Regulatory networks in trees

Abstract

Network analysis involves examining pairwise interactions between individual elements, in the current study genes and proteins. Unlike traditional data analysis methods that focus on individual elements, network analysis is an holistic approach that emphasizes the relationships among all elements and in- vestigates their collective behavior. Here, transcription factors (TFs) of importance in wood formation are identified and examined by looking at specific TF binding motifs (TF motifs) that are enriched in the regulatory promoter regions upstream of genes involved in secondary growth (i.e. wood develop- ment). The enriched TFs provided TF-gene links for inference of gene regulatory networks (GRNs) underlying wood formation in Populus tremula (a seed plant; Angiosperm) and Picea abies (a conifer; Gymnosperm). Multi-omics data (Co-expression and physical protein-protein interactions) of regulator and target genes in TF-gene links and hierarchical TF-TF links unraveled novel NAC and MYB master regulators, homologs of regulators in the non-woody model organism Arabidopsis thaliana, (At) and their NAC-MYB-based gene regulatory network (GRN). These pathways have been proposed to be conserved for the regulation of secondary cell wall (SCW) biosynthesis between herbaceous At and woody plants (Taylor-Teeples et al., 2015), (Li et al., 2024). Our network comparison revealed conserved network motifs in the GRNs of conifers and angiosperms that control SCW genes. This suggests that functional roles have been retained despite > 200 million years of evolutionary divergence between the two lineages and significant anatomical differences in both cell type and cell wall components. Our findings of master regulators represent potential biomarkers for secondary growth in trees and provide natural targets for future functional characterisation studies.

Network analysis involves examining pairwise interactions between individual elements, in the current study genes and proteins. Unlike traditional data analysis methods that focus on individual elements, network analysis is an holistic approach that emphasizes the relationships among all elements and in- vestigates their collective behavior. Here, transcription factors (TFs) of importance in wood formation are identified and examined by looking at specific TF binding motifs (TF motifs) that are enriched in the regulatory promoter regions upstream of genes involved in secondary growth (i.e. wood develop- ment). The enriched TFs provided TF-gene links for inference of gene regulatory networks (GRNs) underlying wood formation in Populus tremula (a seed plant; Angiosperm) and Picea abies (a conifer; Gymnosperm). Multi-omics data (Co-expression and physical protein-protein interactions) of regulator and target genes in TF-gene links and hierarchical TF-TF links unraveled novel NAC and MYB master regulators, homologs of regulators in the non-woody model organism Arabidopsis thaliana, (At) and their NAC-MYB-based gene regulatory network (GRN). These pathways have been proposed to be conserved for the regulation of secondary cell wall (SCW) biosynthesis between herbaceous At and woody plants (Taylor-Teeples et al., 2015), (Li et al., 2024). Our network comparison revealed conserved network motifs in the GRNs of conifers and angiosperms that control SCW genes. This suggests that functional roles have been retained despite > 200 million years of evolutionary divergence between the two lineages and significant anatomical differences in both cell type and cell wall components. Our findings of master regulators represent potential biomarkers for secondary growth in trees and provide natural targets for future functional characterisation studies.