A genetic network coordinated by TCP16 and LHY integrates regulation of the vegetative-reproductive phase transition in Arabidopsis thaliana

Abstract

The transition to flowering in Arabidopsis thaliana is a complex process governed by many biological and environmental stimuli. Although many of the genes which regulate this process have been identified over the past 30 years, it remains unclear how these networks are integrated. In this study, we used the transcriptional responses of Col-0, Ler-1, and three mutant lines, to build a genome wide regulatory network of Arabidopsis thaliana during the flowering transition. The expression profiles of 22,810 genes across five genotypes were collected from the GEO database Series GSE57 from which we assigned flowering-time genes to different interacting modules by an adapted form of Hierarchical Complete Linkage Clustering (HCLC) after reconstruction of regulatory networks according to the Position Weight Matrix (PWM)-based method. Within these modules, we identified 77 core genes and 31 controller or driver genes. We identify two genes, LHY and, less expectedly, the transcription factor TCP16, to be topographically positioned at the regulatory hubs a nine-gene transcriptional control unit, implying they have the capacity to integrate information from across the flowering time pathways which interpret different environmental or endogenous cues during the vegetative-reproductive transition. Interrogating their behaviour across transcriptional datasets, we show that both LHY and TCP16 show transcriptional oscillations during the flowering transition, with a wavelength that varies depending on environmental conditions. We suggest that the transcriptional responses of LHY and TCP16 allow them to regulate the flow of information through the genetic networks which integrates different floral transition cues, and that genetic modelling approaches can provide new insights into the regulation of well-studied biological processes such as the flowering transition. Author summaryHow plants decide when to flower is a critical stage for completing their life cycles. It is also of key agricultural importance, as crops need to flower at the right time of year to allow efficient pollination and harvesting. Many genes are known to affect flowering time control in plants. Here, we use computational approaches to estimate how different genes interact in flowering time control in Arabidopsis, a small plant in the mustard family which is widely used for molecular studies. We use large-scale studies of how gene expression changes in different plant lines which have disrupted or adjusted flowering time to group the many genes involved in flowering into different interacting pathway, which we visualise as sets of coloured nodes controlling one another in a network. We show that two genes may have new rols in integrating information from different pathways, and discuss how their behaviour might help them to function as intregrators of biological information - including the daily oscaillations in their expression.