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Transcription profiling of wild-type and epic2 mutant plants

ABSTRACT: Chromatin and its covalent modifications play important roles during development. However, how different types of chromatin regulators individually control gene expression in different cell types has so far not been investigated in detail. To explore their role in these processes we performed forward and reverse genetic experiments using an epigenetically silenced reporter gene in Arabidopsis. We found three chromatin regulators, each involved in different epigenetic pathways, to control reporter gene expression in distinct tissues and cell-types. Here we report on the roles of the RNA polymerase Pol V, the histone deacetylase HDA6 and the SWI/SNF class chromatin remodeler SPLAYED (SYD) in silencing expression of the reporter in different cell-types. Furthermore, we demonstrate that a highly conserved domain in HDA6 is involved in its target specificity. And we present data showing that SYD controls transcription of epigenetically silenced genes. The results presented here provide evidence supporting the notion that tissue specificity of gene expression and its fine-tuning can be influenced by the activity of different chromatin regulators.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE49935 | GEO | 2020/08/15

REPOSITORIES: GEO

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Project description:DNA 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 respectively, 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 evaluate 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 hypermethylation, 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 are also HDA6-mediated DNA methylated targets. In addition, we observed that HDA6-affected DNA methylation targets are far more than ROS1-demethylation targets at CHG and CHH context, but not at CG context. sRNA analysis showed that HDA6 inhibits LTR/Gypsy and TE gene 24nt siRNA accumulation, while promotes RC/Helitron 24nt siRNA accumulation. Our Mono-nucleosome positioning data further showed that the two hda6 alleles have striking difference on nucleosome positioning, hda6-10 obviously have different nucleosome positioning patterns with hda6-9. Our results indicate HDA6 not only mediates overall DNA methylation at CG, CHG and CHH context, and antagonizes with ROS1 mediated DNA demethylation, but also regulates nucleosome positioning and small RNA accumulation at some genome specific regions.

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Transcription profiling of wild-type and epic2 mutant plants

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