Online Event
September 01-03, 2022 | Online Event
GPMB 2022

Gene regulatory network Inference of crassulacean acid metabolism

Methawi Chomthong, Speaker at Plant Conferences 2022
University of Cambridge, United Kingdom
Title : Gene regulatory network Inference of crassulacean acid metabolism


Recent transcriptomic studies have demonstrated the inverted pattern of gene expression associated with night-time carbon fixation during Crassulacean Acid Metabolism (CAM). This data provides an opportunity to use computational tools to determine the complex Gene Regulatory Network (GRN) of CAM. Gene Regulatory Network inferences and Transcription Factor Binding Site (TFBS) searches have been used to identify potential regulatory candidates of gene expression which will help to define the CAM pathway. The DynGENIE3 algorithm has been adopted to tackle the complex gene regulatory network in an unbiased manner without a priori knowledge. Network inference yielded a ranked list of transcriptional regulatory candidates for key CAM genes, with a particular focus on phosphoenolpyruvate carboxylase kinase (ppck), and the pyrophosphate dikinase regulatory protein gene (ppdk-rp), known to demonstrate an inverted timing relative to C3 species, and also known to have a prominent role in the circadian control of carboxylation and intermediate regeneration, respectively. The GRN was then coupled downstream with TFBS analysis, using the wellestablished computational tool FIMO. Statistically significant transcription factor-target relationships were identified from the combination of two algorithms to provide a list of regulatory candidates on genes of interests. This study focussed on key subnetworks that have implications for the functioning of CAM: namely carboxylation, decarboxylation, circadian control, stomatal function and carbohydrate metabolism. From this analysis we have identified a list of common regulatory candidates across multiple subnetworks to the level of transcription factor families. Furthermore, the identities of the major transcription factor candidates can be specified to the level of unique gene ID for both the candidate transcription factors and their target genes, including but not limited to ppck and ppdk-rp as well as key regulators of the circadian cycle, including HY5, LUX, ELF3, and ELF4.