Dataset Information

Identification and quantification of HDA14-dependent substrates in the Arabidopsis thaliana leaf acetylome of plants grown under low-light conditions

ABSTRACT: Lysine acetylation is a common post-translational modification in eukaryotes and prokaryotes which is known to be involved in the regulation of various cellular processes, such as transcriptional activation, metabolic signaling, and energy homeostasis. Nevertheless, its role in plant primary metabolism, and photosynthesis in particular, is not well understood. Lysine acetylation is catalyzed by acetyltransferases (KATs) and removed by corresponding deacetylases (KDACs). The Arabidopsis thaliana genome encodes for at least 16 KATs and 18 KDACs, belonging to seven different gene families. The cellular functions of these enzymes have been explored only partially, describing effects of single enzymes and their interaction with specific targets. HDA14 is a KDAC expressed primarily in chloroplasts which suggests an involvement in the regulation of photosynthesis or related metabolic processes. In this dataset we aimed to identify substrates of the histone deacetylase 14 in a global manner by comparing the leaf lysine acetylome of a hda14 KO plant to a wild-type under low-light conditions. Proteins were extracted and digested using an adapted FASP procedure, peptides were dimethyl-labeled and lysine-acetylated peptides were antibody-enriched. Peptide identification and quantitative data analysis was carried out using MaxQuant.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Leaf

SUBMITTER: Katharina Kramer

LAB HEAD: Prof. Iris Finkemeier

PROVIDER: PXD006651 | Pride | 2017-10-25

REPOSITORIES: Pride

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Publications

Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in <i>Arabidopsis</i>.

Hartl Markus M Füßl Magdalena M Boersema Paul J PJ Jost Jan-Oliver JO Kramer Katharina K Bakirbas Ahmet A Sindlinger Julia J Plöchinger Magdalena M Leister Dario D Uhrig Glen G Moorhead Greg Bg GB Cox Jürgen J Salvucci Michael E ME Schwarzer Dirk D Mann Matthias M Finkemeier Iris I

Molecular systems biology 20171023 10

Histone deacetylases have central functions in regulating stress defenses and development in plants. However, the knowledge about the deacetylase functions is largely limited to histones, although these enzymes were found in diverse subcellular compartments. In this study, we determined the proteome-wide signatures of the RPD3/HDA1 class of histone deacetylases in <i>Arabidopsis</i> Relative quantification of the changes in the lysine acetylation levels was determined on a proteome-wide scale af ...[more]

PMID: 29061669

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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

Dataset Information

Identification and quantification of HDA14-dependent substrates in the Arabidopsis thaliana leaf acetylome of plants grown under low-light conditions

Publications

Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in <i>Arabidopsis</i>.

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