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Series GSE67873 Query DataSets for GSE67873
Status Public on Apr 15, 2015
Title Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem
Organism Eucalyptus grandis
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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
 
Contributor(s) Hussey SG, Myburg AA
Citation(s) 25957781
Submission date Apr 14, 2015
Last update date May 15, 2019
Contact name Steven Grant Hussey
E-mail(s) steven.hussey@fabi.up.ac.za
Phone +27124206432
Organization name University of Pretoria
Department Genetics
Lab Forest Molecular Genetics
Street address Lynnwood Road, Hatfield
City Pretoria
State/province Gauteng
ZIP/Postal code 0002
Country South Africa
 
Platforms (1)
GPL20030 Illumina HiSeq 2500 (Eucalyptus grandis)
Samples (5)
GSM1657464 H3K4me3_ChIP-seq_rep1
GSM1657465 H3K4me3_ChIP-seq_rep2
GSM1657466 Input_rep1
Relations
BioProject PRJNA281099
SRA SRP057160

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Supplementary file Size Download File type/resource
GSE67873_V5_V11_H3K4me3_pileup.bedGraph.gz 148.7 Mb (ftp)(http) BEDGRAPH
GSE67873_V5_V11_Input_pileup.bedGraph.gz 284.9 Mb (ftp)(http) BEDGRAPH
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