Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors
Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors
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DOI：
10.1128/mcb.24.12.5534-5547.2004
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发表时间：
2004-06-01
影响因子：
5.3
通讯作者：
Hughes, TR
中科院分区：
文献类型：
--
作者：
Grigull, J;Mnaimneh, S;Hughes, TR
使用DNA微阵列，我们比较了全球转录的稳定性配置文件后，化学抑制转录rpb 1 -1（酵母RNA聚合酶II的温度敏感的等位基因）。在所测试的五种抑制剂中，硫代巴比妥和1，10-菲咯啉的作用与rpb 1 -1最相似。比较各种微阵列数据已经在文献中揭示了mRNA的稳定性和转录响应的压力，如热休克之间的相似性，与一般的应激反应，包括一般mRNA转录的瞬时关闭的事实相一致。编码rRNA合成和核糖体组装因子的基因是最不稳定的转录本，在酵母微阵列数据中经常观察到这些基因被协同下调。我们研究了编码去腺苷酸酶组分Ccr 4p和Pan 2 p以及推定的RNA结合蛋白Pub 1 p和Puf 4p的基因缺失对化学物质和/或热应激抑制转录后mRNA稳定性的全基因组模式的影响。这项研究表明，Ccr 4p，主要的酵母mRNA deadenylase，有助于降解的转录编码核糖体蛋白和rRNA合成和核糖体组装因子，并介导了很大一部分的转录响应热应激。Pan 2 p和Puf 4p也有助于转录关闭后这些mRNA的降解速率，而Pub 1 p优先稳定编码核糖体蛋白的转录本。我们的结果表明，核糖体生物合成因子的丰度受控于mRNA稳定性水平。
Using DNA microarrays, we compared global transcript stability profiles following chemical inhibition of transcription to rpb1-1 (a temperature-sensitive allele of yeast RNA polymerase II). Among the five inhibitors tested, the effects of thiolutin and 1,10-phenanthroline were most similar to rpb1-1. A comparison to various microarray data already in the literature revealed similarity between mRNA stability profiles and the transcriptional response to stresses such as heat shock, consistent with the fact that the general stress response includes a transient shutoff of general mRNA transcription. Genes encoding factors involved in rRNA synthesis and ribosome assembly, which are often observed to be coordinately down-regulated in yeast microarray data, were among the least stable transcripts. We examined the effects of deletions of genes encoding deadenylase components Ccr4p and Pan2p and putative RNA-binding proteins Pub1p and Puf4p on the genome-wide pattern of mRNA stability after inhibition of transcription by chemicals and/or heat stress. This examination showed that Ccr4p, the major yeast mRNA deadenylase, contributes to the degradation of transcripts encoding both ribosomal proteins and rRNA synthesis and ribosome assembly factors and mediates a large part of the transcriptional response to heat stress. Pan2p and Puf4p also contributed to the degradation rate of these mRNAs following transcriptional shutoff, while Pub1p preferentially stabilized transcripts encoding ribosomal proteins. Our results indicate that the abundance of ribosome biogenesis factors is controlled at the level of mRNA stability.