The genome-wide abundance of two histone modifications H3K4me3 and H3K9ac (both

The genome-wide abundance of two histone modifications H3K4me3 and H3K9ac (both associated with actively expressed genes) was monitored in Arabidopsis (value ≤ 0. by 35 d a significant proportion continues to be more gradually up-regulated across time points (Fig. 1B). The down-regulated genes only Dasatinib hydrochloride showed a significant overlap across the first two intervals (value < 1.1E-81) indicating that a largely distinct set of genes decreases from 42 to 57 d (Fig. 1C). Figure 1. Gene expression differences during leaf senescence. A Pearson correlation matrix of gene expression data [log2(read counts + 1)] from all RNA-seq libraries. The darker red boxes indicate a higher correlation. Dendrograms were generated by hierarchically ... We sought to generate a high-confidence set of SURGs and senescence down-regulated genes (SDRGs) by requiring that they showed significant changes in expression (≥2-fold ≤ 0.05) in two of six pairwise comparisons (29-35 29 29 35 35 and 42-57 d). This analysis permits the inclusion of genes with significant changes in expression in just one interval; for example the distinct group of genes that is down-regulated between 42 and 57 d (Fig. 1C) will be listed in the 29 to 57 35 to 57 and 42 to 57 d pairwise comparisons. To remove genes with low expression we also required that they have RPKM values (after merging replicate data sets) above the median RPKM value (0.764 for 29 d 0.911 for 35 d 0.79 for 42 d and 0.752 for 57 d) at the time of higher expression. Figure 1 D and Dasatinib hydrochloride E shows the robust up- and down-regulation of expression in the SURGs and SDRGs respectively. Dasatinib hydrochloride As was generally the case the biggest changes in expression occurred between 29 and 35 d but the respective upward and downward trends persisted for the duration of the time course. In contrast to the SURGs and SDRGs the expression distributions of all other genes show no trend indicating that the classification was reasonable (Fig. 1F). Figure 1G shows that setting the threshold at two of six pairwise comparisons resulted in a fair estimate of gene expression changes that represented a good compromise between overly stringent and more lenient criteria. WRKY transcription factor genes usually associated with senescence and thus representing a likely false positive were observed in the down-regulated category when only one of six pairwise comparisons was the threshold; conversely small up-regulated auxin (SAUR) genes down-regulated in senescence and representing a likely false positive were seen at increasing numbers in the up-regulated category when only one of six pairwise comparisons was the threshold. Genes encoding basic helix-loop-helix transcription factors showed no preference for up- or down-regulation during leaf aging and the numbers of these genes became more plentiful as the threshold decreased. The selection procedure described above resulted in 1 432 SURGs (plus 11 pseudo-genes and 6 transposable element genes) and 964 SDRGs (plus 4 pseudo-genes and 5 transposable element genes; Supplemental Data Sets S1 and S2). Small numbers of transposable element genes mostly retroposons and pseudo-genes were both up- and down-regulated during leaf senescence. This contrasts to animal cells where a general increase in expression and mobility of Mouse Monoclonal to MBP tag. transposable element genes has been observed in older somatic cells (De Cecco et al. 2013 Li et al. 2013 A gene ontology (GO) analysis was performed on this list of SURGs and SDRGs and enriched biological processes with false discovery rates below 1% are shown in Table I. Genes related to defense jasmonic acid and transport were enriched in SURGs as expected (Guo et al. 2004 van der Graaff et al. 2006 Breeze et al. 2011 In addition enrichment for indole glucosinolate synthesis genes suggested a role for these secondary metabolites during senescence (Wang et al. 2013 SDRGs were enriched for photosynthesis and growth-related processes such as response to auxin stimulus response to light stimulus response to gibberellin lipid biosynthesis and cell wall organization. Table I. GO enrichment for SURGs and SDRGs ChIP-Seq Analysis for H3K4me3 and H3K9ac Nuclei were prepared from the same tissue used Dasatinib hydrochloride in RNA-seq and ChIP-seq was performed using an antibody that.