Exploring Camelina sativa lipid metabolism regulation by combining gene co-expression and DNA affinity purification analyses

Camelina is an annual oilseed plant that is gaining momentum as a biofuel winter cover crop. Understanding gene regulatory networks (GRNs) is essential to deciphering plant metabolic pathways, including lipid metabolism. Here, we take advantage of a growing collection of gene expression datasets to predict transcription factors (TFs) associated with the control of Camelina lipid metabolism. Also, we performed RNA-seq assays of Camelina's seed at 5, 8, and 11 days post-anthesis (DPA) to improve the transcriptomic resolution of the early stages of the Camelina seed development. We identified ~350 TFs highly co-expressed with lipid-related genes (LRGs). After prioritizing the top 22 TFs for further validation, we identified DNA-binding sites and predicted target genes for 16/22 TF using DNA affinity purification sequencing (DAP-seq). Enrichment analyses supported the co-expression prediction for most TF candidates, and the comparison to Arabidopsis revealed some common themes and aspects unique to Camelina. Altogether, the integration of co-expression data and DNA-binding assays permitted us to generate a high-confident and shortlist of Camelina TFs involved in controlling lipid metabolism during seed development. Examination of gene expression (RNA-seq) during three-time point during early stages of seed development as well as the evaluation of DNA-binding profiles (DAP-seq ) for 22 TF in Camelina sativa. RNA-seq and DAP-seq experiments were performed in triplicate and duplicate. Processed data is not included for Csa17g034220_deM and Csa19g036630_deM samples due to their high correlation with the Halo control.