REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis

Nature Genetics

Volumn 48, Issue 6, 2016, Pages 694-699

  Cui, Xia ^a,g   Lu, Falong ^a,b,h   Qiu, Qi ^a,b   Zhou, Bing ^a,i   Gu, Lianfeng ^a,j   Zhang, Shuaibin ^a,b   Kang, Yanyuan ^a,b   Cui, Xiekui ^a,b   Ma, Xuan ^a,c   Yao, Qingqing ^d,e   Ma, Jinbiao ^d,e   Zhang, Xiaoyu ^f   Cao, Xiaofeng ^a,e  

^a INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^c SHENZHEN UNIVERSITY   (China)

^d FUDAN UNIVERSITY   (China)

^e FUDAN UNIVERSITY   (China)

^f UNIVERSITY OF GEORGIA   (United States)

^g INSTITUTE OF PLANT PROTECTION   (China)

^h BOSTON CHILDREN S HOSPITAL   (United States)

ⁱ UNIVERSITY OF CALIFORNIA   (United States)

^j FUJIAN AGRICULTURE AND FORESTRY UNIVERSITY   (China)

more..

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H3; LYSINE; PROTEIN; RELATIVE OF EARLY FLOWERING 6; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN; ARABIDOPSIS PROTEIN; HISTONE; PLANT DNA; REF6 PROTEIN, ARABIDOPSIS; TRANSCRIPTION FACTOR;

ARABIDOPSIS; ARTICLE; BINDING AFFINITY; CHROMATIN; CONTROLLED STUDY; COTYLEDON; DEMETHYLATION; DNA SEQUENCE; GENE MUTATION; GENE SILENCING; GENETIC TRANSCRIPTION; GENOME-WIDE ASSOCIATION STUDY; IN VITRO STUDY; NONHUMAN; PLANT CELL; PLANT DEVELOPMENT; PLANT GENETICS; PRIORITY JOURNAL; PROTEIN MOTIF; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PLANT GENE;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; DNA, PLANT; GENES, PLANT; HISTONES; TRANSCRIPTION FACTORS;

EID: 84964199681     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3556     Document Type: Article

References (44)

1. Lu, F., Cui, X., Zhang, S., Jenuwein, T., & Cao, X. Arabidopsis REF6 is a histone H3 lysine 27 demethylase. Nat. Genet. 43, 715-719 (2011
2. Holec, S., & Berger, F. Polycomb group complexes mediate developmental transitions in plants. Plant Physiol. 158, 35-43 (2012
3. Margueron, R., & Reinberg, D. The Polycomb complex PRC2 and its mark in life. Nature 469, 343-349 (2011
4. Steffen, P.A., & Ringrose, L. What are memories made of? How Polycomb and Trithorax proteins mediate epigenetic memory. Nat. Rev. Mol. Cell Biol. 15, 340-356 (2014
5. Lafos, M., et al. Dynamic regulation of H3K27 trimethylation during Arabidopsis differentiation. PLoS Genet. 7, e1002040 (2011
6. Sun, B., et al. Timing mechanism dependent on cell division is invoked by Polycomb eviction in plant stem cells. Science 343, 1248559 (2014
7. Wu, M.F., et al. SWI2/SNF2 chromatin remodeling ATPases overcome Polycomb repression and control floral organ identity with the LEAFY and SEPALLATA3 transcription factors. Proc. Natl. Acad. Sci. USA 109, 3576-3581 (2012
8. Zhang, X., et al. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol. 5, e129 (2007
9. Hou, X., et al. Nuclear factor Y-mediated H3K27me3 demethylation of the SOC1 locus orchestrates flowering responses of Arabidopsis. Nat. Commun. 5, 4601 (2014
10. Noh, B., et al. Divergent roles of a pair of homologous jumonji/zinc-finger-class transcription factor proteins in the regulation of Arabidopsis flowering time. Plant Cell 16, 2601-2613 (2004
11. Yu, X., et al. Modulation of brassinosteroid-regulated gene expression by Jumonji domain-containing proteins ELF6 and REF6 in Arabidopsis. Proc. Natl. Acad. Sci. USA 105, 7618-7623 (2008
12. Sun, Y., et al. Integration of brassinosteroid signal transduction with the transcription network for plant growth regulation in Arabidopsis. Dev. Cell 19, 765-777 (2010
13. Yu, X., et al. A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana. Plant J. 65, 634-646 (2011
14. Lu, F., Cui, X., Zhang, S., Liu, C., & Cao, X. JMJ14 is an H3K4 demethylase regulating flowering time in Arabidopsis. Cell Res. 20, 387-390 (2010
15. Larsson, A.S., Landberg, K., & Meeks-Wagner, D.R. The TERMINAL FLOWER2 (TFL2) gene controls the reproductive transition and meristem identity in Arabidopsis thaliana. Genetics 149, 597-605 (1998
16. Klug, A. The discovery of zinc fingers and their applications in gene regulation and genome manipulation. Annu. Rev. Biochem. 79, 213-231 (2010
17. Machanick, P., & Bailey, T.L. MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 27, 1696-1697 (2011
18. Bailey, T.L., & Machanick, P. Inferring direct DNA binding from ChIP-seq. Nucleic Acids Res. 40, e128 (2012
19. Zhang, S., et al. C-terminal domains of a histone demethylase interact with a pair of transcription factors and mediate specific chromatin association. Cell Discovery 1, 15003 (2015
20. van Dijk, K., et al. Dynamic changes in genome-wide histone H3 lysine 4 methylation patterns in response to dehydration stress in Arabidopsis thaliana. BMC Plant Biol. 10, 238 (2010
21. Coleman-Derr, D., & Zilberman, D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genet. 8, e1002988 (2012
22. Sullivan, A.M., et al. Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana. Cell Rep. 8, 2015-2030 (2014
23. Inagaki, S., et al. Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome. EMBO J. 29, 3496-3506 (2010
24. Aida, M., Ishida, T., Fukaki, H., Fujisawa, H., & Tasaka, M. Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant. Plant Cell 9, 841-857 (1997
25. Hibara, K., et al. Arabidopsis CUP-SHAPED COTYLEDON3 regulates postembryonic shoot meristem and organ boundary formation. Plant Cell 18, 2946-2957 (2006
26. Takada, S., Hibara, K., Ishida, T., & Tasaka, M. The CUP-SHAPED COTYLEDON1 gene of Arabidopsis regulates shoot apical meristem formation. Development 128, 1127-1135 (2001
27. Vroemen, C.W., Mordhorst, A.P., Albrecht, C., Kwaaitaal, M.A., & De Vries, S.C. The CUP-SHAPED COTYLEDON3 gene is required for boundary and shoot meristem formation in Arabidopsis. Plant Cell 15, 1563-1577 (2003
28. Crevillén, P., et al. Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state. Nature 515, 587-590 (2014
29. Lu, F., et al. Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice. J. Integr. Plant Biol. 50, 886-896 (2008
30. Amborella Genome Project. The Amborella genome and the evolution of flowering plants. Science 342, 1241089 (2013
31. Najafabadi, H.S., et al. C2H2 zinc finger proteins greatly expand the human regulatory lexicon. Nat. Biotechnol. 33, 555-562 (2015
32. Clough, S.J., & Bent, A.F. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735-743 (1998
33. Bowler, C., et al. Chromatin techniques for plant cells. Plant J. 39, 776-789 (2004
34. Langmead, B., & Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012
35. Li, H., et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009
36. Zhang, Y., et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008
37. Ernst, J., et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49 (2011
38. Grant, C.E., Bailey, T.L., & Noble, W.S. FIMO: scanning for occurrences of a given motif. Bioinformatics 27, 1017-1018 (2011
39. Quinlan, A.R., & Hall, I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010
40. Finnegan, E.J., & Dennis, E.S. Vernalization-induced trimethylation of histone H3 lysine 27 at FLC is not maintained in mitotically quiescent cells. Curr. Biol. 17, 1978-1983 (2007
41. Lin, R., et al. Transposase-derived transcription factors regulate light signaling in Arabidopsis. Science 318, 1302-1305 (2007
42. Johnson, M., et al. NCBI BLAST: a better web interface. Nucleic Acids Res. 36, W5-W9 (2008
43. Thompson, J.D., Higgins, D.G., & Gibson, T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680 (1994
44. Tamura, K., et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739 (2011