Genome-wide correlation analysis to identify amplitude regulators of circadian transcriptome output.
Genome-wide correlation analysis to identify amplitude regulators of circadian transcriptome output.
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DOI：
10.1038/s41598-020-78851-9
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发表时间：
2020-12-14
影响因子：
4.6
通讯作者：
Kojima S
中科院分区：
文献类型：
--
作者：
Littleton ES;Childress ML;Gosting ML;Jackson AN;Kojima S
细胞自主的昼夜节律系统由核心时钟基因组成，产生近24小时的节律，并调节下游节律基因的表达。虽然节奏基因的百分比在小鼠组织中的变化已经很清楚，但仍然不清楚这种变化是如何产生的，特别是当时钟机制在所有组织中几乎相同时。在这项研究中，我们试图描述公开可用的昼夜节律转录组数据集，并确定创建这种变化所涉及的关键组件。我们发现13个基因的相对振幅和197个基因的平均水平与循环基因的百分比相关。其中，Rorc在相对振幅和平均水平上的相关性最强。此外，Per2AS（一种在第2阶段基因座表达的新型非编码转录物）的水平也呈线性相关，尽管与Rorc相比程度要小得多。总的来说，我们的研究提供了对小鼠组织中时钟控制基因百分比变化的深入了解，并表明Rorc和潜在的Per2AS参与调节昼夜节律转录组输出的幅度。
Cell-autonomous circadian system, consisting of core clock genes, generates near 24-h rhythms and regulates the downstream rhythmic gene expression. While it has become clear that the percentage of rhythmic genes varies among mouse tissues, it remains unclear how this variation can be generated, particularly when the clock machinery is nearly identical in all tissues. In this study, we sought to characterize circadian transcriptome datasets that are publicly available and identify the critical component(s) involved in creating this variation. We found that the relative amplitude of 13 genes and the average level of 197 genes correlated with the percentage of cycling genes. Of those, the correlation of Rorc in both relative amplitude and the average level was one of the strongest. In addition, the level of Per2AS, a novel non-coding transcript that is expressed at the Period 2 locus, was also linearly correlated, although with a much lesser degree compared to Rorc. Overall, our study provides insight into how the variation in the percentage of clock-controlled genes can be generated in mouse tissues and suggests that Rorc and potentially Per2AS are involved in regulating the amplitude of circadian transcriptome output.
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DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
影响因子：
12.3
作者：
Marchese FP;Raimondi I;Huarte M
通讯作者：
Huarte M
影响因子：
14.9
作者：
The Gene Ontology Consortium
通讯作者：
The Gene Ontology Consortium
影响因子：
4.5
作者：
Liu AC;Tran HG;Zhang EE;Priest AA;Welsh DK;Kay SA
通讯作者：
Kay SA
影响因子：
4.6
作者：
Matsumura R;Okamoto A;Node K;Akashi M
通讯作者：
Akashi M