Transcriptome profile of barley aleurone differs between total and polysomal RNAs: implications for proteome modeling

Abstract

Microarray analysis of mRNA populations is routinely conducted with total RNA. However, such analyses would probably represent the translated genome (proteome) more accurately if conducted with polysomal RNA. An accurate assessment of the proteome is essential where microarray analysis is used to produce molecular markers for breeding programs. In order to determine whether significant variation occurs between these two RNA populations, the relative abundance of transcripts was analyzed in barley aleurones of intact 3.5 day old germinated seedlings, comparing total and polysomal RNAs. A total of 13,744 transcripts was detected among both populations. Of these, 714 were detected only in total RNA, and 1,541 were detected only in polysomal RNA. A surprising number of transcripts detected in both populations (6,312 gene calls or 46% of the compared transcripts) differed significantly between populations. Almost half of these (2,987) were more abundant by at least two-fold, depending on the RNA source, and expression was often biased toward specific functional classes of genes. Transcripts encoding hydrolytic enzymes for the mobilization of stored seed macromolecules were more highly represented in total RNA, rather than polysomal RNA. These included proteinases, nucleases and carbohydrases. Genes for ribonucleoprotein complexes, nucleic acid binding and components of ribosomes were more abundant in polysomal RNA. Among genes with signal intensities of 1,000 or more, hydrolases were greatly over-represented in total RNA, whereas ubiquitin, histone and kinase related genes were mainly represented in polysomal RNA.