Genome-wide Evaluation of Histone Methylation Changes Associated with Leaf Senescence in Arabidopsis

Major changes in gene expression accompany leaf senescence which is the orderly dismantling of older tissue that allows recycling of nutrients to developing portions of the plant.  This study utilizes ChIP-seq to classify activating H3K4me3 and silencing H3K27me3 marks on a genome-wide scale for soil-grown mature and naturally senescent Arabidopsis leaves.  Data are displayed in a publicly available database (http://genomes.mcdb.ucla.edu/).   ChIPnorm was used to normalize data sets and identify genomic regions with significant differences in the two histone methylation patterns, and the differences were correlated to changes in gene expression.  Genes that showed an increase in the H3K4me3 mark in older leaves were senescence up-regulated, while genes that showed a decrease in the H3K4me3 mark in the older leaves were senescence down-regulated.  For the H3K27me3 modification, genes that lost the H3K27me3 mark in older tissue were senescence up-regulated.   Recently, a T-DNA insertion disrupting a gene encoding a putative H3K4me3 demethylase was shown to result in early expression of senescence up-regulated genes suggesting that active H3K4me3 demethylation maintains certain target genes in a silenced state.  T-DNA disruptions in other putative H3K4me3 demethylases and H3K4me3 methyl transferases are currently being evaluated for expression of senescence up- and down-regulated genes.   Additional studies in progress include utilizing more time points and determining patterns of histone acetylation in mature and senescing leaf tissue.