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H3K36 Methylation Is Involved in Promoting Rice Flowering

2012; Elsevier BV; Volume: 6; Issue: 3 Linguagem: Inglês

10.1093/mp/sss152

1674-2052

Pengfei Sui, Jinlei Shi, Xueying Gao, Wen‐Hui Shen, Aiwu Dong,

Plant Reproductive Biology

Dear Editor, Histone H3 lysine 36 (H3K36) methylation is a conserved epigenetic mark in all eukaryotes (Berr et al., 2011Berr A. Shafiq S. Shen W.H Histone modifications in transcriptional activation during plant development.Biochim. Biophys. Acta. 2011; 1809: 567-576Crossref PubMed Scopus (171) Google Scholar; Wagner and Carpenter, 2012Wagner E.J. Carpenter P.B Understanding the language of Lys36 methylation at histone H3.Nat. Rev. Mol. Cell Biol. 2012; 13: 115-126Crossref PubMed Scopus (631) Google Scholar). Reverse genetic analysis in Arabidopsis had uncovered a crucial role of H3K36 di- and tri-methylation (H3K36me2 and H3K36me3) in flowering-time regulation (reviewed in Berr et al., 2011Berr A. Shafiq S. Shen W.H Histone modifications in transcriptional activation during plant development.Biochim. Biophys. Acta. 2011; 1809: 567-576Crossref PubMed Scopus (171) Google Scholar). The Arabidopsis SET DOMAIN GROUP 8 (SDG8), also known as EARLY FLOWERING IN SHORT DAYS (EFS), encodes a SET-domain protein showing similarity to the yeast SET2 and the Drosophila ASH1 and the human NSD1 proteins. The sdg8 loss-of-function mutants exhibit an early-flowering phenotype associated with reduced levels of H3K36me2 and H3K36me3 at chromatin and suppression of FLOWERING LOCUS C (FLC), a key flowering repressor in Arabidopsis (Kim et al., 2005Kim S.Y. He Y. Jacob Y. Noh Y.S. Michaels S. Amasino R Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyl transferase.Plant Cell. 2005; 17: 3301-3310Crossref PubMed Scopus (188) Google Scholar; Zhao et al., 2005Zhao Z. Yu Y. Meyer D. Wu C. Shen W.H Prevention of early flowering by expression of FLOWERING LOCUS C requires methylation of histone H3 K36.Nat. Cell Biol. 2005; 7: 1256-1260Crossref PubMed Scopus (238) Google Scholar; Xu et al., 2008Xu L. Zhao Z. Dong A. Soubigou-Taconnat L. Renou J.P. Steinmetz A. Shen W.H Di- and tri- but not monomethylation on histone H3 lysine 36 marks active transcription of genes involved in flowering time regulation and other processes in Arabidopsis thaliana.Mol. Cell Biol. 2008; 28: 1348-1360Crossref PubMed Scopus (242) Google Scholar). Flowering time is a critical trait in plant life history and is fine-tuned by complex gene networks (Tsuji et al., 2011Tsuji H. Taoka K. Shimamoto K Regulation of flowering in rice: two florigen genes, a complex gene network, and natural variation.Curr. Opin. Plant Biol. 2011; 14: 45-52Crossref PubMed Scopus (242) Google Scholar; He, 2012He Y Chromatin regulation of flowering.Trends Plant Sci. 2012; 17: 556-562Abstract Full Text Full Text PDF PubMed Scopus (135) Google Scholar). Because of a lack of FLC homolog in rice, it is of great interest to examine the role of H3K36 methylation in flowering-time control in this economic important plant. Previously, we reported that the rice SDG725 encodes a close homolog of SDG8 exhibiting H3K36-specific histone methyltransferase activity in vitro and in vivo, and is involved in promotion of brassinosteroid-related gene expression (Sui et al., 2012Sui P. Jin J. Ye S. Mu C. Gao J. Feng H. Shen W.H. Yu Y. Dong A H3K36 methylation is critical for brassinosteroid-regulated plant growth and development in rice.Plant J. 2012; 70: 340-347Crossref PubMed Scopus (72) Google Scholar). In this study, we show that SDG725 is involved in promoting rice flowering. To investigate flowering time, we grew side by side the 725Ri-1 mutant line, which exhibits a knockdown of over 80% of SDG725 transcripts by a RNAi construct (Sui et al., 2012Sui P. Jin J. Ye S. Mu C. Gao J. Feng H. Shen W.H. Yu Y. Dong A H3K36 methylation is critical for brassinosteroid-regulated plant growth and development in rice.Plant J. 2012; 70: 340-347Crossref PubMed Scopus (72) Google Scholar), together with wild-type (WT) in two latitude places: Shanghai with a subtropical climate and long-day (LD) photoperiods and Sanya with tropical climate and short-day (SD) photoperiods. At both places, the 725Ri-1 mutant plants showed a late-flowering phenotype compared to WT (Figure 1A) and the average heading time of the 725Ri-1 mutant compared to WT was considerably delayed (Figure 1B). We next investigated expression levels of several genes, including OsGI, Hd1, Ehd3, Ehd2 (also named RID1 or OsId1), OsMADS50, OsMADS51, Ghd7, Ehd1, Hd3a, and RFT1, from different flowering regulatory pathways (Figure 1C; Tsuji et al., 2011Tsuji H. Taoka K. Shimamoto K Regulation of flowering in rice: two florigen genes, a complex gene network, and natural variation.Curr. Opin. Plant Biol. 2011; 14: 45-52Crossref PubMed Scopus (242) Google Scholar). Leaf samples were collected 2 h after dawn from 45-day-old plants grown in a growth chamber under LD (14-h light/10-h dark) as well as from 35-day-old plants grown under SD (10-h light/14-h dark) growth conditions. They were subjected to quantitative RT–PCR analysis using gene-specific primers. No significant differences in the levels of OsGI and Hd1 transcripts were observed between 725Ri-1 and WT under either SD or LD conditions (shown for LD in Figure 1D). Remarkably, the expression levels of Ehd3, Ehd2, OsMADS50, OsMADS51, Ehd1, Hd3a, and RFT1 all were drastically reduced in 725Ri-1 compared with WT under either SD or LD conditions (shown for LD in Figure 1D). In agreement with a previous report showing that Ehd3 functions as a repressor of Ghd7 (Matsubara et al., 2011Matsubara K. Yamanouchi U. Nonoue Y. Sugimoto K. Wang Z. Minobe Y. Yano M Ehd3, encoding a plant homeodomain finger-containing protein, is a critical promoter of rice flowering.Plant J. 2011; 66: 603-612Crossref PubMed Scopus (143) Google Scholar), Ghd7 expression was elevated in 725Ri-1 (Figure 1D). To investigate histone methylation status in chromatin of flowering genes, we performed chromatin immunoprecipitation (ChIP) experiments using commercially available antibodies specifically recognizing H3K36me1, H3K36me2, H3K36me3, H3K4me2, or H3K4me3. We chose to analyze histone methylation levels at Ehd3, Ehd2, OsMADS50, Hd3a, and RFT1 genes located at different positions within the flowering regulatory pathways (Figure 1C). As shown in Figure 1E, 725Ri-1 mutant compared with WT exhibited reduced H3K36me2 and H3K36me3 levels accompanied by increased H3K36me1 levels at all examined flowering genes, with each gene analyzed at two different regions using specific PCR primers. In contrast, H3K4me2 levels were unaffected and H3K4me3 levels were increased in some regions in 725Ri-1 mutant compared with WT (Figure 1E). Using the SDG725-specific antibody (Sui et al., 2012Sui P. Jin J. Ye S. Mu C. Gao J. Feng H. Shen W.H. Yu Y. Dong A H3K36 methylation is critical for brassinosteroid-regulated plant growth and development in rice.Plant J. 2012; 70: 340-347Crossref PubMed Scopus (72) Google Scholar), we found that the chromatin-binding levels of the SDG725 protein at flowering genes were significantly reduced in 725Ri-1 mutant compared with WT (Figure 1E). These results indicate that SDG725 is recruited and is specifically required for deposition of H3K36me2/3, which is associated with active transcription of flowering genes. Taken together, this study establishes a crucial function of SDG725 in rice flowering-time regulation via H3K36me2/3-mediated activation of several genes within photoperiodic pathways. Recently, Sun et al., 2012Sun C. Fang J. Zhao T. Xu B. Zhang F. Liu L. Tang J. Zhang G. Deng X. Chen F The histone methyltransferase SDG724 mediates H3K36me2/3 deposition at MADS50 and RFT1 and promotes flowering in rice.Plant Cell. 2012; 24: 3235-3247Crossref PubMed Scopus (92) Google Scholar reported that SDG724, encoding a SET-domain protein much smaller than SDG725, is required for deposition of H3K36me2/3 at OsMADS50 and RFT1 but not Hd3a chromatin. Thus, SDG724 and SDG725 show both overlapped and specific functions in regulation of different flowering genes. Both studies on SDG724 and SDG725 demonstrate that H3K36me2/3 promotes rice flowering, which is in sharp contrast to the previously known function of these epigenetic marks in Arabidopsis flowering suppression (Zhao et al., 2005Zhao Z. Yu Y. Meyer D. Wu C. Shen W.H Prevention of early flowering by expression of FLOWERING LOCUS C requires methylation of histone H3 K36.Nat. Cell Biol. 2005; 7: 1256-1260Crossref PubMed Scopus (238) Google Scholar; Xu et al., 2008Xu L. Zhao Z. Dong A. Soubigou-Taconnat L. Renou J.P. Steinmetz A. Shen W.H Di- and tri- but not monomethylation on histone H3 lysine 36 marks active transcription of genes involved in flowering time regulation and other processes in Arabidopsis thaliana.Mol. Cell Biol. 2008; 28: 1348-1360Crossref PubMed Scopus (242) Google Scholar). The difference resides in H3K36me2/3-mediated transcription activation of FLC, a key flowering repressor present in Arabidopsis but absent in rice. This comparative observation remarkably illustrates an example of how a similar epigenetic regulatory mechanism could lead to distinct physiological/phenotypical outcomes between two plant species. The finding of histone methylation in rice flowering-time control intrigues future research about their roles in rice domestication and possible application in rice breeding. This work was funded by the National Basic Research Program of China (973 Program, grant no. 2012CB910500). No conflict of interest declared.