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

• Published in: Nature genetics Vol. 48; no. 6; pp. 687 - 693
• Main Authors: Li, Chenlong, Gu, Lianfeng, Gao, Lei, Chen, Chen, Wei, Chuang-Qi, Qiu, Qi, Chien, Chih-Wei, Wang, Suikang, Jiang, Lihua, Ai, Lian-Feng, Chen, Chia-Yang, Yang, Songguang, Nguyen, Vi, Qi, Yanhua, Snyder, Michael P, Burlingame, Alma L, Kohalmi, Susanne E, Huang, Shangzhi, Cao, Xiaofeng, Wang, Zhi-Yong, Wu, Keqiang, Chen, Xuemei, Cui, Yuhai
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.06.2016; Nature Publishing Group
• Subjects: 38/35; 38/39; 38/77; 38/91; 631/449/1659; 631/449/2491; 82/58; Adenosine Triphosphatases - genetics; Agriculture; Animal Genetics and Genomics; Arabidopsis; Arabidopsis - enzymology; Arabidopsis - genetics; Arabidopsis Proteins - genetics; Base Sequence; Biomedicine; Cancer Research; Chromatin; Chromatin Assembly and Disassembly; Deoxyribonucleic acid; DNA; Gene expression; Gene Expression Regulation, Enzymologic; Gene Expression Regulation, Plant; Gene Function; Genetic aspects; Genome, Plant; Genomes; Genomics; Human Genetics; letter; Localization; Mass spectrometry; Observations; Oxidoreductases; Properties; Proteins; Scientific imaging; Transcription Factors - genetics
• ISSN: 1061-4036; 1546-1718
• DOI: 10.1038/ng.3555

Yuhai Cui and colleagues report that the H3K27 demethylase REF6 targets genomic loci containing a specific DNA motif via its zinc-finger domains. They show that REF6 facilitates the recruitment of BRM and that deleting the DNA motif from a target gene in Arabidopsis makes it inaccessible to REF6. SWI/SNF-type chromatin remodelers, such as BRAHMA (BRM), and H3K27 demethylases both have active roles in regulating gene expression at the chromatin level 1 , 2 , 3 , 4 , 5 , 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 6 , 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.