Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions.
Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions.
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DOI：
10.1038/s41598-018-26170-5
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发表时间：
2018-05-21
影响因子：
4.6
通讯作者：
Hubbard SJ
中科院分区：
文献类型：
--
作者：
Talavera D;Kershaw CJ;Costello JL;Castelli LM;Rowe W;Sims PFG;Ashe MP;Grant CM;Pavitt GD;Hubbard SJ
酵母细胞对不同胁迫的转录反应通常包括基因激活和抑制。特定的胁迫防御、柠檬酸循环和氧化磷酸化基因被激活，而蛋白质合成基因被协同抑制。这一观点是通过比较转录实验得出的，这些实验描绘了一组基因，这些基因的表达随着特定的压力而发生很大变化。人们较少注意到1)RNA水平在多种情况下持续变化，尽管变化不大，以及2)在比较众多全基因组研究时观察到的全球基因表达相关性的生物学意义。为了解决这个问题，我们在酵母中进行了1379个基于微阵列的实验的荟萃分析，并确定了1388个RNA块，它们的表达变化在多种不同的条件下相关。其中许多块代表了一组功能相关的RNA，它们在正常和应激条件下以协调的方式发挥作用，并映射到全球细胞防御和生长反应。随后，我们使用这些模块来分析新的RNA-SEQ实验，展示了它们的实用性，并证实了从荟萃分析得出的结论。我们的结果为理解基因表达变化的生物学意义提供了一个新的框架：‘原型’转录块，它以一种协调的方式调节对外部刺激的反应。
The transcriptional responses of yeast cells to diverse stresses typically include gene activation and repression. Specific stress defense, citric acid cycle and oxidative phosphorylation genes are activated, whereas protein synthesis genes are coordinately repressed. This view was achieved from comparative transcriptomic experiments delineating sets of genes whose expression greatly changed with specific stresses. Less attention has been paid to the biological significance of 1) consistent, albeit modest, changes in RNA levels across multiple conditions, and 2) the global gene expression correlations observed when comparing numerous genome-wide studies. To address this, we performed a meta-analysis of 1379 microarray-based experiments in yeast, and identified 1388 blocks of RNAs whose expression changes correlate across multiple and diverse conditions. Many of these blocks represent sets of functionally-related RNAs that act in a coordinated fashion under normal and stress conditions, and map to global cell defense and growth responses. Subsequently, we used the blocks to analyze novel RNA-seq experiments, demonstrating their utility and confirming the conclusions drawn from the meta-analysis. Our results provide a new framework for understanding the biological significance of changes in gene expression: ‘archetypal’ transcriptional blocks that are regulated in a concerted fashion in response to external stimuli.
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影响因子：
5.3
作者：
GABER, RF;COPPLE, DM;BARD, M
通讯作者：
BARD, M
影响因子：
5.8
作者：
Hibbs, Matthew A.;Hess, David C.;Troyanskaya, Olga G.
通讯作者：
Troyanskaya, Olga G.
影响因子：
12.3
作者：
Costello JL;Kershaw CJ;Castelli LM;Talavera D;Rowe W;Sims PFG;Ashe MP;Grant CM;Hubbard SJ;Pavitt GD
通讯作者：
Pavitt GD
影响因子：
10.5
作者：
FORSBURG, SL;GUARENTE, L
通讯作者：
GUARENTE, L
影响因子：
7
作者：
Bellay, Jeremy;Atluri, Gowtham;Myers, Chad L.
通讯作者：
Myers, Chad L.