Abstract

SWI/SNF-type chromatin remodelers, such as BRAHMA (BRM), and H3K27 demethylases both have active roles in regulating gene expression at the chromatin level1,2,3,4,5, 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 demethylase6, 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.

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Acknowledgements

We thank the Arabidopsis Biological Resource Center (ABRC) for seeds for T-DNA insertion lines; A. Molnar for help with figure preparation; X. Shi of the Clinical Genomics Centre at Mount Sinai Hospital for overseeing the next-generation sequencing; and S. Rothstein for critical reading of the manuscript. C.C. is supported by a graduate fellowship from the Chinese Scholarship Council. This work was supported by funding from the Agriculture and Agri-Food Canada A-base and the National Science and Engineering Research Council of Canada (R4019A01) to Y.C., the Natural Science Foundation of China (31128001 to K.W. and Y.C. and 31210103901 to X. Cao and X. Chen), the State Key Laboratory of Plant Genomics (2015B0129-01 to X. Cao), and the US National Institutes of Health to X. Chen (GM061146) and Z.-Y.W. (R01GM066258).

Author information

Affiliations

  1. Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, Canada.

    • Chenlong Li
    • , Chen Chen
    • , Vi Nguyen
    •  & Yuhai Cui
  2. Department of Biology, Western University, London, Ontario, Canada.

    • Chenlong Li
    • , Chen Chen
    • , Susanne E Kohalmi
    •  & Yuhai Cui
  3. Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, China.

    • Lianfeng Gu
  4. Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, California, USA.

    • Lianfeng Gu
    • , Lei Gao
    • , Suikang Wang
    •  & Xuemei Chen
  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.

    • Lianfeng Gu
    • , Qi Qiu
    •  & Xiaofeng Cao
  6. Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA.

    • Chuang-Qi Wei
    • , Chih-Wei Chien
    •  & Zhi-Yong Wang
  7. Life Science College, Hebei Normal University, Shijiazhuang, China.

    • Chuang-Qi Wei
  8. State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China.

    • Suikang Wang
    •  & Yanhua Qi
  9. Department of Genetics, Stanford University, Stanford, California, USA.

    • Lihua Jiang
    •  & Michael P Snyder
  10. Hebei Entry–Exit Inspection and Quarantine Bureau, Shijiazhuang, China.

    • Lian-Feng Ai
  11. Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan.

    • Chia-Yang Chen
    •  & Keqiang Wu
  12. Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.

    • Songguang Yang
  13. Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.

    • Alma L Burlingame
  14. School of Life Sciences, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-sen University, Guangzhou, China.

    • Shangzhi Huang
  15. Collaborative Innovation Center of Genetics and Development, Shanghai, China.

    • Xiaofeng Cao
  16. CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.

    • Xiaofeng Cao
  17. Howard Hughes Medical Institute, University of California, Riverside, Riverside, California, USA.

    • Xuemei Chen

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Contributions

C.L. and Y.C. conceived the project. C.L. performed most of the experiments. C.-Q.W., L.-F.A., C.-W.C., M.P.S., L.J., A.L.B., and Z.-Y.W. performed BRM-GFP IP–MS assays. L. Gu, L. Gao, C.L., and C.C. conducted bioinformatics analyses. C.L., Q.Q., S.W., Y.Q., S.Y., C.-Y.C., V.N., S.E.K., S.H., X. Cao., and K.W. analyzed data. C.L., Y.C., and X. Chen wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Yuhai Cui.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–15 and Supplementary Tables 1 and 2.

Excel files

  1. 1.

    Supplementary Data 1

    List of genes occupied by BRM in 14-d-old Col seedlings.

  2. 2.

    Supplementary Data 2

    List of genes occupied by REF6 in 14-d-old Col seedlings.

  3. 3.

    Supplementary Data 3

    List of genes co-occupied by BRM and REF6.

  4. 4.

    Supplementary Data 4

    List of genes showing REF6-dependent BRM occupancy.

  5. 5.

    Supplementary Data 5

    List of genes differentially expressed in brm-1, ref6-1, and brm-1 ref6-1 compared to wild-type seedlings by RNA-seq.

Image files

  1. 1.

    Supplementary Data 6

    Uncropped immunoblot images.

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DOI

https://doi.org/10.1038/ng.3555

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