SET DOMAIN GROUP 708, a histone H3 lysine 36‐specific methyltransferase, controls flowering time in rice (Oryza sativa)

Abstract

SummaryAs a key epigenetic modification, the methylation of histone H3 lysine 36 (H3K36) modulates chromatin structure and is involved in diverse biological processes.To better understand the language of H3K36 methylation in rice (Oryza sativa), we chose potential histone methylation enzymes for functional exploration. In particular, we characterized rice SET DOMAIN GROUP 708 (SDG708) as an H3K36-specific methyltransferase possessing the ability to deposit up to three methyl groups on H3K36.Compared with the wild-type, SDG708-knockdown rice mutants displayed a late-flowering phenotype under both long-day and short-day conditions because of the down-regulation of the key flowering regulatory genes Heading date 3a (Hd3a), RICE FLOWERING LOCUS T1 (RFT1), and Early heading date 1 (Ehd1). Chromatin immunoprecipitation experiments indicated that H3K36me1, H3K36me2, and H3K36me3 levels were reduced at these loci in SDG708-deficient plants. More importantly, SDG708 was able to directly target and effect H3K36 methylation on specific flowering genes. In fact, knockdown of SDG708 led to misexpression of a set of functional genes and a genome-wide decrease in H3K36me1/2/3 levels during the early growth stages of rice.SDG708 is a methyltransferase that catalyses genome-wide deposition of all three methyl groups on H3K36 and is involved in many biological processes in addition to flowering promotion.

SIP1 participates in regulation of flowering time in rice by recruiting OsTrx1 to Ehd1

“…SDG701, related to Arabidopsis SDG2/ATRX3, regulates the tri‐methylation of H3K4 at Hd3a and RFT1 (Liu et al ., 2017). SDG724 , SDG725 and SDG708 encode proteins belong to SET domain family II; members of this family function in H3K36me2/3 modifications (Sun et al ., 2012; Sui et al ., 2013; Choi et al ., 2014; Liu et al ., 2016). Loss of function of any of these proteins results in late flowering in both LD and SD conditions.…”

“…SDG724 is required for the deposition of H3K36me2/3 at more flowering gene loci, such as Ehd3 , Ehd2 , OsMADS50 , Hd3a and RFT1 , whereas SDG725 is only required for H3K36me2/3 deposition at RFT1 (Sui et al ., 2013; Sun et al ., 2014). SDG708 is indispensible for H3K36me2/3 at Hd3a , RFT1 and Ehd1 (Liu et al ., 2016). …”

SET DOMAIN GROUP701 encodes a H3K4‐methytransferase and regulates multiple key processes of rice plant development

“…Identification and characterization of enzymes involved in histone methylation constitute an importance step in elucidating epigenetic regulatory mechanisms in diverse organisms. In rice, several SET‐domain group (SDG) proteins have been identified as enzymes involved in methylation of H3K9 (SDG714 and SDG728) (Ding et al ., ,b; Qin et al ., ), H3K36 (SDG708, SDG724 and SDG725) (Sui et al ., ; Sun et al ., ; Liu et al ., ), or H3K27 (SDG711 and SDG718) (Nallamilli et al ., ; Liu et al ., ). Consistent with the knowledge that H3K27me2/me3 are catalyzed by SDG within a multiprotein complex called Polycomb Repressive Complex 2 (PRC2), several PRC2 homologs (in addition to SDG711 and SDG718) are found to be necessary for H3K27me3 deposition in rice (Zhang et al ., ; Nallamilli et al ., ; Wang et al ., ; Yang et al ., ; Conrad et al ., ; Shi et al ., ).…”

The COMPASS-Like Complex Promotes Flowering and Panicle Branching in Rice

“…Ghd7 is 94 activated by EL1 (Early flowering 1)/Hd16, which encodes a casein kinase I protein 95 (Dai and Xue, 2010), and suppressed by Ehd3 (Matsubara et al, 2011). 96 The activation of flowering time also requires the histone methylation modulated 97 by SET-domain group proteins (SDG) (Sun et al, 2012;Sui et al, 2013;Choi et al, 98 2014; Liu et al, 2015). SDG701, related to Arabidopsis SDG2, regulates the 99 tri-methylation of lysine 4 of histone 3 (H3K4me3) at Hd3a and RFT1 (Liu et al,100 2017).…”

“…SDG724, SDG725,and 103 SDG708 encode proteins that belong to SET domain family II, which function in di-104 and tri-methylation modifications of lysine 36 of H3 (H3K36me2/3). Loss of function 105 of any of these proteins results in late flowering in both LD and SD (Sun et al, 2012; 106 Sui et al, 2013;Choi et al, 2014;Liu et al, 2015).…”