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SRX994837: GSM1657464: H3K4me3_ChIP-seq_rep1; Eucalyptus grandis; ChIP-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 21.9M spots, 1.4G bases, 1.1Gb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem
show Abstracthide Abstract
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. Overall design: Examination of H3K4me3 in developing secondary xylem tissue from two clonal individuals of E. grandis growing in the field
Sample: H3K4me3_ChIP-seq_rep1
SAMN03482964 • SRS909318 • All experiments • All runs
Instrument: Illumina HiSeq 2500
Strategy: ChIP-Seq
Selection: ChIP
Layout: PAIRED
Construction protocol: Developing secondary xylem was ground to a powder in liquid nitrogen and fixed in 1% formaldehyde for 30 min on ice. Chromatin isolation and sonication was performed using standard protocols (Kaufman et al. 2010. Nature Prot. 5:457–472). ChIP-seq was performed as described (Adli & Bernstein. 2011. Nature Prot. 6:1656-1668) ChIP and input DNA was amplified (Adli & Bernstein. 2011. Nature Prot. 6:1656-1668), digested with BciVI to yield 3' A overhangs and ligated to standard Illumina HiSeq 2500 adapters (library construction and sequencing service provided by Beijing Genome Institute)
Experiment attributes:
GEO Accession: GSM1657464
External link:
Runs: 1 run, 21.9M spots, 1.4G bases, 1.1Gb
Run# of Spots# of BasesSizePublished


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