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

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.

A Genome-Wide Chronological Study of Gene Expression and Two Histone Modifications, H3K4me3 and H3K9ac, during Developmental Leaf Senescence

“…S6B), suggesting that H3K4me3 modifications in the promoter can be associated with changes in gene expression. This differed from our previous study, in which SAG12 was not marked by H3K4me3 (Brusslan et al, 2012). The other gene that was reported to be strongly up-regulated that did not have H3K4me3 marks, At1g73220, was devoid of both marks in this study ( Supplemental Fig.…”

“…The abundance of H3K4me3 and H3K9ac histone modifications changes at specific loci during numerous developmental transitions in plants (Kim et al, 2008(Kim et al, , 2009a(Kim et al, , 2012Charron et al, 2009;Adrian et al, 2010;Anzola et al, 2010;van Dijk et al, 2010;Brusslan et al, 2012;Malapeira et al, 2012;López-González et al, 2014;Molitor et al, 2014;Schenke et al, 2014), and thus, it is likely that the final stage of leaf development, leaf senescence, would be accompanied by changes in these two well-characterized histone modifications that positively correlate with gene expression. Leaves were harvested from progressively more senescent plants and subject to RNA-seq and ChIP-seq, so that a direct correlation between gene expression and Table II.…”

“…Plant Growth, Nuclei Isolation, ChIP, ChIP Library Preparation, RNA Isolation, and RNA-Seq Library preparation Plants were grown as described (Brusslan et al, 2012), with the exceptions that the light intensity was 30 mmol photons m 22 s 21 at 22°C and the diurnal cycle was 20 h of light and 4 h of dark. The low light intensity was chosen, because the leaves of older plants grown at standard light intensities (120-150 mmol photons m 22 s 21 for 16 h is recommended by the Arabidopsis Biological Resource Center) became purple and stressed; to compensate for the low light intensity, a longer light period of 20 h was used.…”

“…The H3K9ac antibody (07-352) and H3K4me3 antibody (17-678) were purchased from Millipore. The H3K4me3 ChIP library was prepared for sequencing as described previously (Brusslan et al, 2012), and the H3K9ac library was prepared using the Illumina TruSeq ChIP Sample Preparation Kit-Set A. RNA was isolated using Trizol Reagent (Life Technologies), and RNA was prepared for sequencing using the Illumina TruSeq RNA Sample Prep Kit v2-SetA. Sequencing was performed at the University of California, Los Angeles using an Illumina HiSeq2000 to produce 50-bp single reads from both the ChIP-seq and RNA-seq libraries.…”

“…In a previous study, changes in two euchromatin histone modifications, trimethylation of Lys-4 in Histone H3 (H3K4me3; Zhang et al, 2009) and trimethylation of Lys-27 in Histone H3 (H3K27me3; Zhang et al, 2007), were measured on a genome-wide scale by chromatin immunoprecipitation Illumina sequencing (ChIP-seq) in young and old leaves (Brusslan et al, 2012). This study did not have accompanying gene expression data, and published microarray data (van der Graaff et al, 2006) were used to compare gene expression and changes in histone methylation status.…”