Project description:DNA methylation is an important epigenetic modification involved in many biological processes, and active DNA demethylation plays critical roles in regulating expression of genes and anti-silencing of transgenes. In this study, we isolated mutations in one arabidopsis gene, ROS5, which causes the silencing of transgenic 35S-NPTII because of DNA hypermethylation, but no effect on transgenic RD29A-LUC. ROS5 encodes an atypical small heat shock protein. ROS5 can physically interact with IDM1 and is required for preventing DNA hypermethylation of some endogenous genes that are also regualated by IDM1 and ROS1. We propose that ROS5 may regulate active DNA demethylation by interacting with IDM1, thereby creating a friendly chromatin environment that facilitates the binding of ROS1 to erase DNA methylation.

2014-08-28 | E-MTAB-4323 | biostudies-arrayexpress

Arabidopsis thaliana

Project description:NaCl: Plant Small RNAs

| PRJNA108069 | ENA

Endogenous small RNAs from Arabidopsis thaliana wild-type, dcl4 mutant and dcl4 mutant expressing nuclear or cytoplasmic DCL4

Project description:Parallel RNA silencing pathways regulate gene expression in plants, either by transcriptional gene silencing via RNA-dependent DNA methylation (RdDM), or by post-transcriptional silencing targeting mRNAs. Both pathways rely on distinct Dicer-like proteins to cleave double-stranded RNA into small-interfering RNAs. Experiments to determine the subcellular localization of Dicer-like proteins in Arabidopsis revealed that DCL4 is predominantly expressed as a transcriptional start site isoform that encodes a cytoplasmic protein. A second, longer DCL4 transcript isoform encodes a nuclear-localization signal and its expression is repressed by DNA methylation. Consequently this isoform is induced when promoter methylation decreases due to infection with a bacterial pathogen or during silique development. Nuclear DCL4 produces unique populations of small RNAs, called DCL4NLS isoform-dependent siRNAs (disiRNAs), which function via a post-transcriptional silencing effector, but whose precursors are generated by the RdDM pathway. Arabidopsis cells can thus respond to genome methylation changes by modulating DCL4 localization, which in turn recruits PTGS factors to reinforce RNA silencing.

2016-11-14 | GSE74731 | GEO

Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana

Project description:In plants, transposons and non-protein-coding repeats are epigenetically silenced by CG and non-CG methylation. This pattern of methylation is mediated in part by small RNAs and two specialized RNA polymerases, Pol IV and Pol V, in a process called RNA-directed DNA methylation. By contrast, many protein-coding genes transcribed by Pol II contain in their gene bodies exclusively CG methylation that is independent of small RNAs and Pol IV/Pol V activities. It is unclear how the different methylation machineries distinguish between transposons and genes. Here we report on a group of atypical genes that display in their coding region a transposon-like methylation pattern, which is associated with gene silencing in sporophytic tissues. We performed a methylation-sensitive amplification polymorphism analysis to search for targets of RNA-directed DNA methylation in Arabidopsis thaliana and identified several members of a gene family encoding cysteine-rich peptides (CRPs). We also examined small RNA abundance at individual CRP genes in the wild type plant, nrpd1, and rdr2 mutant plants.

2012-11-22 | E-GEOD-34207 | biostudies-arrayexpress

Bisulfite-Seq and RNA-seq in rootstock of Arabidopsis thaliana grafts

Project description:RNA silencing is a mechanism for regulating gene expression at the transcriptional and post-transcriptional levels. Its functions include regulating endogenous gene expression and protecting the cell against viruses and invading transposable elements (TEs). A key component of the mechanism is small RNAs (sRNAs) of 21-24 nucleotides (nt) in length, which direct the silencing machinery in a sequence specific manner to target nucleic acids. sRNAs of 24 nt are involved in methylation of cytosine residues of target loci in three sequence contexts (CG, CHG and CHH), referred to as RNA-directed DNA methylation (RdDM). We previously demonstrated that 24 nt sRNAs are mobile from shoot to root in Arabidopsis thaliana. In this study we demonstrated that methylation of thousands of loci in root tissues is dependent upon mobile sRNAs from the shoot. Furthermore, we found that mobile sRNA-dependent DNA methylation occurs predominantly in non-CG contexts. These findings were made using base-resolution next generation sequencing approaches and genome wide analyses. Specific classes of short TEs are the predominant targets of mobile sRNA-dependent DNA methylation; classes typically found in gene-rich euchromatic regions. Mobile sRNA-regulated genes were also identified. Mechanistically, we demonstrate that mobile sRNA-dependent non-CG methylation is largely independent of the CMT2/3 RdDM pathway but dependent upon the DRM1/DRM2 RdDM pathway. This is in contrast to non-mobile sRNA-dependent DNA methylation, which predominantly depends upon the CMT2/3 RdDM pathway. These data are complementary to the small RNA sequencing data from Arabidopsis root grafts described in Molnar et al (Science, 2010 May 14;328(5980):872-5).

2016-01-04 | E-MTAB-3473 | biostudies-arrayexpress

Arabidopsis thaliana

Project description:Thermoresponive small RNAs in Arabidopsis thalinana

| PRJNA407271 | ENA

Arabidopsis thaliana

Project description:Small RNAs in stv-1 mutant

| PRJNA356639 | ENA