Synechococcus elongatus is an important cyanobacterium that serves as a versatile and robust model for studying circadian biology and photosynthetic metabolism. Its transcriptional regulatory network (TRN) is of fundamental interest, as it orchestrates the cell’s adaptation to the environment, including its response to sunlight. Despite the previous characterization of constituent parts of the S. elongatus TRN, a comprehensive layout of its topology remains to be established. Here, we decomposed a compendium of 300 high-quality RNA sequencing datasets of the model strain PCC 7942 using independent component analysis. We obtained 57 independently modulated gene sets, or iModulons, that explain 67% of the variance in the transcriptional response and 1) accurately reflect the activity of known transcriptional regulations, 2) capture functional components of photosynthesis, 3) provide hypotheses for regulon structures and functional annotations of poorly characterized genes, and 4) describe the transcriptional shifts under dynamic light conditions. This transcriptome-wide analysis of S. elongatus provides a quantitative reconstruction of the TRN and presents a knowledge base that can guide future investigations. Our systems-level analysis also provides a global TRN structure for S. elongatus PCC 7942.

中文翻译：

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机器学习揭示了 Synechococcus elongatus PCC 7942 的转录调控网络和昼夜节律动力学


Synechococcus elongatus 是一种重要的蓝藻，是研究昼夜节律生物学和光合代谢的多功能和稳健模型。它的转录调节网络 （TRN） 具有根本意义，因为它协调细胞对环境的适应，包括对阳光的反应。尽管之前对 S. elongatus TRN 的组成部分进行了表征，但其拓扑结构的全面布局仍有待建立。在这里，我们使用独立成分分析分解了模型菌株 PCC 7942 的 300 个高质量 RNA 测序数据集的纲要。我们获得了 57 个独立调制的基因集或 iModulons，它们解释了 67% 的转录反应方差，并且 1） 准确反映了已知转录调控的活性，2） 捕获光合作用的功能成分，3） 为表征不佳的基因的调节子结构和功能注释提供假设，以及 4） 描述动态光照条件下的转录变化。这种对 S. elongatus 的转录组范围分析提供了 TRN 的定量重建，并提供了可以指导未来调查的知识库。我们的系统级分析还提供了 S. elongatus PCC 7942 的全局 TRN 结构。