Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem

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Authors

Hussey, Steven Grant
Mizrachi, Eshchar
Groover, Andrew
Berger, David Kenneth
Myburg, Alexander Andrew

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Volume Title

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BioMed Central

Abstract

BACKGROUND : 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. RESULTS : 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. CONCLUSIONS : In this first genome-wide analysis of a modified histone in a woody tissue, we 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.

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Additional file 1: Supplementary Note S1.
Additional file 2: Figure S1, Figure S2, Figure S3, Figure S4, Figure S5, Figure S6, Figure S6, Figure S7, Figure S8, Figure S9, Figure S10, Figure S11, Figure S12, Figure S13, Figure S14, Figure S15, Figure S16.
Additional file 3: Table S1, Table S2, Table S3, Table S4, Table S5, Table S6, Table S7.
Additional file 4: Genomic locations and fragment coverage of significant H3K4me3 peaks.
Additional file 5: Genomic locations of annotated genes overlapping with significant H3K4me3 peaks.
Additional file 6: Genomic locations of low-confidence gene models overlapping with significant H3K4me3 peaks.

Keywords

ChIP-seq, H3K4me3, Histone, Secondary cell wall (SCW), Xylogenesis, Eucalyptus

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Citation

Hussey, SG, Mizrachi, E, Groover, A, Berger, DK & Myburg, AA 2015, 'Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing', BMC Plant Biology, vol. 15, no. 117, pp. 1-14.