Project description:Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. We investigated the role of the modified histone H3K4me3 (trimethylated lysine 4 of histone H3) in gene expression during the early stages of wood formation using ChIP-seq in Eucalyptus grandis, a woody biomass model. Plant chromatin fixation and isolation protocols were optimized for developing xylem tissue collected from field-grown E. grandis trees. A “nano-ChIP-seq” procedure was employed for ChIP DNA amplification. Over 9 million H3K4me3 ChIP-seq and 18 million control paired-end reads were mapped to the E. grandis reference genome for peak-calling using Model-based Analysis of ChIP-Seq. The 12,177 significant H3K4me3 peaks identified covered ~1.5% of the genome and overlapped some 9,623 protein-coding genes and 38 noncoding RNAs. H3K4me3 library coverage, peaking ~600 - 700 bp downstream of the transcription start site, was highly correlated with gene expression levels measured with RNA-seq. Overall, H3K4me3-enriched genes tended to be less tissue-specific than unenriched genes and were overrepresented for general cellular metabolism and development gene ontology terms. Relative expression of H3K4me3-enriched genes in developing secondary xylem was higher than unenriched genes, however, and highly expressed secondary cell wall-related genes were enriched for H3K4me3 as validated using ChIP-qPCR. In this first genome-wide analysis of a modified histone in a woody tissue, we developed optimized a ChIP-seq procedure suitable for field-collected samples. In developing E. grandis xylem, H3K4me3 enrichment is an indicator of active transcription, consistent with its known role in sustaining pre-initiation complex formation in yeast. The H3K4me3 ChIP-seq data from this study paves the way to understanding the chromatin landscape and epigenomic architecture of xylogenesis in plants, and complements RNA-seq evidence of gene expression for the future improvement of the E. grandis genome annotation. Examination of H3K4me3 in developing secondary xylem tissue from two clonal individuals of E. grandis growing in the field
Project description:We investigated the chromatin modifications H3K4me3 and H3K27me3 in the A. thaliana shoot apical meristem using INTACT reporter lines. Samples were collected in two biological replications.
Project description:Chromatin immunoprecipitation and hybridization to a chromosome-wide DNA tiling array (ChIP-chip)was performed to identify the targets of the chromatin protein TERMINAL FLOWER 2/LIKE HETEROCHROMATIN PROTEIN 1. Epigenomic profiling was also carried out for three histone H3 modifications: H3K27me3, H3K9me2 and H3K9me3. Experiments were done using two independent biological replicates.
Project description:The study set out to assess the genome-wide distribution of the chromatin modifications H3K4me3 and H3K27me3 in mature thymic epithelial cells. ChIP and input DNA was prepared from biological replicated FACS sorted mature mTEC samples and sequenced.
Project description:Chromatin immunoprecipitation and hybridization to a chromosome-wide DNA tiling array (ChIP-chip)was performed to compare the distribution pattern of H3K9me2 between nrpd1a-4_nrpd1b-11 and wild type. Experiments were done using two independent biological replicates.<br>
Project description:Chromatin immunoprecipitation and hybridization to a chromosome-wide DNA tiling array (ChIP-chip)was performed to compare the distribution of H3K4me2 in nrpd1a-4_nrpd1b-11 double mutant and in the wild type. Experiments were done using two independent biological replicates.<br><br>
Project description:After characterizing super-enhancer-associated chromatin dynamics accompanied by malignant progression of skin stem cells, we show that ETS family members auto-regulate themselves and a cohort of cancer-associated super-enhancer transcription factors which together are essential for tumor maintenance. Control and ETS2(T72D) super-activated epidermal basal stem cells were FACS-purified for ChIP-sequencing.
Project description:We investigated the chromatin modifications H3K4me3 and H3K27me3 in the A. thaliana shoot phloem companion cells using INTACT reporter lines. Samples were collected in two biological replications.