Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana
Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana
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DOI：
10.1105/tpc.107.055046
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发表时间：
2007-11-01
期刊：
影响因子：
11.6
通讯作者：
Whelan, James
中科院分区：
文献类型：
--
作者：
Narsai, Reena;Howell, Katharine A.;Whelan, James
为了全面了解拟南芥中 mRNA 的衰减情况，用转录抑制剂处理悬浮细胞培养物，并使用微阵列来测量随时间变化的转录丰度。推断的 mRNA 半衰期差异很大，从几分钟到 >24 小时。转录本的三个特征显示出与衰减率相关：（1）具有至少一个内含子的基因产生的mRNA转录本比无内含子的基因显着更稳定，并且这与总长度、序列组成或内含子的数量无关； (2) 39个非翻译区的各种序列元件在短寿命和长寿命转录本中富集，它们的多重出现表明转录本衰减的组合控制； (3) 作为 microRNA 靶标的转录物通常半衰期较短。转录本的衰减率与编码蛋白质的亚细胞定位和功能相关。对拟南芥、酵母和人类之间编码直系同源蛋白质的基因转录本衰减率的分析表明，酵母和人类具有较高比例的半衰期较短的转录本，并且来自编码参与细胞周期、转录、翻译和能量代谢的蛋白质的基因的转录本的相对稳定性是保守的。将衰减率与各种非生物胁迫下转录丰度的变化进行比较表明，一组转录因子以与衰减率相似的动力学下调，这表明对其转录的抑制是对非生物胁迫的重要早期反应。
To gain a global view of mRNA decay in Arabidopsis thaliana, suspension cell cultures were treated with a transcriptional inhibitor, and microarrays were used to measure transcript abundance over time. The deduced mRNA half-lives varied widely, from minutes to >24 h. Three features of the transcript displayed a correlation with decay rates: (1) genes possessing at least one intron produce mRNA transcripts significantly more stable than those of intronless genes, and this was not related to overall length, sequence composition, or number of introns; (2) various sequence elements in the 39 untranslated region are enriched among short- and long-lived transcripts, and their multiple occurrence suggests combinatorial control of transcript decay; and (3) transcripts that are microRNA targets generally have short half-lives. The decay rate of transcripts correlated with subcellular localization and function of the encoded proteins. Analysis of transcript decay rates for genes encoding orthologous proteins between Arabidopsis, yeast, and humans indicated that yeast and humans had a higher percentage of transcripts with shorter half-lives and that the relative stability of transcripts from genes encoding proteins involved in cell cycle, transcription, translation, and energy metabolism is conserved. Comparison of decay rates with changes in transcript abundance under a variety of abiotic stresses reveal that a set of transcription factors are downregulated with similar kinetics to decay rates, suggesting that inhibition of their transcription is an important early response to abiotic stress.