[KSCI] Korea Science Citation Index Service

http://dx.doi.org/10.1007/s10059-009-0054-7

Temporal and Spatial Expression Patterns of Nine Arabidopsis Genes Encoding Jumonji C-Domain Proteins

Hong, Eun-Hye (School of Biological Sciences, Seoul National University)
Jeong, Young-Min (School of Biological Sciences, Seoul National University)
Ryu, Jee-Youn (School of Biological Sciences, Seoul National University)
Amasino, Richard M. (Global Research Laboratory for Floral Regulatory Signaling, Seoul National University)
Noh, Bosl (Global Research Laboratory for Floral Regulatory Signaling, Seoul National University)
Noh, Yoo-Sun (School of Biological Sciences, Seoul National University)

Abstract

Diverse posttranslational modifications of histones, such as acetylation and methylation, play important roles in controlling gene expression. Histone methylation in particular is involved in a broad range of biological processes, including heterochromatin formation, X-chromosome inactivation, genomic imprinting, and transcriptional regulation. Recently, it has been demonstrated that proteins containing the Jumonji (Jmj) C domain can demethylate histones. In Arabidopsis, twenty-one genes encode JmjC domain-containing proteins, which can be clustered into five clades. To address the biological roles of the Arabidopsis genes encoding JmjC-domain proteins, we analyzed the temporal and spatial expression patterns of nine genes. RT-PCR analyses indicate all nine Arabidopsis thaliana Jmj (AtJmj) genes studied are actively expressed in various tissues. Furthermore, studies of transgenic plants harboring AtJmj:: ${\beta}$ -glucuronidase fusion constructs reveal that these nine AtJmj genes are expressed in a developmentally and spatially regulated manner.

Keywords

Arabidopsis; demethylase; epigenetics; histone demethylation; Jumonji;

Citations & Related Records

Times Cited By KSCI : 1 (Citation Analysis)
Times Cited By Web Of Science : 8 (Related Records In Web of Science)

Reference
Cited By KSCI

1	Byvoet, P. (1972). In vivo turnover and distribution of radio-N-methyl in arginine-rich histones from rat tissues. Arch. Biochem. Biophys. 152, 887-888 DOI PUBMED ScienceOn
2	Kosarev, P., Mayer, K.F., and Hardtke, C.S. (2002). Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome. Genome Biol. 3, RESEARCH0016
3	Noh, B., Lee, S.H., Kim, H.J., Yi, G., Shin, E.A., Lee, M., Jung, K.J., Doyle, M.R., Amasino, R.M., and Noh, Y.S. (2004). 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 DOI ScienceOn
4	Pagnussat, G.C., Yu, H.J., Ngo, Q.A., Rajani, S., Mayalagu, S., Johnson, C.S., Capron, A., Xie, L.F., Ye, D., and Sundaresan, V. (2005). Genetic and molecular identification of genes required for female gametophyte development and function in Arabidopsis. Development 132, 603-614 DOI ScienceOn
5	Shi, Y., Lan, F., Matson, C., Mulligan, P., Whetstine, J.R., Cole, P.A., Casero, R.A., and Shi, Y. (2004). Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119, 941–953 DOI ScienceOn
6	Tsukada, Y., Fang, J., Erdjument-Bromage, H., Warren, M.E., Borchers, C.H., Tempst, P., and Zhang, Y. (2006). Histone demethylation by a family of JmjC domain-containing proteins. Nature 439, 811-816 DOI ScienceOn
7	Whetstine, J.R., Nottke, A., Lan, F., Huarte, M., Smolikov, S., Chen, Z., Spooner, E., Li, E., Zhang, G., Colaiacovo, M., et al. (2006). Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell 125, 467-481 DOI ScienceOn
8	Kouzarides, T. (2007). Chromatin modifications and their function. Cell 128, 693-705 DOI PUBMED ScienceOn
9	Lu, F., Li, G., Cui, X., Liu, C., Wang, X.J., and Cao, X. (2008). Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice. J. Int. Plant Biol. 50, 886-896 DOI ScienceOn
10	Clissold, P.M., and Ponting, C.P. (2001). JmjC: cupin metalloenzymelike domains in jumonji, hairless and phospholipase A2beta. Trends Biochem. Sci. 26, 7-9 DOI PUBMED ScienceOn
11	Zhou, X., and Ma, H. (2008). Evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence. BMC Evol. Biol. 8, 294 DOI PUBMED ScienceOn
12	Duerre, J.A., and Lee, C.T. (1974). in vivo methylation and turnover of rat brain histones. J. Neurochem. 23, 541-547 DOI PUBMED
13	Klose, R.J., Kallin, E.M., and Zhang, Y. (2006). JmjC-domaincontaining proteins and histone demethylation. Nat. Rev. Genet. 7, 715-727 DOI ScienceOn
14	Musco, G., and Peterson, P. (2008). PHD finger of autoimmune regulator: An epigenetic link between the histone modifications and tissue-specific antigen expression in thymus. Epigenetics 3, 310-314 DOI ScienceOn
15	Martin, C., and Zhang, Y. (2005). The diverse functions of histone lysine methylation. Nat. Rev. Mol. Cell. Biol. 6, 838-849 DOI ScienceOn
16	Chen, Z., Zang, J., Whetstine, J., Hong, X., Davrazou, F., Kutateladze, T.G., Simpson, M., Mao, Q., Pan, C.H., Dai, S., et al. (2006). Structural insights into histone demethylation by JMJD2 family members. Cell 125, 691-702 DOI ScienceOn
17	Saze, H., Shiraishi, A., Miura, A., and Kakutani, T. (2008). Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana Science 319, 462-465 DOI PUBMED ScienceOn
18	Chang, B., Chen, Y., and Bruick, R.K. (2007). JMJD6 is a histone arginine demethylase, Science 318, 444-447 DOI PUBMED ScienceOn
19	Jefferson, R.A., Kavanagh, T.A., and Bevan, M.W. (1987). GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO J. 6, 3901-3907 PUBMED
20	Cloos, P.A.C., Christensen, J., Agger, K., Maiolica, A., Rappsilber, J., Antal, T., Hansen, K.H., and Helin, K. (2006). The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3. Nature 442, 307-311 DOI ScienceOn
21	Clough, S.J., and Bent, A.F. (1998). Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735-743 DOI ScienceOn
22	Yamane, K., Toumazou, C., Tsukada, Y., Erdjument-Bromage, H., Tempst, P., Wong, J., and Zhang, Y. (2006). JHDM2A, a JmjCcontaining H3K9 demethylase, facilitates transcription activation by androgen receptor. Cell 125, 483-495 DOI ScienceOn
23	Noh, Y.S., and Amasino, R.M. (2003). mfbN, an fptf family gene, is required for ci` activation and floral repression in Arabidopsis. Plant Cell 15, 1671-1682 DOI ScienceOn
24	Xiang, Y., Zhu, Z., Han, G., Ye, X., Xu, B., Peng, Z., Ma, Y., Yu, Y. Lin, H., Chen, A.P., et al. (2007). JARID1B is a histone H3 lysine 4 demethylase up-regulated in prostate cancer. Proc. Natl. Acad. Sci. USA 103, 19226-19231
25	Malamy, J., and Benfey, P. (1997). Organization and cell differentiation. Development 124, 33-44 PUBMED
26	Finn, R.D., Mistry, J., Schuster-Bockler, B., Griffiths-Jones, S., Hollich, V., Lassmann, T., Moxon, S., Marshall, M., Khanna, A., Durbin, R., et al. (2006). Pfam: clans, web tools and services. Nucleic Acids Res. 34, D247-251 DOI ScienceOn
27	Thompson, J.D., Higgins, D.G.I and Gibson, T.J. (1994). 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 DOI ScienceOn
28	Agger, K., Cloos, P.A., Christensen, J., Pasini, D., Rose, S., Rappsilber, J., Issaeva, I., Canaani, E., Salcini, A.E., and Helin, K. (2007). UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. Nature 449, 731-734 DOI ScienceOn
29	Cuthbert, G.L., Daujat, S., Snowden, A.W., Erdjument-Bromage, H., Hagiwara, T., Yamada, M., Schneider, R., Gregory, P.D., Tempst, P., Bannister, A.J., et al. (2004). Histone deimination antagonizes arginine methylation. Cell 118, 545-553 DOI ScienceOn
30	Kwon, S.H., and Workman, J.L. (2008). The heterochromatin protein 1 (HP1) family: put away a bias toward HP1. Mol. Cells 26, 217-227 PUBMED

11	(2009) PLoS ONE Repression of <I>FLOWERING LOCUS T</I> Chromatin by Functionally Redundant Histone H3 Lysine 4 Demethylases in <I>Arabidopsis</I> / 4 (11) , e8033
2	(2011) Plant physiology The Jumonji C Domain-Containing Protein JMJ30 Regulates Period Length in the Arabidopsis Circadian Clock / 155 (2) , 906
6	(2009) Plant signaling & behavior Chromatin remodeling and the circadian clock : Jumonji C-domain containing proteins / 6 (6) , 810
18	(2009) Nucleic acids research IBM1, a JmjC domain-containing histone demethylase, is involved in the regulation of RNA-directed DNA methylation through the epigenetic control of RDR2 and DCL3 expression in Arabidopsis / 40 (18) , 8905
4	(2012) PLoS genetics A Companion Cell–Dominant and Developmentally Regulated H3K4 Demethylase Controls Flowering Time in <I>Arabidopsis</I> via the Repression of <I>FLC</I> Expression / 8 (4) , e1002664
1	David Re？ak. (2009) Sexual plant reproduction Wide-scale screening of T-DNA lines for transcription factor genes affecting male gametophyte development in Arabidopsis / 25 (1) , 39
3	(2009) PLoS ONE Genome-Wide Evaluation of Histone Methylation Changes Associated with Leaf Senescence in Arabidopsis / 7 (3) , e33151
4	(2009) Developmental cell Control of Seed Germination by Light-Induced Histone Arginine Demethylation Activity / 22 (4) , 736
1	(2014) Nature communications Jumonji demethylases moderate precocious flowering at elevated temperature via regulation of FLC in Arabidopsis / 5 (1) , 5098
None	(2009) Frontiers in plant science Over-expression of histone H3K4 demethylase gene <I>JMJ15</I> enhances salt tolerance in <I>Arabidopsis</I> / 5 (None) , 290
9	(2015) Plant signaling & behavior Dynamics of H3K27me3 methylation and demethylation in plant development / 10 (9) , e1027851
6	(2017) The Plant journal : for cell and molecular biology JMJ27, an Arabidopsis H3K9 histone demethylase, modulates defense against <I>Pseudomonas syringae</I> and flowering time / 91 (6) , 1015
6	(2009) The Plant journal : for cell and molecular biology JMJ30‐mediated demethylation of H3K9me3 drives tissue identity changes to promote callus formation in Arabidopsis / 95 (6) , 961
4	(2009) PLoS genetics The H3K27me3 demethylase REF6 promotes leaf senescence through directly activating major senescence regulatory and functional genes in <I>Arabidopsis</I> / 15 (4) , e1008068
23	(2009) Development Conditional effects of the epigenetic regulator JUMONJI 14 in <I>Arabidopsis</I> root growth / 146 (23) , dev183905
3	(2009) The New phytologist <I>Arabidopsis</I> JMJ17 promotes cotyledon greening during de‐etiolation by repressing genes involved in tetrapyrrole biosynthesis in etiolated seedlings / 231 (3) , 1023