Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression
Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression
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DOI：
10.1261/rna.039081.113
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发表时间：
2013-06-01
期刊：
影响因子：
4.5
通讯作者：
Black, Douglas L.
中科院分区：
文献类型：
--
作者：
Pandya-Jones, Amy;Bhatt, Dev M.;Black, Douglas L.
真核 mRNA 的表达是通过一系列复杂的分子过程实现的，这些过程提供了调节最终基因产物产生的许多步骤。然而，人们对 mRNA 生物合成的各个步骤及其发生速率之间的关系知之甚少。通过将 RNA-seq 应用于来自脂质 A 刺激的巨噬细胞的 RNA 的染色质相关和可溶核质部分，我们检查了外显子连接和转录物从染色质释放相对于转录诱导的时间。我们发现，对于脂质 A 反应中的一部分基因，某些外显子对的连接相对于完整转录本的合成被延迟。相反，一旦转录延伸通过切割位点，3'端切割和聚腺苷酸化就会迅速发生。我们的数据表明，这些具有延迟剪接的转录本直到所有内含子都被切除后才从染色质部分释放。这些不寻常的动力学导致完全转录和 3' 加工转录本的染色质相关池尚未完全剪接。我们还发现，与转录本中的其他内含子相比，含有抑制外显子（将从最终 mRNA 中排除）的长内含子的切除速度特别慢。这些结果表明剪接和转录物释放的动力学有助于炎症反应的多个基因的表达时间。
The expression of eukaryotic mRNAs is achieved though an intricate series of molecular processes that provide many steps for regulating the production of a final gene product. However, the relationships between individual steps in mRNA biosynthesis and the rates at which they occur are poorly understood. By applying RNA-seq to chromatin-associated and soluble nucleoplasmic fractions of RNA from Lipid A-stimulated macrophages, we examined the timing of exon ligation and transcript release from chromatin relative to the induction of transcription. We find that for a subset of genes in the Lipid A response, the ligation of certain exon pairs is delayed relative to the synthesis of the complete transcript. In contrast, 3' end cleavage and polyadenylation occur rapidly once transcription extends through the cleavage site. Our data indicate that these transcripts with delayed splicing are not released from the chromatin fraction until all the introns have been excised. These unusual kinetics result in a chromatin-associated pool of completely transcribed and 3'-processed transcripts that are not yet fully spliced. We also find that long introns containing repressed exons that will be excluded from the final mRNA are excised particularly slowly relative to other introns in a transcript. These results indicate that the kinetics of splicing and transcript release contribute to the timing of expression for multiple genes of the inflammatory response.