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Deciphering the origins of gene expression bursts at dawn, using computer-aided experimental design

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Abstract: Eukaryotes are able to change gene expression within minutes, but it is difficult to identify regulatory targets for genes that are only expressed for a very short length of time. To help resolve these regulatory relationships, we sought to create a high-resolution time course to capture these transient expression changes, but also obtain a large number of genetic and environmental perturbation experiments to discriminate between causative and correlative relationships between genes. Because the large number of samples required for a high resolution time course under many conditions rapidly becomes unpractical, we have created a general-purpose tool, New Investigation Time Point Picker (NITPicker), to aide in the design of experiments that require both fine-scale temporal resolution and many perturbation experiments. NIT Picker identifies subsets of time points within a high resolution time course which would be most informative to sample in perturbation experiments, taking into account lab budget and experimental requirements. In particular, we apply this tool to help identify the how plants rapidly adjust their transcriptomes at the onset of dawn, when the circadian clock is entrained by light and when plants are most resilient to many environmental stressors. By using a high-resolution RNA -seq time course (sampled every 2 minutes), as well as RNA -seq time course experiments in which the circadian clock, light perception, and temperature response are perturbed, we determined that there are numerous waves of gene expression after dawn, and that plants employ a ‘multi-threading’ approach to coordinate environmental and circadian signals.

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