DNA methylation repels targeting of Arabidopsis REF6
DNA methylation repels targeting of Arabidopsis REF6
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DNA甲基化排斥拟南芥REF6的靶向
DOI：
10.1038/s41467-019-10026-1
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发表时间：
2019-05-02
影响因子：
16.6
通讯作者：
Cao, Xiaofeng
中科院分区：
文献类型：
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作者：
Qiu, Qi;Mei, Hailiang;Cao, Xiaofeng
EARLY FLOWERING 6 (REF6/JMJ12) 的亲戚，一种包含 Jumonji C (JmjC) 结构域的 H3K27me3 组蛋白去甲基化酶，通过其锌指 (ZnF) 结构域直接识别 CCTTGYTY 基序，在拟南芥基因组中找到其目标位点。 REF6 倾向于结合位于活性染色质状态的基序，这些基序因异染色质修饰而被耗尽。然而，其根本机制仍不清楚。在这里，我们表明 REF6 在体内优先结合低甲基化的 CTCTGYTY 基序，并且 CHG 甲基化降低了 REF6 DNA 体外结合亲和力。此外，ZnF簇与DNA寡核苷酸复合物的晶体结构表明5-甲基胞嘧啶不利于REF6结合。在 drm1 drm2 cmt2 cmt3 (ddcc) 四重突变体中，非 CG 甲基化显着减少，REF6 可以异位结合少量新的靶位点，其中大多数位于常染色质区域中的短 TE 中或与短 TE 相邻。总的来说，我们的研究结果表明，DNA 甲基化可能与其他表观遗传修饰结合作用，可以部分解释为什么 REF6 结合在异染色质位点中被耗尽。
RELATIVE OF EARLY FLOWERING 6 (REF6/JMJ12), a Jumonji C (JmjC)-domain-containing H3K27me3 histone demethylase, finds its target loci in Arabidopsis genome by directly recognizing the CTCTGYTY motif via its zinc-finger (ZnF) domains. REF6 tends to bind motifs located in active chromatin states that are depleted for heterochromatic modifications. However, the underlying mechanism remains unknown. Here, we show that REF6 preferentially bind to hypo-methylated CTCTGYTY motifs in vivo, and that CHG methylation decreases REF6 DNA binding affinity in vitro. In addition, crystal structures of ZnF-clusters in complex with DNA oligonucleotides reveal that 5-methylcytosine is unfavorable for REF6 binding. In drm1 drm2 cmt2 cmt3 (ddcc) quadruple mutants, in which non-CG methylation is significantly reduced, REF6 can ectopically bind a small number of new target loci, most of which are located in or neighbored with short TEs in euchromatic regions. Collectively, our findings reveal that DNA methylation, likely acting in combination with other epigenetic modifications, may partially explain why REF6 binding is depleted in heterochromatic loci.