GSE136193 Characterizing epigenetic effects of HISTONE DEACETYLASE 6 on DNA methylation, siRNA biogenesis and nucleosome positioning using two hda6 alleles in ros1 background

Contributors : Shoudong Zhang ; Huan Zhong ; Qianwen WangSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencing ; Methylation profiling by high throughput sequencingOrganism : Arabidopsis thalianaDNA cytosine methylation is a hallmark of epigenetic gene silencing. DNA demethylation requires ROS1, a bifunctional  DNA glycosylase/lyases and open chromatin status mediated by IDM1. HDA6 is a RDP3-like histone deacetylase and was confirmed to mediate DNA methylation. In previous screening for ros1 suppressor, we identified two hda6 mutants reverting ros1-caused hypermethylation at RD29A and 35S promoters resp ectively, indicating the antagonization of DNA methylation between HDA6 and ROS1. To learn antagonized effects between HDA6 and ROS1 at DNA cytosine methylation genome-wide, we performed whole genome bisulfite sequencing to search antagonized targets of HDA6 and ROS1 and their specific targets to ev aluate their roles on DNA methylation. To evaluate HDA6’s roles in sRNA biogenesis and nucleosome positioning, we also performed small RNA sequencing and genome-wide mapping of nucleosome positioning of C24, ros1, hda6-9 and hda6-10. Our results indicate that around 43% ros1-caused CG hypermethyl ation, 74.5% and 84.5% ros1-caused CHG and CHH hypermethylation were reverted by the two hda6 alleles in the ros1 background respectively. These results indicate that most of ROS1-demethylated targets...
Source: GEO: Gene Expression Omnibus - Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Methylation profiling by high throughput sequencing Arabidopsis thaliana Source Type: research