Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis.
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.
Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada.|Department of Biology, Western University, London, Ontario, Canada.
Chenlong
0000-0003-3405-6056
C
Li
Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, China.|Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, USA.|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.
Lianfeng
L
Gu
Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, USA.
Lei
L
Gao
Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada.|Department of Biology, Western University, London, Ontario, Canada.
Chen
C
Chen
Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA.|Life Science College, Hebei Normal University, Shijiazhuang, China.
Chuang-Qi
CQ
Wei
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.
Qi
Q
Qiu
Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA.
Chih-Wei
CW
Chien
Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, USA.|State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China.
Suikang
S
Wang
Department of Genetics, Stanford University, Stanford, California, USA.
Lihua
L
Jiang
Hebei Entry-Exit Inspection and Quarantine Bureau, Shijiazhuang, China.
Lian-Feng
LF
Ai
Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan.
Chia-Yang
CY
Chen
Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
Songguang
S
Yang
Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada.
Vi
V
Nguyen
State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China.
Yanhua
Y
Qi
Department of Genetics, Stanford University, Stanford, California, USA.
Michael P
MP
Snyder
Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.
Alma L
AL
Burlingame
Department of Biology, Western University, London, Ontario, Canada.
Susanne E
SE
Kohalmi
School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-sen University, Guangzhou, China.
Shangzhi
S
Huang
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.|Collaborative Innovation Center of Genetics and Development, Shanghai, China.|CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
Xiaofeng
X
Cao
Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA.
Zhi-Yong
ZY
Wang
Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan.
Keqiang
0000-0002-5791-3594
K
Wu
Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, USA.|Howard Hughes Medical Institute, University of California, Riverside, Riverside, California, USA.
Xuemei
X
Chen
Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada.|Department of Biology, Western University, London, Ontario, Canada.
Yuhai
0000-0002-3675-3288
Y
Cui
D000251:Adenosine Triphosphatases / Q000235:genetics*; D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics*; D001483:Base Sequence; D042002:Chromatin Assembly and Disassembly; D015971:Gene Expression Regulation, Enzymologic; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D014157:Transcription Factors / Q000235:genetics*
D029681:Arabidopsis Proteins; C529524:REF6 protein, Arabidopsis; D014157:Transcription Factors; D000251:Adenosine Triphosphatases; C514541:BRM protein, Arabidopsis