Monitoring endoplasmic reticulum stress responsive mRNAs by RNA sequencing
Monitoring endoplasmic reticulum stress responsive mRNAs by RNA sequencing
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通过 RNA 测序监测内质网应激反应 mRNA
DOI：
10.1016/j.gene.2012.03.048
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发表时间：
2012
期刊：
影响因子：
3.5
通讯作者：
Sugano S
中科院分区：
文献类型：
--
作者：
Okuda T;Wakaguri H;Suzuki Y;Sugano S
通过使用来自HT 29细胞的多聚核糖体或细胞质的RNA的mRNA的深度鸟枪测序（DSSR）来分析内质网（ER）应激后的基因表达谱。使用两个时间点，衣霉素处理后4 h（IRE 1 α信号通路活跃时）和处理后16 h（IRE 1 α信号通路失活时）。在多核糖体中短片段（<1000 bp）的mRNA比例短暂下降，而在胞质中则短暂增加。尽管有这样的总体变化和多聚核糖体总量的减少，但分析的6966个基因中的大多数在其表达中具有小于2倍的变化。我们寻找在多核糖体和细胞质中表达量增加2倍或更多的基因，并用RT-PCR证实了结果。其中7个基因仅在4 h（组I）升高，20个基因仅在16 h（组II）升高，7个基因在4 h和16 h（组III）均升高。I组中有3个基因参与核糖体RNA生物合成，III组中有2个基因参与mTOR控制。这与核糖体是处理内质网应激的重要位点的概念一致。DSSR是寻找内质网应激反应基因的有效工具。
Gene expression profile upon endoplasmic reticulum (ER) stress was analyzed by deep shotgun sequencing of mRNAs (DSSR) using RNAs from polysomes or cytoplasm of the HT29 cell. Two time points, 4h after tunicamycin treatment when IRE1α signaling pathway is active and 16h after the treatment when it is inactive, were used. There was a transient decrease in the proportion of shorter mRNA species (<1000bp) in polysome, while it increased transiently in the cytoplasm. Despite such an overall change and decrease in total amount of polysomes, the majority of the 6966 genes analyzed had less than 2 fold change in their expressions. We searched for the genes whose expression was elevated by 2 folds or more in both polysome and cytoplasm and confirmed the results with RT-PCR. There were 7 genes elevated only at 4h (Group I), 20 genes only at 16h (Group II) and 7 genes both at 4 and 16h (Group III). There were 3 genes involved in ribosomal RNA biogenesis in Group I and 2 genes involved mTOR control in Group III. This was consistent with the concept that the ribosome is the essential site for managing ER stress. DSSR is a useful tool for the search of candidates of ER stress responsive genes.