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Genome-wide gene expression profiling to investigate molecular phenotypes of Arabidopsis mutants deprived in distinct histone methyltransferases and demethylases.

ABSTRACT: Histone lysine (K) methylation is a type of epigenetic modification involved in regulation of DNA-based processes, including transcription, replication and repair. It can either activate or repress transcription depending on the histone K residue on which methylation occurs and on chromatin context of additional other modifications. In both animals and plants, methylation on one histone K residue can be deposited by several different histone methyltransferases and vice versa removed by different histone demethylases. It is of great interest to know which histone enzyme regulates which genes in the genome. Here we describe in details the contents and quality controls for the gene expression data of Arabidopsis mutants deprived in distinct histone methyltransferases (SDG26, SDG25, ATX1, CLF) and histone demethylases (LDL1, LDL2), in association with the study recently published by Berr and colleagues in The Plant Journal (Berr et al., 2015). The microarray dataset has been deposited in Gene Expression Omnibus with accession number GSE55167.

SUBMITTER: Zhao W

PROVIDER: S-EPMC4535660 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature

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Genome-wide gene expression profiling to investigate molecular phenotypes of Arabidopsis mutants deprived in distinct histone methyltransferases and demethylases.

Zhao Wei W Shafiq Sarfraz S Berr Alexandre A Shen Wen-Hui WH

Genomics data 20150414

Histone lysine (K) methylation is a type of epigenetic modification involved in regulation of DNA-based processes, including transcription, replication and repair. It can either activate or repress transcription depending on the histone K residue on which methylation occurs and on chromatin context of additional other modifications. In both animals and plants, methylation on one histone K residue can be deposited by several different histone methyltransferases and vice versa removed by different ...[more]

PMID: 26484201

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Project description:Dynamic histone lysine methylation, regulated by methyltransferases and demethylases, plays fundamental roles in chromatin structure and gene expression in a wide range of eukaryotic organisms. A large number of SET-domain-containing proteins make up the histone lysine methyltransferase (HKMT) family, which catalyses the methylation of different lysine residues with relatively high substrate specificities. Another large family of Jumonji C (JmjC)-domain-containing histone lysine demethylases (JHDMs) reverses histone lysine methylation with both lysine site and methyl-state specificities. Through bioinformatic analysis, at least nine SET-domain-containing genes were found in the malaria parasite Plasmodium falciparum and its sibling species. Phylogenetic analysis separated these putative HKMTs into five subfamilies with different putative substrate specificities. Consistent with the phylogenetic subdivision, methyl marks were found on K4, K9 and K36 of histone H3 and K20 of histone H4 by site-specific methyl-lysine antibodies. In addition, most SET-domain genes and histone methyl-lysine marks displayed dynamic changes during the parasite asexual erythrocytic cycle, suggesting that they constitute an important epigenetic mechanism of gene regulation in malaria parasites. Furthermore, the malaria parasite and other apicomplexan genomes also encode JmjC-domain-containing proteins that may serve as histone lysine demethylases. Whereas prokaryotic expression of putative active domains of four P. falciparum SET proteins did not yield detectable HKMT activity towards recombinant P. falciparum histones, two protein domains expressed in vitro in a eukaryotic system showed HKMT activities towards H3 and H4, respectively. With the discovery of these Plasmodium SET- and JmjC-domain genes in the malaria parasite genomes, future efforts will be directed towards elucidation of their substrate specificities and functions in various cellular processes of the parasites.

Dataset Information

Genome-wide gene expression profiling to investigate molecular phenotypes of Arabidopsis mutants deprived in distinct histone methyltransferases and demethylases.

Publications

Genome-wide gene expression profiling to investigate molecular phenotypes of Arabidopsis mutants deprived in distinct histone methyltransferases and demethylases.

Similar Datasets

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