The distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana resolve the Central Dogma’s information flow

A label-free proteomics dataset from our investigation of the interplay of constitutive gene-body CpG methylation (gbM), tRNA abundance and codon composition on mRNA and protein expression, in the plant Arabidopsis thaliana. We performed genomic profiling in rosette leaves of two Arabidopsis accessions, Col-0 and Can-0, and re-assembled and re-annotated their genomes using long reads. We measured gene and protein expression levels in multiple biological replicates grown in a constant environment, also measuring ribosome-associated transcript levels and tRNA abundance. We fitted models to explain variation in gbM, tRNA, gene and protein expression in the paper.