SIZ1-Mediated SUMOylation of ROS1 Enhances Its Stability and Positively Regulates Active DNA Demethylation in Arabidopsis

The 5-methylcytosine DNA glycosylase/lyase REPRESSOR OF SILENCING 1(ROS1)-mediated active DNA demethylation is critical for shaping the genomic DNA methylation landscape in Arabidopsis.Whether and how the stability of ROS1 may be regulated by post-translational modifications is unknown.Using a methylation-sensitive PCR(CHOP-PCR)-based forward genetic screen forArabidopsis DNA hyper-methyl-ation mutants,we identified the SUMO E3 ligase SIZ1 as a critical regulator of active DNA demethylation.Dysfunction of SIZ1 leads to hyper-methylation at approximately 1000 genomic regions.SIZ1 physically in-teracts with ROS1 and mediates the SUMOylation of ROS1.The SUMOylation of ROS1 is reduced in siz1 mutant plants.Compared with that in wild-type plants,the protein level of ROS1 is significantly decreased,whereas there is an increased level of ROS1 transcripts in siz1 mutant plants.Our results suggest that SIZ1-mediated SUMOylation of ROS1 promotes its stability and positively regulates active DNA demethylation.

Molecules and mechanisms controlling the active DNA demethylation of the mammalian zygotic genome

The active DNA demethylation in early embryos is essential for subsequent development. Although the zygotic genome is globally demethylated, the DNA methylation of imprinted regions, part of repeat sequences and some gamete-specific regions are maintained. Recent evidence has shown that multiple proteins and biological pathways participate in the regulation of active DNA demethylation, such as TET proteins, DNA repair pathways and DNA methyltransferases. Here we review the recent understanding regarding proteins associated with active DNA demethylation and the regulatory networks controlling the active DNA demethylation in early embryos.

Roles of DEMETER in regulating DNA methylation in vegetative tissues and pathogen resistance

DNA methylation is an epigenetic mark important for genome stability and gene expression.In Arabidopsis thaliana,the 5-methylcytosine DNA glycosylase/demethylase DEMETER(DME)controls active DNA demethylation during the reproductive stage;however,the lethality of loss-of-function dme mutations has made it difficult to assess DME function in vegetative tissues.Here,we edited DME using clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9 and created three weak dme mutants that produced a few viable seeds.We also performed central cell-specific complementation in a strong dme mutant and combined this line with mutations in the other three Arabidopsis demethylase genes to generate the dme ros1 dml2 dml3(drdd)quadruple mutant.A DNA methylome analysis showed that DME is required for DNA demethylation at hundreds of genomic regions in vegetative tissues.A transcriptome analysis of the drdd mutant revealed that DME and the other three demethylases are important for plant responses to biotic and abiotic stresses in vegetative tissues.Despite the limited role of DME in regulating DNA methylation in vegetative tissues,the dme mutants showed increased susceptibility to bacterial and fungal pathogens.Our study highlights the important functions of DME in vegetative tissues and provides valuable genetic tools for future investigations of DNA demethylation in plants.

Genome-wide antagonism between 5-hydroxymethylcytosine and DNA methylation in the adult mouse brain

Mounting evidence points to critical roles for DNA modifications, including 5-methylcytosine （5mC） and its oxidized forms, in the development, plasticity and disorders of the mammalian nervous system. The novel DNA base 5- hydroxymethylcytosine （5hmC） is known to be capable of initiating passive or active DNA demethylation, but whether and how extensively 5hmC functions in shaping the post-mitotic neuronal DNA methylome is unclear. Here we report the genome-wide distribution of 5hmC in dentate granule neurons from adult mouse hippocampus in vivo. 5hmC in the neuronal genome is highly enriched in gene bodies, especially in exons, and correlates with gene expression. Direct genome-wide comparison of 5hmC distribution between embryonic stem cells and neurons reveals extensive differences, reflecting the functional disparity between these two cell types. Importantly, integrative analysis of 5hmC, overall DNA methylation and gene expression profiles of dentate granule neurons in vivo reveals the genome-wide antagonism between these two states of cytosine modifications, supporting a role for 5hmC in shaping the neuronal DNA methylome by promoting active DNA demethylation.