Abstract
Leaf senescence is the orderly dismantling of older tissue that allows recycling of nutrients to developing portions of the plant and is accompanied by major changes in gene expression. Histone modifications correlate to levels of gene expression, and 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. 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. Only a small number of genes gained the H3K27me3 mark, and these were senescence down-regulated. Approximately 50% of senescence up-regulated genes lacked the H3K4me3 mark in both mature and senescent leaf tissue. Two of these genes, SAG12 and At1g73220, display strong senescence up-regulation without the activating H3K4me3 histone modification. This study provides an initial epigenetic framework for the developmental transition into senescence.
Highlights
Arabidopsis thaliana, similar to most crop plants, is a monocarpic species that undergoes whole plant senescence to maximize energy input into reproductive structures
Data are displayed on a mirror UCSC genome browser under Senescence chromatin immunoprecipitation (ChIP)-seq and tracks are displayed in the following order, from top to bottom: H3K4me3_23d, H3K4me3_52d, K4_diff, H3K27me3_23d, H3K27me3_52d, and K27_diff
Senescence is the orderly, final process of leaf development, and this study aimed to determine if there were any epigenetic changes that marked the chromatin of the senescent leaf and if these correlated to changes in gene expression
Summary
Arabidopsis thaliana, similar to most crop plants, is a monocarpic species that undergoes whole plant senescence to maximize energy input into reproductive structures. Global gene expression has been characterized in senescent Arabidopsis tissue [1,2,3,4], and senescence up-regulated genes (SURGs) are enriched for autophagy, response to reactive oxygen species, chlorophyll and lipid catabolism as well as carbohydrate and nitrogen transport. Transcription factors that play a role in these global changes in gene expression have been identified. Genetic and biochemical evidence support a role for WRKY53 (Locus:2128514) and NAC family members VNI2 (Locus:2179877) and AtNAP (Locus:2007166) as positive regulators of senescence [6,7,8,9,10] , and microarray analysis reveals over-representation for the AP2-EREBP, bZIP, C3H, CCAAT, NAC and WRKY transcription factor families as senescence progresses [1]
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