Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA222364 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1005390.fastq.gz | Fastqsanger.gz | |||
| SRR1005400.fastq.gz | Fastqsanger.gz | |||
| SRR1005410.fastq.gz | Fastqsanger.gz | |||
| SRR1005420.fastq.gz | Fastqsanger.gz | |||
| SRR1005391.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 48 |
Similar Datasets
Project description:DNA methylation occurs in both CG and non-CG sequence contexts. Non-CG methylation is abundant in plants, and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM) proteins; however its roles remain poorly understood. Here we characterize the roles of non-CG methylation in Arabidopsis thaliana. We show that a poorly characterized methyltransferase, CMT2, is a functional methyltransferase in vitro and in vivo. CMT2 specifically binds histone H3 lysine 9 (H3K9) dimethylation and methylates non-CG cytosines at sites that are also regulated by H3K9 dimethylation. By generating different combinations of non-CG methylation mutants, we reveal the contributions and redundancies between each methyltransferase in DNA methylation patterning and in regulating transposable elements (TEs) and protein-coding genes. We also demonstrate extensive dependencies of small RNA accumulation and H3K9 methylation patterning on non-CG methylation, suggesting self-reinforcing mechanisms between these epigenetic factors. The results suggest that non-CG methylation patterns are critical in shaping the histone modification and small non-coding RNA landscapes.
2013-12-15 | GSE51304 | GEO
Project description:In diverse eukaryotes, constitutively silent sequences, such as transposons and repeats, are marked by methylation at histone H3 lysine 9 (H3K9me). Despites the conservation and importance in the genome integrity, mechanisms to exclude H3K9m from active genes remained largely unexplored. Here we show in Arabidopsis that the exclusion depends on a histone demethylase gene, IBM1 (increase in BONSAI methylation); loss-of-function ibm1 mutation caused ectopic H3K9me in thousands of genes, which accompanies genic DNA methylation at non-CG sites. The ibm1-induced genic H3K9me depended on both histone methylase KYP/SUVH4 and DNA methylase CMT3, suggesting interdependence of two epigenetic marks – H3K9me and non-CG methylation. Notably, IBM1 enhanced loss of H3K9m in transcriptionally de-repressed sequences. Furthermore, disruption of transcription in genes induced ectopic non-CG methylation, mimicking the loss of IBM1 function. We propose that active chromatin is stabilized by the autocatalytic loop of transcription and H3K9 demethylation. This process counteracts accumulation of silent epigenetic marks, H3K9me and non-CG methylation, which is also autocatalytic.
2010-09-21 | GSE22953 | GEO
Project description:Comparative Epigenomics Reveals Hierarchical Regulation of Non-CG Methylation in Arabidopsis
| PRJNA386485 | ENA
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 | GSE183986 | GEO
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 | GSE183985 | GEO
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
Project description:DNA methylation occurs in both CG and non-CG sequence contexts. Non-CG methylation is abundant in plants, and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM) proteins; however its roles remain poorly understood. Here we characterize the roles of non-CG methylation in Arabidopsis thaliana. We show that a poorly characterized methyltransferase, CMT2, is a functional methyltransferase in vitro and in vivo. CMT2 specifically binds histone H3 lysine 9 (H3K9) dimethylation and methylates non-CG cytosines at sites that are also regulated by H3K9 dimethylation. By generating different combinations of non-CG methylation mutants, we reveal the contributions and redundancies between each methyltransferase in DNA methylation patterning and in regulating transposable elements (TEs) and protein-coding genes. We also demonstrate extensive dependencies of small RNA accumulation and H3K9 methylation patterning on non-CG methylation, suggesting self-reinforcing mechanisms between these epigenetic factors. The results suggest that non-CG methylation patterns are critical in shaping the histone modification and small non-coding RNA landscapes. Eighteen mRNA-seq samples, five smRNA-seq samples, five bisulfite-seq samples, twenty ChIP-seq samples. Bisulfite-seq data for cmt2-7 single mutants, cmt3 single mutants, drm1/2 double mutants, drm1/2 cmt3 triple mutants are deposited in GSE39901. Processed wiggle format files for all datasets can be downloaded at http://genomes.mcdb.ucla.edu/AthBSseq/
2013-12-15 | E-GEOD-51304 | biostudies-arrayexpress
Project description:Major alleles of CDCA7α shape CG-methylation in Arabidopsis thaliana
| PRJNA1197390 | ENA
Project description:In diverse eukaryotes, constitutively silent sequences, such as transposons and repeats, are marked by methylation at histone H3 lysine 9 (H3K9me). Despites the conservation and importance in the genome integrity, mechanisms to exclude H3K9m from active genes remained largely unexplored. Here we show in Arabidopsis that the exclusion depends on a histone demethylase gene, IBM1 (increase in BONSAI methylation); loss-of-function ibm1 mutation caused ectopic H3K9me in thousands of genes, which accompanies genic DNA methylation at non-CG sites. The ibm1-induced genic H3K9me depended on both histone methylase KYP/SUVH4 and DNA methylase CMT3, suggesting interdependence of two epigenetic marks – H3K9me and non-CG methylation. Notably, IBM1 enhanced loss of H3K9m in transcriptionally de-repressed sequences. Furthermore, disruption of transcription in genes induced ectopic non-CG methylation, mimicking the loss of IBM1 function. We propose that active chromatin is stabilized by the autocatalytic loop of transcription and H3K9 demethylation. This process counteracts accumulation of silent epigenetic marks, H3K9me and non-CG methylation, which is also autocatalytic. Leaves of 4-week-old plants were fixed as described previously (Saze et al, 2008). Chromatin immunoprecipitation (ChIP) was performed as described previously (Kimura et al, 2008), using antibody against H3K9me2 (CMA307, Kimura et al, 2008, PMID: 18227620). Non-immunoprecipitated DNA (input DNA) and ChIP samples were amplified, labeled, and hybridized to microarray according to the manufacturer’s instruction (Protocols for Chromatin Immunoprecipitation and Amplification, NimbleGen). Input DNA and ChIP DNA were differentially labeled with Cy3 and Cy5, respectively, and competitively hybridized to a microarray chip. We used NimbleGen 2.1M HD2 array covering entire genome of A. thaliana.
2010-09-21 | E-GEOD-22953 | biostudies-arrayexpress
Project description:Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated by the DNA glycosylase DEMETER, but the extent of the methylation changes is not known. Here we show that virtually the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of siRNA-targeted sequences. Mutation of DEMETER partially restores endosperm CG methylation to levels found in other tissues, indicating that CG demethylation is specific to maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation of embryo transposable elements. Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo. Keywords: Epigenetics; bisulfite sequencing Examination of DNA methylation in four Arabidopsis tissues Description of processed data and raw data file contents can be found in the attached README.txt file
2009-06-16 | E-GEOD-15922 | biostudies-arrayexpress