Ontology highlight
ABSTRACT:
PROVIDER: PRJEB22323 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Kitasatospora papulosa CG 893 genome sequencing
| PRJNA330490 | ENA
Project description:Streptomyces microflavus DSM 40593 Genome sequencing
| PRJNA192408 | ENA
Project description:Streptomyces microflavus NBRC 13062 genome sequencing project
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Project description:Streptomyces sp. CG 926 Genome sequencing and assembly
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Project description:Streptococcus pneumoniae isolate 893
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Project description:To examine the relationship of reduced CG methylation and gene expression in Lsh KO MEFs, we computed mean CG methylation levels at promoter regions of protein-coding genes. About 60% of TSS regions of protein-coding genes display a difference of CG methylation values greater than 0.3 (WT CG methylation minus KO CG methylation) indicating that Lsh deletion has widespread effects at promoter regions. RNA-seq analysis detects similar transcript steady state levels in WT and KO samples. To determine the relationship of Pol II binding and CG methylation reduction in KO MEFs, Pol II Chip-seq was performed. Protein coding genes were ranked according their CG methylation differences between WT MEFs and KO MEFs. The greatest loss of CG methylation is found at promoter with low CG density. Pol II association is inversely related to the number of CpG sites within promoter regions. KO MEFs show less Pol II association at CG rich promoter regions. However, RNA-seq reads are indistinguishable comparing WT and KO samples, suggesting similar transcriptional efficiency in the absence of Lsh. To explore other molecular mechanisms that may preserve low transcription activity or repression at CG hypomethylated promoter regions, we examined H3K27me3 and H3K4me3 modifications by ChIP-seq. Genome wide computation of histone modifications at 5kb tiles shows no increase of H3K27me3 level in KO MEFs. When we ranked 5kb tiles based on CG methylation differences between WT and KO, we observed alterations in H3K27me3 distribution, while H3K4me3 modifications are unremarkable. Regions with moderate CG methylation reduction exhibit concomitant decreases in H3K27me3. mRNA profiles and Genome-wide maps of H3K27me3, H3K4me3 and Pol II in wildtype (WT) and Lsh KO primary MEFs.
2014-06-24 | E-GEOD-57419 | biostudies-arrayexpress
Project description:This study compared the genome of Streptomyces rimosus rimosus against that of Streptomyces coelicolor. It also compared 4 strains with changes in oxytetracycline production and derived from G7, the type strain, against G7. Keywords: Comparative genomic hybridization
2008-01-11 | GSE10126 | 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