Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation
Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation
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DOI：
10.1101/gr.912603
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发表时间：
2003-02-01
期刊：
影响因子：
7
通讯作者：
Rosenow, C
中科院分区：
文献类型：
--
作者：
Selinger, DW;Saxena, RM;Rosenow, C
亚基因分辨率寡核苷酸微阵列用于研究野生型大肠杆菌 MG1655 中的整体 RNA 降解。测量了 1036 个开放阅读框 (ORF) 和 329 个已知和预测操纵子的 RNA 化学半衰期。在测试条件下总mRNA的半衰期为6.8分钟。我们还观察到基因功能分配和转录稳定性之间的显着关系。出乎意料的是，单个操纵子 (tdcABCDEFG) 的转录对利福平相对不敏感，并且在添加利福平后 2.5 分钟显示出显着增加。这支持了 tdc 操纵子的一种新的转录机制，其启动子缺乏任何可识别的西格玛结合位点。对所有已知和预测的操纵子的逐个探针分析表明，操纵子的 5' 末端平均降解速度比转录物的其余部分更快，并且稳定性在 3' 方向上增加，支持并进一步推广了当前的净 5' 到 3' 方向性降解的模型。操纵子降解模式的层次聚类分析表明，这种模式占主导地位，但不是排他性的。我们发现相邻操纵子区域的降解之间存在微弱但高度显着的相关性，这表明稳定性是由局部和整个操纵子稳定性决定因素的组合决定的。 16 ORF dcw 基因簇具有复杂的启动子结构和部分表征的降解模式，以高分辨率进行研究，可以对其丰度和降解进行详细和综合的描述。我们讨论了亚基因分辨率 DNA 微阵列分析在研究 RNA 转录和加工的整体机制中的应用。
Subgenic-resolution oligonucleotide microarrays were used to study global RNA degradation in wild-type Escherichia coli MG1655. RNA chemical half-lives were measured for 1036 open reading frames (ORFs) and for 329 known and predicted operons. The half-life of total mRNA was 6.8 min under the conditions tested. We also observed significant relationships between gene functional assignments and transcript stability. Unexpectedly, transcription of a single operon (tdcABCDEFG) was relatively rifampicin-insensitive and showed significant increases 2.5 min after rifampicin addition. This supports a novel mechanism of transcription for the tdc operon, whose promoter lacks any recognizable sigma binding sites. Probe by probe analysis of all known and predicted operons showed that the 5' ends of operons degrade, on average, more quickly than the rest of the transcript, with stability increasing in a 3' direction, supporting and further generalizing the current model of a net 5' to 3' directionality of degradation. Hierarchical clustering analysis of operon degradation patterns revealed that this pattern predominates but is not exclusive. We found a weak but highly significant correlation between the degradation of adjacent operon regions, suggesting that stability is determined by a combination of local and operon-wide stability determinants. The 16 ORF dcw gene cluster, which has a complex promoter structure and a partially characterized degradation pattern, was studied at high resolution, allowing a detailed and integrated description of its abundance and degradation. We discuss the application of subgenic resolution DNA microarray analysis to study global mechanisms of RNA transcription and processing.