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Creators/Authors contains: "Lee, Jaehoon"

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  1. ; ; ; ; ; ; ; ; ; ; et al ( , BMC Plant Biology)
    Abstract Background

    H2A.X is an H2A variant histone in eukaryotes, unique for its ability to respond to DNA damage, initiating the DNA repair pathway. H2A.X replacement within the histone octamer is mediated by the FAcilitates Chromatin Transactions (FACT) complex, a key chromatin remodeler. FACT is required for DEMETER (DME)-mediated DNA demethylation at certain loci inArabidopsis thalianafemale gametophytes during reproduction. Here, we sought to investigate whether H2A.X is involved in DME- and FACT-mediated DNA demethylation during reproduction.

     Results

    H2A.X is encoded by two genes in Arabidopsis genome,HTA3andHTA5. We generatedh2a.xdouble mutants, which displayed a normal growth profile, whereby flowering time, seed development, and root tip organization, S-phase progression and proliferation were all normal. However,h2a.xmutants were more sensitive to genotoxic stress, consistent with previous reports. H2A.X fused to Green Fluorescent Protein (GFP) under theH2A.Xpromoter was highly expressed especially in newly developing Arabidopsis tissues, including in male and female gametophytes, where DME is also expressed. We examined DNA methylation inh2a.xdeveloping seeds and seedlings using whole genome bisulfite sequencing, and found that CG DNA methylation is decreased genome-wide inh2a.xmutant endosperm. Hypomethylation was most striking in transposon bodies, and occurred on both parental alleles in the developing endosperm, but not the embryo or seedling.h2a.x-mediated hypomethylated sites overlapped DME targets, but also included other loci, predominately located in heterochromatic transposons and intergenic DNA.

     Conclusions

    Our genome-wide methylation analyses suggest that H2A.X could function in preventing access of the DME demethylase to non-canonical sites. Overall, our data suggest that H2A.X is required to maintain DNA methylation homeostasis in the unique chromatin environment of the Arabidopsis endosperm.

     
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  2. ; ; ; ( , Inventiones mathematicae)
    Full Text Available 
  3. ; ; ; ; ; ( , Conference on Neural Information Processing Systems)
    Accepted Manuscript Full Text Available
  4. ; ; ; ; ; ; ; ( , Proceedings of the 2021 SIAM International Conference on Data Mining (SDM))
    null (Ed.)
    Graph synthesis is a long-standing research problem. Many deep neural networks that learn about latent characteristics of graphs and generate fake graphs have been proposed. However, in many cases their scalability is too high to be used to synthesize large graphs. Recently, one work proposed an interesting scalable idea to learn and generate random walks that can be merged into a graph. Due to its difficulty, however, the random walk-based graph synthesis failed to show state-of-the-art performance in many cases. We present an improved random walk-based method by using negative random walks. In our experiments with 6 datasets and 8 baseline methods, our method shows the best performance in almost all cases. We achieve both high scalability and generation quality. 
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  5. ; ; ; ; ; ; ; ; ; ; et al ( , Transactions on machine learning research)
    Accepted Manuscript Full Text Available