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1.
Plant Signal Behav ; 8(9)2013 Sep.
Article in English | MEDLINE | ID: mdl-23857353

ABSTRACT

Gene promoters perceive numerous signals and integrate this information into a single response, the transcriptional activity of a gene. It was speculated that covalent modification of histones on the promoters might have an important function in storage and integration of signals. Using the genes for the core proteins of C4 metabolism in maize as a model, we associated the perception of specific signals with the establishment of individual histone modifications. Core elements of the histone code defined in these studies are conserved on all C4 genes and on other maize genes that respond to similar stimuli. Moreover, the code is used in independent C4 lineages. However, our data also advise caution because interpretation of histone modifications might differ dependent on the promoter position of the modification. The model provided here constitutes a starting point for genome-wide decoding of stimulus-modification pairs in epigenetic gene regulation.


Subject(s)
Promoter Regions, Genetic , Signal Transduction/genetics , Zea mays/genetics , Acetylation/radiation effects , Gene Expression Regulation, Plant/radiation effects , Genes, Plant , Histones/metabolism , Light , Methylation/radiation effects , Phylogeny , Protein Processing, Post-Translational/genetics , Protein Processing, Post-Translational/radiation effects , Zea mays/radiation effects
2.
Plant Physiol ; 162(1): 456-69, 2013 May.
Article in English | MEDLINE | ID: mdl-23564230

ABSTRACT

C4 photosynthesis evolved more than 60 times independently in different plant lineages. Each time, multiple genes were recruited into C4 metabolism. The corresponding promoters acquired new regulatory features such as high expression, light induction, or cell type-specific expression in mesophyll or bundle sheath cells. We have previously shown that histone modifications contribute to the regulation of the model C4 phosphoenolpyruvate carboxylase (C4-Pepc) promoter in maize (Zea mays). We here tested the light- and cell type-specific responses of three selected histone acetylations and two histone methylations on five additional C4 genes (C4-Ca, C4-Ppdk, C4-Me, C4-Pepck, and C4-RbcS2) in maize. Histone acetylation and nucleosome occupancy assays indicated extended promoter regions with regulatory upstream regions more than 1,000 bp from the transcription initiation site for most of these genes. Despite any detectable homology of the promoters on the primary sequence level, histone modification patterns were highly coregulated. Specifically, H3K9ac was regulated by illumination, whereas H3K4me3 was regulated in a cell type-specific manner. We further compared histone modifications on the C4-Pepc and C4-Me genes from maize and the homologous genes from sorghum (Sorghum bicolor) and Setaria italica. Whereas sorghum and maize share a common C4 origin, C4 metabolism evolved independently in S. italica. The distribution of histone modifications over the promoters differed between the species, but differential regulation of light-induced histone acetylation and cell type-specific histone methylation were evident in all three species. We propose that a preexisting histone code was recruited into C4 promoter control during the evolution of C4 metabolism.


Subject(s)
Histone Code , Histones/metabolism , Plant Proteins/metabolism , Setaria Plant/metabolism , Sorghum/metabolism , Zea mays/metabolism , Acetylation , Gene Expression Regulation, Plant , Histones/genetics , Light , Methylation , Plant Proteins/genetics , Promoter Regions, Genetic/genetics , Setaria Plant/genetics , Setaria Plant/radiation effects , Sorghum/genetics , Sorghum/radiation effects , Species Specificity , Zea mays/genetics , Zea mays/radiation effects
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