An Integrated System-Wide Maize Atlas: From Transcriptome to Proteome Networks

Integrated molecular atlases make possible systems biology approaches aimed at understanding biological phenomena.  Using RNA-seq and quantitative mass spectrometry we generated an atlas comprised of 62,547 mRNAs, 17,862 non-modified proteins, and 6,227 phosphoproteins harboring 31,595 phosphorylation sites, quantified across maize development.  Analysis of the atlas has revealed complex spatiotemporal patterns of gene activity.  For example, there is poor correlation between protein and mRNA levels and for many of the most abundant proteins there is little to no detectable cognate mRNA. The atlas has also enabled generation and interrogation of a number of different types of regulatory networks including mRNA and protein co-expression networks, and gene regulatory networks (GRN). Together, these studies highlight the complex interplay of transcriptional, translational and post-translational events in proteome dynamics.