Co-expression networks from gene expression variability between genetically identical seedlings can reveal novel regulatory relationships

Abstract

Co-expression networks are a powerful tool to understand gene regulation. They have been used to identify new regulation and function of genes involved in plant development and their response to the environment. Up to now, co-expression networks have been inferred using transcriptomes generated on plants experiencing genetic or environmental perturbation, or from expression time series. We propose a new approach by showing that co-expression networks can be constructed in the absence of genetic and environmental perturbation, for plants at the same developmental stage. For this we used transcriptomes that were generated from genetically identical individual plants that were grown in the same conditions and for the same amount of time. Twelve time points were used to cover the 24h light/dark cycle. We used variability in gene expression between individual plants of the same time point to infer a co-expression network. We show that this network is biologically relevant and use it to suggest new gene functions and to identify new targets for the transcription factors GI, PIF4 and PRR5. Moreover, we find different co-regulation in this network based on changes in expression between individual plants, compared to the usual approach requiring environmental perturbation. Our work shows that gene co-expression networks can be identified using variability in gene expression between individual plants, without the need for genetic or environmental perturbations. It will allow further exploration of gene regulation in contexts with subtle differences between plants, which could be closer to what individual plants in a population might face in the wild. Author summaryPlant development and response to changes in the environment are strongly regulated at the level of gene expression. That is why understanding how gene expression is regulated is key, and transcriptome approaches have allowed the analysis of transcription for all genes of the genome. Extracting useful information from the high amount of data generated by transcriptomes is a challenge, and gene co-expression networks are a powerful tool to do this. The principle is to find genes that co-vary in expression in different conditions and to pair them together. Communities of genes that are more closely linked are then identified and this is the starting point to look for their implication in the same pathway. Co-expression networks have been used to identify new regulation and function of genes involved in plant development and their response to the environment. They were constructed using transcriptomes generated on plants experiencing genetic or environmental perturbation. We show that co-expression networks can in fact be constructed in the absence of genetic and environmental perturbation. Our work will allow further exploration of gene co-regulation in contexts with subtle differences between plants, which could be closer to what individual plants in a population might face in the wild.