Project description:Photoperiod is a circannual signal measured by biological systems to align growth and reproduction with the seasons. To understand the effect of photoperiod of gene expression in Arabidopsis thaliana in the absence of exogenous sugar under constant light intensity, we performed time course mRNA-seq analysis on 13-day old seedlings across three photoperiods with triplicates to identify photoperiod-regulated genes.
Project description:Histone acetylation and methylation regulate gene expression in eukaryotes, but their effects on the transcriptome of a multicellular organism and on the transcriptomic divergence between species are still poorly understood. Here we present the first genome-wide 1-bp resolution maps of histone acetylation, histone methylation and core histone in Arabidopsis thaliana and a comprehensive analysis of these maps and gene expression data in A. thaliana, A. arenosa and allotetraploids. H3K9 acetylation (H3K9ac) and H3K4 trimethylation (H3K4me3) are correlated, and their high densities near transcriptional start sites determine constitutive expression of genes involved in translation. In contrast, broad distributions of these modifications toward coding regions determine expression variation, especially in genes involved in photosynthesis, carbohydrate metabolism, and defense responses. A dispersed distribution of H3K27me3 and depletion of H3K9ac and H3K4me3 are associated with developmentally repressed genes. Finally, genes affected by histone deacetylase mutation and species divergence tend to show high expression variation. In conclusion, changes in histone acetylation and methylation modulate developmental and environmental gene expression variation within and between species. ChIP-Seq: Identification of distribution of H3K9ac, H3K4me3 and H3 in Arabidopsis thaliana leaf. Expression: Gene expression in the histone deacetylase 1 mutant was generated using t-DNA insertion. mRNA expressions in leaf and flower of the AtHD1 mutant were compared with those of the wild type plants. We conducted 8 replicates of dual-channel microarrays, including 4 biological replicates and individual dye swaps.
Project description:The objective of the study is to profile histone H3 lysine nine di-methylation (H3K9me2) in Arabidopsis thaliana and to correlate it with DNA methylation.
Project description:Histone acetylation and methylation regulate gene expression in eukaryotes, but their effects on the transcriptome of a multicellular organism and on the transcriptomic divergence between species are still poorly understood. Here we present the first genome-wide 1-bp resolution maps of histone acetylation, histone methylation and core histone in Arabidopsis thaliana and a comprehensive analysis of these maps and gene expression data in A. thaliana, A. arenosa and allotetraploids. H3K9 acetylation (H3K9ac) and H3K4 trimethylation (H3K4me3) are correlated, and their high densities near transcriptional start sites determine constitutive expression of genes involved in translation. In contrast, broad distributions of these modifications toward coding regions determine expression variation, especially in genes involved in photosynthesis, carbohydrate metabolism, and defense responses. A dispersed distribution of H3K27me3 and depletion of H3K9ac and H3K4me3 are associated with developmentally repressed genes. Finally, genes affected by histone deacetylase mutation and species divergence tend to show high expression variation. In conclusion, changes in histone acetylation and methylation modulate developmental and environmental gene expression variation within and between species.