Circadian Cycles of Gene Expression in the Coral, Acropora millepora

BackgroundCircadian rhythms regulate many physiological, behavioral and reproductive processes. These rhythms are often controlled by light, and daily cycles of solar illumination entrain many clock regulated processes. In scleractinian corals a number of different processes and behaviors are associated with specific periods of solar illumination or non-illumination—for example, skeletal deposition, feeding and both brooding and broadcast spawning. Methodology/Principal FindingsWe have undertaken an analysis of diurnal expression of the whole transcriptome and more focused studies on a number of candidate circadian genes in the coral Acropora millepora using deep RNA sequencing and quantitative PCR. Many examples of diurnal cycles of RNA abundance were identified, some of which are light responsive and damped quickly under constant darkness, for example, cryptochrome 1 and timeless, but others that continue to cycle in a robust manner when kept in constant darkness, for example, clock, cryptochrome 2, cycle and eyes absent, indicating that their transcription is regulated by an endogenous clock entrained to the light-dark cycle. Many other biological processes that varied between day and night were also identified by a clustering analysis of gene ontology annotations. Conclusions/SignificanceCorals exhibit diurnal patterns of gene expression that may participate in the regulation of circadian biological processes. Rhythmic cycles of gene expression occur under constant darkness in both populations of coral larvae that lack zooxanthellae and in individual adult tissue containing zooxanthellae, indicating that transcription is under the control of a biological clock. In addition to genes potentially involved in regulating circadian processes, many other pathways were found to display diel cycles of transcription.

【背景】昼夜节律（circadian rhythms）调控诸多生理、行为与生殖过程。这类节律通常受光信号调控，日光的每日光照周期可同步众多受生物钟调控的生命过程。在石珊瑚（scleractinian corals）中，诸多不同的生理过程和行为与特定的光照或非光照时段紧密相关——例如骨骼沉积、摄食，以及育幼繁殖与散播式产卵（broadcast spawning）。【方法与主要发现】本研究借助深度RNA测序（deep RNA sequencing）与定量PCR（quantitative PCR）技术，对千孔鹿角珊瑚（Acropora millepora）的全转录组昼夜表达模式开展了系统性分析，并针对多个候选昼夜节律基因展开了针对性研究。研究团队鉴定出大量RNA丰度呈现昼夜周期变化的基因：其中一部分受光调控，并在持续黑暗环境中快速衰减，例如隐花色素1（cryptochrome 1）与timeless基因；另一部分则在持续黑暗条件下仍能维持稳健的周期表达，例如时钟基因（clock）、隐花色素2（cryptochrome 2）、周期基因（cycle）与眼睛缺失基因（eyes absent），这表明这些基因的转录过程受光暗周期同步的内源生物钟调控。通过对基因本体（gene ontology，GO）注释结果进行聚类分析，本研究还鉴定出诸多其他呈现昼夜差异的生物学过程。【结论与意义】珊瑚的基因表达呈现昼夜模式，该模式可能参与调控昼夜节律相关的生物学过程。在缺乏虫黄藻（zooxanthellae）的珊瑚幼虫群体，以及含有虫黄藻的成年珊瑚组织中，均观测到基因表达的周期性节律在持续黑暗条件下依然存在，这证实基因转录过程受生物生物钟的调控。除了潜在参与昼夜节律调控的基因外，本研究还发现诸多其他通路的转录过程同样呈现昼夜周期变化。