Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

On the Origin and Evolutionary Consequences of Gene Body DNA Methylation

ABSTRACT: In plants, CG DNA methylation is prevalent in the transcribed regions of constitutively expressed genes (“gene body methylation; gbM”), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum, has lost gbM from its genome, the first known instance for a flowering plant. Of all known DNA methyltransferases, only CHROMOMETHYLTRANSFERASE 3 (CMT3) is missing from E. salsugineum, indicating that CMT3 may be required for the establishment of gbM. Detailed analyses of gene expression, the histone variant H2A.Z and various histone modifications in E. salsugineum and Arabidopsis thaliana epiRILs turned up no evidence in support of any role for gbM in regulating transcription or affecting the composition and modifications of chromatin over evolutionary time scales.

ORGANISM(S): Arabidopsis thaliana Brassica rapa Eutrema salsugineum Arabidopsis lyrata Capsella rubella Brassica oleracea

PROVIDER: GSE75071 | GEO | 2016/07/11

SECONDARY ACCESSION(S): PRJNA302602

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation

Project description:In many plant species, a subset of transcribed genes are characterized by strictly CG-context DNA methylation, referred to as gene body methylation (gbM). The mechanisms that establish gbM are unclear, yet flowering plant species naturally without gbM lack the DNA methyltransferase, CMT3, which maintains CHG (H=A, C, or T) and not CG methylation at constitutive heterochromatin. Here, we identify the mechanistic basis for gbM establishment by expressing CMT3 in a species naturally lacking CMT3. CMT3 expression reconstituted gbM through a progression of de novo CHG methylation on expressed genes, followed by the accumulation of CG methylation that could be inherited even following loss of the CMT3 transgene. Thus, gbM originates from the simultaneous targeting of loci by pathways that promote euchromatin and heterochromatin, which primes genes for the formation of stably inherited epimutations in the form of CG DNA methylation.

2019-08-06 | GSE128687 | GEO

Dual Binding of Chromomethylase Domains to H3K9me2-containing Nucleosomes Mediates DNA Methylation in Plants

Project description:DNA methylation and histone modification exert epigenetic control over gene expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly understood. Here, we report multiple lines of evidence that CMT3 interacts with H3K9me2-containing nucleosomes. CMT3 genome locations nearly perfectly correlated with H3K9me2 and CMT3 stably associated with H3K9me2-containing nucleosomes. Crystal structures of maize CMT3 homologue, ZMET2, in complex with H3K9me2 peptides, showed that ZMET2 binds H3K9me2 via both BAH and chromo domains. The structures reveal an aromatic cage within both BAH and chromo domains as interaction interfaces that capture H3K9me2. Mutations that abolish either interaction disrupt CMT3 binding to nucleosomes, and show a complete loss of CMT3 activity in vivo. Our study establishes dual recognition of H3K9me2 marks by BAH and chromo domains, and reveals a novel mechanism of interplay between DNA methylation and histone modification.

2012-11-11 | GSE39097 | GEO

Dual Binding of Chromomethylase Domains to H3K9me2-containing Nucleosomes Mediates DNA Methylation in PlantsM-BM-

2012-11-11 | E-GEOD-39097 | biostudies-arrayexpress

DNA Methylation shapes histone modification landscape for transcription regulation in Arabidopsis [ChIP-Seq]

Project description:DNA methylation and histone modifications cooperate to shape the epigenetic landscape for transcription regulation, but their orchestration is not fully understood due to the lack of met1 drm1 drm2 cmt2 cmt3 mutants (mddcc), in which total DNA methylation were eliminated. This is the first time to generate mddcc that allow us to elucidate the roles of DNA methylation in the upheaval of histone modification landscape, transposon activity and gene expression. We found that DNA methylation elimination-triggered genome-wide transcriptional reprogramming is largely orchestrated by the redistribution and conversion of histone modifications. We also distinguished the contribution of CG and non-CG methylation to the histone modification landscape. Furthermore, we reveal histone modifications can serve as an independent regulatory system despite the influence of DNA methylation. Taken together, we provide comprehensive insights into the roles of DNA methylation in shaping epigenomic landscape for genome transcription, which deep understanding of epigenomic regulation.

2022-08-19 | GSE183957 | GEO

DNA Methylation shapes histone modification landscape for transcription regulation in Arabidopsis [WGBS]

2022-08-19 | GSE183986 | GEO

DNA Methylation shapes histone modification landscape for transcription regulation in Arabidopsis [RNA-Seq]

2022-08-19 | GSE183985 | GEO

Meiotic cohesin, chromatin and expression profiling of Arabidopsis thaliana floral buds from wild type and non-CG DNA methylation/H3K9me2 pathway mutant plants (ChIP-seq)

Project description:We generated and sequenced ChIP libraries for the meiotic cohesin subunit REC8 and four histone modifications (H3K4me1, H3K4me2, H3K9me2 and H3K27me1) to investigate their relationships with meiotic chromosome architecture and recombination in Arabidopsis thaliana. REC8 and H3K9me2 ChIP-seq were performed using meiotic-stage floral buds from wild type (Col-0) and non-CG DNA methylation/H3K9me2 pathway mutant (kyp/suvh4 suvh5 suvh6 or cmt3) plants to examine the role of heterochromatin assembly in meiotic cohesin distribution.

2020-01-21 | E-MTAB-7370 | biostudies-arrayexpress

Chromatin and siRNA pathways cooperate to maintain DNA methylation

Project description:DNA methylation occurs at preferred sites in eukaryotes, although the basis for preference is not known. We use a microarray-based profiling method to explore the involvement of Arabidopsis CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related RNA silencing component (AGO4) in methylating target loci. We find that KYP targets are also CMT3 targets, suggesting that histone methylation maintains CNG methylation genome-wide. CMT3 and KYP targets show similar proximal distributions that corresponds to the overall distribution of transposable elements of all types, whereas DRM targets are distributed more distally along the chromosome. We find an inverse relationship between element size and loss of methylation in ago4 and drm mutants. Our results suggest that RNA-directed DNA methylation is required to silence isolated elements that may be too small to be maintained in a silent state by a chromatin-based mechanism. Thus, parallel pathways would be needed to maintain silencing of transposable elements. Keywords: Methylation profiling using Msp I enzyme

2005-10-25 | GSE3109 | GEO

Bisulfite-seq of the Solanum lycopersicum sulfurea paramutation in the cmt3 mutant background and upon reintroduction of WT CMT3

Project description:Whole genome bisulfite sequencing was done in F3 plants resulting from a cross between Solanum lycopersicum plants bearing the sulfurea epiallele and cmt3 mutants. 6 F3 plants were sequenced: 3 WT and 3 cmt3. The F3 WT plants had methylation levels (quantified with McrBC-qPCR) consistent with the TAB2sulf epiallele and the cmt3 plants had methylation levels consistent with TAB2+ (low DNA methylation). cmt3 mutants from the F2 generation were backcrossed with WT cv M82 plants to restore CMT3 activity and followed for 2 generations (BC2). 4 BC2 plants were sequenced 2 WT and 2 cmt3. The aim of the experiment was to compare DNA methylation levels in all contexts between cmt3 and WT F3 plants with particular interest on SlTAB2 (Solyc02g005200) which has been previously associated with paramutation in the sulfurea background. The stability of DNA methylation upon CMT3 reintroduction was assessed in the BC2 plants. WT cv M82, cmt3 and sulfurea controls were added in single replicates.

2021-06-24 | E-MTAB-10568 | biostudies-arrayexpress

Dynamic evolution of the heterochromatin sensing histone demethylase IBM1

Project description:Heterochromatin constitutes a fundamental aspect of genomes that is crucial for maintaining genome stability. In flowering plants, maintenance of heterochromatin relies on a positive feedback loop involving the histone 3 lysine nine methyltransferase (H3K9), KRYPTONITE (KYP), and the DNA methyltransferase, CHROMOMETHYLASE3 (CMT3). An H3K9 demethylase, INCREASED IN BONSAI METHYLATION 1 (IBM1), has evolved to modulate the activity of KYP-CMT3 within transcribed genes. The absence of IBM1 activity results in aberrant methylation of gene bodies, which is deleterious. This study demonstrates extensive genetic and gene expression variations in KYP, CMT3, and IBM1 within and between flowering plant species. IBM1 activity in Arabidopsis thaliana is uniquely regulated by the abundance of H3K9me2 in a repetitive sequence within an intron preceding the histone demethylase domain. This mechanism enables IBM1 to monitor global levels of H3K9me2. We discovered that the methylated intron is prevalent across flowering plants, however, its underlying sequence exhibits dynamic evolution. Its absence in species lacking gene body DNA methylation suggests its primary role in sensing H3K9me2 and preventing its integration into these constitutively expressed genes. Furthermore, our investigation uncovered Arabidopsis thaliana accessions resembling weak ibm1 mutants, several Brassicaceae species with reduced IBM1 expression, and a potential IBM1 deletion. Evolution towards reduced IBM1 activity in some flowering plants could explain the frequent natural occurrence of diminished or lost CMT3 activity, as cmt3 mutants in A. thaliana mitigate the deleterious effects of IBM1.

2024-05-10 | GSE252913 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data