CG and CHG Methylation Contribute to the Transcriptional Control of OsPRR37-Output Genes in Rice

Abstract

Plant circadian clock coordinates endogenous transcriptional rhythms with diurnal changes of environmental cues. OsPRR37, a negative component in the rice circadian clock, reportedly regulates transcriptome rhythms, and agronomically important traits. However, the underlying regulatory mechanisms of OsPRR37-output genes remain largely unknown. In this study, whole genome bisulfite sequencing and high-throughput RNA sequencing were applied to verify the role of DNA methylation in the transcriptional control of OsPRR37-output genes. We found that the overexpression of OsPRR37 suppressed rice growth and altered cytosine methylations in CG and CHG sequence contexts in but not the CHH context (H represents A, T, or C). In total, 35 overlapping genes were identified, and 25 of them showed negative correlation between the methylation level and gene expression. The promoter of the hexokinase gene OsHXK1 was hypomethylated at both CG and CHG sites, and the expression of OsHXK1 was significantly increased. Meanwhile, the leaf starch content was consistently lower in OsPRR37 overexpression lines than in the recipient parent Guangluai 4. Further analysis with published data of time-course transcriptomes revealed that most overlapping genes showed peak expression phases from dusk to dawn. The genes involved in DNA methylation, methylation maintenance, and DNA demethylation were found to be actively expressed around dusk. A DNA glycosylase, namely ROS1A/DNG702, was probably the upstream candidate that demethylated the promoter of OsHXK1. Taken together, our results revealed that CG and CHG methylation contribute to the transcriptional regulation of OsPRR37-output genes, and hypomethylation of OsHXK1 leads to decreased starch content and reduced plant growth in rice.

Increased DNA methylation contributes to the early ripening of pear fruits during domestication and improvement

“…This result indicates that CG methylation and CHG methylation are usually coupled to regulate gene expression, and CG and CHG methylation may show co-evolution during crop domestication. For example, the promoter of OsHXK1 is hypomethylated at CG and CHG sites, which leads to an increase in OsHXK1 expression, which in turn leads to a decrease in the starch content in rice [39]. While DNA methyltransferases maintain cytosine methylation in specific contexts, four DNA demethylases in A. thaliana (ROS1, DME, DML2, and DML3) can erase the methylation status of cytosines in all sequence contexts.…”

The role of circadian rhythm in osteoporosis; a review

“…We found that the number of articles in the past two or 3 years has increased significantly, as shown in the figure below (Figure 5). In vivo, circadian rhythms are regulated and maintained by endogenous clock genes (Oishi et al, 2005;Liu et al, 2022), which are involved in several physiological activities, including metabolism (Peek et al,FIGURE 4 Human studies of melatonin and osteoclast differentiation.…”

“…We found that the number of articles in the past two or 3 years has increased significantly, as shown in the figure below ( Figure 5 ). In vivo , circadian rhythms are regulated and maintained by endogenous clock genes ( Oishi et al, 2005 ; Liu et al, 2022 ), which are involved in several physiological activities, including metabolism ( Peek et al, 2017 ), cell cycle ( Han et al, 2016 ; Dong et al, 2019 ), sleep wake cycle ( Ikegami et al, 2019 ), bone formation ( Fu et al, 2005 ; Sato et al, 2007 ; Hirata et al, 2022 ; Zhao et al, 2022 ), and heart rate and blood pressure ( Wang et al, 2008 ). However, when clock gene expression is aberrant, the body experience abnormalities and possible disease, including sleep disorders ( Patke et al, 2017 ), diabetes ( Marcheva et al, 2010 ), obesity ( Paschos et al, 2012 ; Chaix et al, 2019 ), osteoporosis ( Tang et al, 2020 ), and tumors ( Altman et al, 2015 ).…”