间接靶标，在转录抑制后的1小时时间窗内，用高密度阵列探测野生型（Nmd+）和突变型（Nmd−）菌株的总RNA。统计模型被开发来描述RNA衰变的动力学。预测NMD靶向的45% ± 5%的RNA是Nmd−菌株中衰变率改变的直接靶标。使用传统方法进行平行实验，以经验检验全球实验的预测。结果表明，该总体测定可靠地区分了直接与间接靶标。研究了不同类型的靶标，包括含有相邻的、禁用的开放阅读框、上游开放阅读框的转录物，以及倾向于框外翻译起始的转录物。已知的瞄准机制未能解释国家导弹防御系统的所有直接目标，这表明其他瞄准机制仍有待阐明。30%的NMD蛋白质编码靶点属于两个广泛定义的功能主题：影响染色体结构和行为的那些和影响细胞表面动力学的那些。总的来说，这些结果为多细胞真核生物中的表达谱如何受到NMD的影响提供了一个预览。此外，在全球范围内分析衰变率的方法为研究任何生物体中mRNA衰变途径的新方法提供了蓝图，其中培养的细胞系可用。基因通过转录和翻译来决定蛋白质的结构，其中基因的RNA拷贝（mRNA）被制造出来，然后被翻译成蛋白质。细胞蛋白水平反映了mRNA合成和降解的相对速率，这受到多层控制。还存在确保每个mRNA的质量的机制。一种称为无义介导的mRNA衰变（NMD）的质量控制机制触发含有编码错误的mRNA的快速降解，否则会导致产生无功能或潜在有害的蛋白质。NMD发生在酵母、植物、苍蝇、蠕虫、小鼠和人类中。在人类中，NMD通过影响携带致病突变的基因的表达来影响遗传疾病的病因。除了质量保证，NMD还通过控制数百种没有编码错误的正常mRNA的丰度在基因表达中发挥另一种作用。在这篇论文中，作者使用DNA阵列来监测芽殖酵母中所有mRNA的相对衰减率，并发现了一个衰减率依赖于NMD的子集。许多相应的蛋白质执行相关的功能作用，影响染色体的结构和行为以及细胞表面的结构和完整性。
Nonsense-mediated mRNA decay (NMD) is a eukaryotic mechanism of RNA surveillance that selectively eliminates aberrant transcripts coding for potentially deleterious proteins. NMD also functions in the normal repertoire of gene expression. In Saccharomyces cerevisiae, hundreds of endogenous RNA Polymerase II transcripts achieve steady-state levels that depend on NMD. For some, the decay rate is directly influenced by NMD (direct targets). For others, abundance is NMD-sensitive but without any effect on the decay rate (indirect targets). To distinguish between direct and indirect targets, total RNA from wild-type (Nmd+) and mutant (Nmd−) strains was probed with high-density arrays across a 1-h time window following transcription inhibition. Statistical models were developed to describe the kinetics of RNA decay. 45% ± 5% of RNAs targeted by NMD were predicted to be direct targets with altered decay rates in Nmd− strains. Parallel experiments using conventional methods were conducted to empirically test predictions from the global experiment. The results show that the global assay reliably distinguished direct versus indirect targets. Different types of targets were investigated, including transcripts containing adjacent, disabled open reading frames, upstream open reading frames, and those prone to out-of-frame initiation of translation. Known targeting mechanisms fail to account for all of the direct targets of NMD, suggesting that additional targeting mechanisms remain to be elucidated. 30% of the protein-coding targets of NMD fell into two broadly defined functional themes: those affecting chromosome structure and behavior and those affecting cell surface dynamics. Overall, the results provide a preview for how expression profiles in multi-cellular eukaryotes might be impacted by NMD. Furthermore, the methods for analyzing decay rates on a global scale offer a blueprint for new ways to study mRNA decay pathways in any organism where cultured cell lines are available. Genes determine the structure of proteins through transcription and translation in which an RNA copy of the gene is made (mRNA) and then translated to make the protein. Cellular protein levels reflect the relative rates of mRNA synthesis and degradation, which are subject to multiple layers of controls. Mechanisms also exist to ensure the quality of each mRNA. One quality control mechanism called nonsense-mediated mRNA decay (NMD) triggers the rapid degradation of mRNAs containing coding errors that would otherwise lead to the production of non-functional or potentially deleterious proteins. NMD occurs in yeasts, plants, flies, worms, mice, and humans. In humans, NMD affects the etiology of genetic disorders by affecting the expression of genes that carry disease-causing mutations. Besides quality assurance, NMD plays another role in gene expression by controlling the abundance of hundreds of normal mRNAs that are devoid of coding errors. In this paper, the authors used DNA arrays to monitor the relative decay rates of all mRNAs in budding yeast and found a subset where decay rates were dependent on NMD. Many of the corresponding proteins perform related functional roles affecting both the structure and behavior of chromosomes and the structure and integrity of the cell surface.
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影响因子：
10.5
作者：
Czaplinski, K;Ruiz-Echevarria, MJ;Peltz, SW
通讯作者：
Peltz, SW
影响因子：
5.6
作者：
ALTAMURA, N;GROUDINSKY, O;SLONIMSKI, PP
通讯作者：
SLONIMSKI, PP
影响因子：
64.8
作者：
Amrani, N;Ganesan, R;Jacobson, A
通讯作者：
Jacobson, A
影响因子：
4.8
作者：
Dickinson, JR;Eshantha, L;Hewlins, MJE
通讯作者：
Hewlins, MJE
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y