Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Expression data for the mom1-2 mutant of Arabidopsis

ABSTRACT: Heterochromatin is an inert region in the genome and composed of mainly remnants of transposons and repetitive elements. In Arabidopsis, the major heterchromatin regions are present at around centromeres (pericentromeric regions) and at a region on the short arm of chromosome 4 (heterochromatin knob). Histones and DNAs in heterochromatin have characteristic features with abundant H3H9me2 and cytosine methylation, respectively. Here, by using a genome tiling array, we showed that a subset of heterochromatin loci are silenced by the action of Morpheus' molecule 1 (MOM1) that is an epigeneic regulator for transcriptional gene silencing independent of global DNA and histone modification. Most of the up-regulated loci in the mom1 mutant carried sequences related to transposable elements but none of them was annotated as functional transposons. No specific subclass of transposons was targeted by MOM1 and loci that were unrelated to transposons but flanked by short tandem repeats were also shown to be under the control of MOM1. The results suggest the presence of an unknown level of regulatory network maintaining the silent state of heterochromain in the genome. Keywords: Epigenetic regulation of endogenous loci by Morpheus' Molecule 1 (MOM1) Three-week-old Arabidopsis plants (Col-0 and mom1-2) grown on soil were subjected to RNA extraction and the total RNA samples were used for the microarray hybridization. Three replicative hybridization experiments for each strand array were carried out using the independent biological RNA samples.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Motoaki Seki

PROVIDER: E-GEOD-13092 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transduction of RNA-directed DNA methylation signals to repressive histone marks in Arabidopsis thaliana.

Numa Hisataka H Kim Jong-Myong JM Matsui Akihiro A Kurihara Yukio Y Morosawa Taeko T Ishida Junko J Mochizuki Yoshiki Y Kimura Hiroshi H Shinozaki Kazuo K Toyoda Tetsuro T Seki Motoaki M Yoshikawa Manabu M Habu Yoshiki Y

The EMBO journal 20091210 2

RNA-directed modification of histones is essential for the maintenance of heterochromatin in higher eukaryotes. In plants, cytosine methylation is an additional factor regulating inactive chromatin, but the mechanisms regulating the coexistence of cytosine methylation and repressive histone modification remain obscure. In this study, we analysed the mechanism of gene silencing mediated by MORPHEUS' MOLECULE1 (MOM1) of Arabidopsis thaliana. Transcript profiling revealed that the majority of up-re ...[more]

PMID: 20010696

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Project description:Epigenetic gene silencing is of central importance to maintain genome integrity and is mediated by an elaborate interplay between DNA methylation, histone posttranslational modifications and chromatin remodeling complexes. DNA methylation and repressive histone marks usually correlate with transcriptionally silent heterochromatin, however there are exceptions to this interdependence. In Arabidopsis, mutation of MORPHEUS MOLECULE 1 (MOM1) causes transcriptional derepression of heterochromatin independently of changes in DNA methylation. More recently, two Arabidopsis homologs of mouse Microrchidia (MORC) have also been implicated in gene silencing and heterochromatin condensation without altering genome-wide DNA methylation patterns. In this study, we show that AtMORC6 physically interacts with AtMORC1 and with its close homologue AtMORC2 in two mutually exclusive protein complexes. RNA-seq analysis of high-order mutants indicates that AtMORC1 and AtMORC2 act redundantly to repress a common set of loci. We also examined the genetic interactions between AtMORC6 and MOM1 pathways. Although AtMORC6 and MOM1 control the silencing of a very similar set of genomic loci, we observed synergistic transcriptional regulation in the mom1/atmorc6 double mutant, suggesting that these epigenetic regulators act mainly by independent silencing mechanisms. RNA-seq libraries were prepared for two suites of mutants to allow direct comparisons between mutants within each set. The two sets consisted of the following samples: Set_1) A wildtype (Col) control, the morc1 mutant, the morc2 mutant, the morc1 morc2 double mutant, the morc6 mutant, and the morc1 morc2 morc6 triple mutant ; Set_2) A wildtpe (Col) control, the morc6 mutant, the mom1 mutant, and the mom1 morc6 double mutant. For each sample, two biological replicates were performed (denoted "bio_replicate_1" or "bio_replicate_2"). Whole genome bisulifte libraries were sequenced from material grown in parallel.

Dataset Information

Expression data for the mom1-2 mutant of Arabidopsis

Publications

Transduction of RNA-directed DNA methylation signals to repressive histone marks in Arabidopsis thaliana.

Similar Datasets

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