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Nat Genet. 2016 Jun;48(6):687-93. doi: 10.1038/ng.3555. Epub 2016 Apr 25.

Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis.

Author information

1
Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada.
2
Department of Biology, Western University, London, Ontario, Canada.
3
Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, China.
4
Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, USA.
5
State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
6
Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA.
7
Life Science College, Hebei Normal University, Shijiazhuang, China.
8
State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China.
9
Department of Genetics, Stanford University, Stanford, California, USA.
10
Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang, China.
11
Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan.
12
Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
13
Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.
14
School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-sen University, Guangzhou, China.
15
Collaborative Innovation Center of Genetics and Development, Shanghai, China.
16
CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
17
Howard Hughes Medical Institute, University of California, Riverside, Riverside, California, USA.

Abstract

SWI/SNF-type chromatin remodelers, such as BRAHMA (BRM), and H3K27 demethylases both have active roles in regulating gene expression at the chromatin level, but how they are recruited to specific genomic sites remains largely unknown. Here we show that RELATIVE OF EARLY FLOWERING 6 (REF6), a plant-unique H3K27 demethylase, targets genomic loci containing a CTCTGYTY motif via its zinc-finger (ZnF) domains and facilitates the recruitment of BRM. Genome-wide analyses showed that REF6 colocalizes with BRM at many genomic sites with the CTCTGYTY motif. Loss of REF6 results in decreased BRM occupancy at BRM-REF6 co-targets. Furthermore, REF6 directly binds to the CTCTGYTY motif in vitro, and deletion of the motif from a target gene renders it inaccessible to REF6 in vivo. Finally, we show that, when its ZnF domains are deleted, REF6 loses its genomic targeting ability. Thus, our work identifies a new genomic targeting mechanism for an H3K27 demethylase and demonstrates its key role in recruiting the BRM chromatin remodeler.

PMID:
27111034
PMCID:
PMC5134324
DOI:
10.1038/ng.3555
[Indexed for MEDLINE]
Free PMC Article

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