Reprogramming feedback strength in gibberellin biosynthesis highlights conditional regulation by the circadian clock and carbon dioxide

The phytohormone gibberellin (GA) is an important regulator of plant morphology and reproduction, and the biosynthesis and distribution of GA in planta is agriculturally relevant to past and current breeding efforts. Tools like biosensors, extensive molecular genetic resources in reference plants and mathematical models have greatly contributed to current understanding of GA homeostasis; however, these tools are difficult to tune or repurpose for engineering crop plants. Previously, we showed that a GA-regulated Hormone Activated CAS9-based Repressor (GAHACR) functions in planta (Khakhar et al., 2018). Here, we use GAHACRs to modulate the strength of feedback on endemic GA regulated genes, and to directly test the importance of transcriptional feedback in GA signaling. We first adapted existing mathematical models to predict the impact of targeting a GAHACR to different nodes in the GA biosynthesis pathway, and then implemented a perturbation predicted by the mo..., RNA-Seq
For ambient carbon dioxide concentrations, T4 seedlings were cultured on plates for 4 days without drug selection, and then transplanted to LS0 plates without drug for 10 days in either ambient or carbon dioxide-supplemented Conviron (Pembina, North Dakota) growth chambers. RNA was extracted using the Illustra RNAspin Mini Kit from GE, and RNA-Seq was performed by Amaryllis Nucleics (Oakland CA). In brief, RNA was checked for quality and quantity on a Bioanalyzer, and poly(A) mRNA was purified from total RNA. The library was constructed using the Amaryllis proprietary construction kit, followed by QC by E-gel & Bioanalyzer. Libraries were pooled and run on an Illumina NextSeq 500 SR75, with a target of approximately 20 million reads per sample. Read preprocessing, mapping, and differential gene expression were performed by Amaryllis, in addition to independent differential gene expression analysis in-house using EdgeR and DESeq2. Network analysis was performed in cytoscape. ..., , # Reprogramming feedback strength in gibberellin biosynthesis highlights conditional regulation by the circadian clock and carbon dioxide

[https://doi.org/10.5061/dryad.547d7wmgr](https://doi.org/10.5061/dryad.547d7wmgr)

## Description of the data and file structure

**Dataset overview:**

Counts tables for differential gene expression performed in the analysis of 'reprogramming feedback strength in gibberellin biosynthesis highlights conditional regulation by the circadian clock and carbon dioxide' are provided for RNA-Seq experiments performed on Arabidopsis seedlings. We performed these at both Ambient and elevated (750ppm) carbon dioxide levels, with and without the GAHACR genetic perturbation, using GAHACRs to modulate the strength of feedback on endemic GA regulated genes, and to directly test the importance of transcriptional feedback in GA signaling. In order to facilitate future researchers to most easily incorporate our RNA-seq results, we have shared the count tables genera...,