6JNL

REF6 ZnF2-4-NAC004 complex

Summary for 6JNL

• Entry DOI: 10.2210/pdb6jnl/pdb
• Descriptor: Lysine-specific demethylase REF6, DNA (5'-D(*TP*TP*CP*TP*CP*TP*GP*TP*TP*TP*TP*G)-3'), DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*A)-3'), ... (8 entities in total)
• Functional Keywords: ref6, zinc finger, 5mc, dna complex, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Arabidopsis thaliana (Mouse-ear cress); More
• Total number of polymer chains: 3
• Total formula weight: 19679.58

Authors

Yao, Q.Q.,Wu, B.X.,Ma, J.B. (deposition date: 2019-03-17, release date: 2019-03-27, Last modification date: 2024-05-29)

Primary citation

Qiu, Q.,Mei, H.,Deng, X.,He, K.,Wu, B.,Yao, Q.,Zhang, J.,Lu, F.,Ma, J.,Cao, X.
DNA methylation repels targeting of Arabidopsis REF6.
Nat Commun, 10:2063-2063, 2019

PubMed Abstract: 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.

PubMed: 31048693
DOI: 10.1038/s41467-019-10026-1

Experimental method

X-RAY DIFFRACTION (2.15 Å)