Unknown,Transcriptomics,Genomics,Proteomics

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Comparative histone modification profiling revealed developmentally regulated acetylation on upstream promoters of C4 genes and potential C4 regulators

ABSTRACT: We analysed genome-wide histone H3 lysine 4 trimethylation and histone H3 lysine 9 acetylation, two modifications typically associated with active genes, in meristematic cells at the base and expanding cells in the maturing zone of the maize (Zea mays) leaf. These data were compared to transcript levels of associated genes. Our data revealed that for individual genes fold-changes in histone modification and transcript abundance were much better correlated than absolute intensities. When focusing on regulated modification sites, we identified secondary upstream H3 lysine 9 acetylation peaks (SUPs) on upstream promoter regions of approximately 6% of all acetylated genes. SUPs showed stronger regulation than the previously described acetylation peaks at transcription initiation sites, were more often found on genes that were upregulated towards the maturing zone than on downregulated genes, and were significantly enriched on photosynthetic genes. We identified SUPs on all genes encoding enzymes of the C4 cycle. Moreover, SUPs were enriched in four lists of candidate C4-associated genes that were derived from previous transcriptomic studies. Based on these data, we used highly regulated SUPs as an epigenetic mark to identify new genes potentially involved in C4 metabolism. This approach also allowed the identification of ethylene response elements as highly enriched cis-acting elements in SUP regions. Our data suggest co-evolution of epigenetic promoter elements during the establishment of C4 photosynthesis. Comparative analysis of H3K9ac, H3K4me3 and the transcription between two developmental zones within one maize leaf.

ORGANISM(S): Zea mays

SUBMITTER: Christoph Peterhansel

PROVIDER: E-GEOD-67551 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Photosynthetic Genes and Genes Associated with the C4 Trait in Maize Are Characterized by a Unique Class of Highly Regulated Histone Acetylation Peaks on Upstream Promoters.

Perduns Renke R Horst-Niessen Ina I Peterhansel Christoph C

Plant physiology 20150625 4

Histone modifications contribute to gene regulation in eukaryotes. We analyzed genome-wide histone H3 Lysine (Lys) 4 trimethylation and histone H3 Lys 9 acetylation (two modifications typically associated with active genes) in meristematic cells at the base and expanded cells in the blade of the maize (Zea mays) leaf. These data were compared with transcript levels of associated genes. For individual genes, regulations (fold changes) of histone modifications and transcript levels were much bette ...[more]

PMID: 26111542

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Project description:To gain novel molecular insights into quantitative late blight resistance, we performed a high-resolution quantitative analysis of gene expression using potato cultivars with contrasting SNP alleles at the StAOS2 locus associated with maturity corrected resistance (MCR). SuperSAGE samples were generated from uninfected and infected plants of the selected genotypes under controlled environmental conditions. Genotypes were pooled to reduce the influence of the genetic background on the transcriptome. Nine SuperSAGE samples were prepared from artificially inoculated plants in a growth chamber using total RNA of the pooled 14, 6 and 9 genotypes in groups A1, A2 and B2, respectively, at three infection time points T0, T1 and T2. Combining the tag counts of both NlaIII and DpnII libraries resulted in 1.1 to 6.2 million tags per sample. Of total 266361 unique tags (unitags), 52.6% matched to the potato genome sequence when up to three mismatches per 26 base pairs were allowed, and 23.3% matched without mismatch. Fifteen pair wise comparisons were performed between the nine SuperSAGE samples to identify transcripts that were differentially expressed in response to infection (six comparisons) or between three genotype pools at the infection time points T0, T1 and T2 (nine comparisons). The number of unitags per comparison ranged from 127 000 to 182 000 (average 158 000). Between 2100 and 11800 tags were differentially expressed in pair wise comparisons, depending on arbitrary cut-off p-values for a significant difference. The highest number of differences was observed for the comparison between genotype pools A1 and A2 one day after infection (A1-T1 vs A2-T1), and the lowest between genotype pools A2 and B2 two days after infection (B2-T2 vs A2-T2). The number of differences in response to infection and between genotype pools even before infection (T0) was in the same order of magnitude. Based on the annotations in the DFCI potato gene index, in the potato genome and in few cases by BLASTX searches against the protein database at NCBI, transcripts that showed reproducible differential expression over the infection time course or between genotype pools A1, A2 and B2 were grouped in 16 functional categories, with overlaps between categories. Genes with genotype dependent, constitutive differential expression provide excellent targets for developing novel diagnostic markers for breeding cultivars with improved quantitative resistance to late blight and possibly other biotic and abiotic stresses. Relevant in this respect appear, besides numerous genes of unknown or ill-defined function, genes with known function involved in stress responses, photosynthesis, protein biosynthesis, protein degradation via the 26S proteasome, transport of proteins, lipids, ions and other small molecules, cell wall structure and many others. Eighteen SuperSAGE libraries were constructed based on nine leaf samples from one infection experiment. For each time point (T0, T1 and T2) one leaflet each of 14, 6 and 9 SL genotypes in genotypic groups A1, A2 and B2, respectively, were pooled. Frozen pooled leaf tissue was powdered in a CryoMill. SuperSAGE libraries were generated at GenXPro GmbH (Frankfurt, Germany) essentially as described (Matsumura et al. 2010). To prevent amplification biases the TrueQuant technology was applied as described by B. Rotter (Patent application Nr. WO2009152928). Besides NlaIII (recognition site: 5M-bM-^@M-^Y-CATG-3M-bM-^@M-^Y), DpnII (recognition site: 5M-bM-^@M-^Y-GATC-3M-bM-^@M-^Y) was used as second anchoring enzyme, to capture transcripts without a NlaIII site. Therefore, the 26 bp tags carry either CATG or GATC at their 5M-bM-^@M-^Y end. The libraries were pooled and sequenced by Solexa/Illumina technology (Illumina, Inc., USA).