DNA Methylation Plays a Role in Defining the Developmental Expression Profile of QQS, an Arabidopsis thaliana de novo Originated Gene

DNA methylation is an epigenetic modification involved in transposon silencing and regulation of gene expression. In plants, developmentally induced re-programming of DNA methylation profiles are critical for gene imprinting in the germline and for early embryo development. Yet, little is known about the integration of DNA methylation control and vegetative development. We have recently identified several spontaneous stably-inherited epialleles of the de novo Qua-Quine Starch (QQS, At3g30720) gene of Arabidopsis thaliana. Since the expression of the methylated QQS epiallele varies during vegetative growth and between different organs we thought to use QQS as a probe to explore the interplay between vegetative developmental programs and DNA methylation pathways. The expression levels of different QQS epialleles and their corresponding methylation profile were determined along development  in different plant organs. The expression of QQS was quite contrasted between the epialleles throughout development and correlated inversely with their DNA methylation levels. Relative expression analysis revealed that the methylated epialles presented more pronounced expression  differences between different organs than their demethylated counterparts. Moreover, higher expression of methylated QQS epiallele in leaves as compared to other organs was correlated with  reduced QQS promoter methylation. Based on our data we raised the hypothesis that DNA demethylation takes place while organs develop from the vegetative meristem. Other evidences suggest that  DNA methylation changes are not sufficient to explain all changes in QQS expression. Thus, these results indicate that DNA methylation and developmentally-regulated transcription factors play a role in the establishment of QQS expression pattern throughout Arabidopsis vegetative development.