Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem.
Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem.
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DOI：
10.1186/s12870-015-0499-0
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发表时间：
2015-05-10
影响因子：
5.3
通讯作者：
Myburg AA
中科院分区：
文献类型：
--
作者：
Hussey SG;Mizrachi E;Groover A;Berger DK;Myburg AA
组蛋白修饰在植物发育中起着不可或缺的作用，但在木本植物中的研究却很少。研究木材形成组织中的染色质组织及其在调控基因表达中的作用，使我们能够了解木质部发生（木材形成）过程中细胞分化的机制，并确定植物基因组中的新功能区域。然而，木本组织提出了独特的挑战，使用高通量染色质免疫沉淀（ChIP）技术研究全基因组组的组蛋白修饰在体内。我们研究了修饰的组蛋白H3 K4 me 3（组蛋白H3的三甲基化赖氨酸4）在木材形成早期阶段的基因表达中的作用，使用ChIP-seq在巨桉（一种木本生物量模型）中。植物染色质的固定和分离方案进行了优化，从野外生长的E。巨树使用“nano-ChIP-seq”程序进行ChIP DNA扩增。超过900万个H3 K4 me 3 ChIP-seq和1800万个对照配对末端读数被映射到E. grandis参考基因组的峰值调用使用基于模型的分析ChIP-Seq。鉴定的12，177个显著H3 K4 me 3峰覆盖约1.5%的基因组，并与约9，623个蛋白质编码基因和38个非编码RNA重叠。在转录起始位点下游约600 - 700 bp处达到峰值的H3 K4 me 3文库覆盖率与用RNA-seq测量的基因表达水平高度相关。总的来说，H3 K4 me 3富集基因往往比未富集基因的组织特异性更低，并且对于一般细胞代谢和发育基因本体论术语而言代表性过高。H3 K4 me 3富集基因在发育中的次生木质部中的相对表达高于未富集的基因，然而，使用ChIP-qPCR验证，高表达的次生细胞壁相关基因富集H3 K4 me 3。在这第一次对木本组织中修饰的组蛋白进行全基因组分析时，我们优化了适合现场收集样品的ChIP-seq程序。在开发E.在巨木木质部中，H3 K4 me 3富集是活性转录的指示物，与其在维持酵母中的前起始复合物形成中的已知作用一致。本研究的H3 K4 me 3 ChIP-seq数据为理解植物木质化的染色质景观和表观基因组结构铺平了道路，并补充了基因表达的RNA-seq证据，用于未来改进E. Grandis基因组注释。本文的在线版本（doi：10.1186/s12870-015-0499-0）包含补充材料，可供授权用户使用。
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 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. The online version of this article (doi:10.1186/s12870-015-0499-0) contains supplementary material, which is available to authorized users.
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