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.
Highlights
Plant DNA methylation occurs in the sequence context of CG, CHG, and CHH (Zhang et al, 2006)
We observed that rice growth was retarded in OsPRR37 overexpression lines (OE)
The growth of OE5 and OE9 was significantly repressed compared to the growth of Guangluai 4 (GL) and NIL-OsPRR37 on these days (Figures 1A–F)
Summary
Plant DNA methylation occurs in the sequence context of CG, CHG, and CHH (where H is A, C, or T) (Zhang et al, 2006). Pseudo-Response Regulators (PRRs) are key components of transcription-translation feedback loops in plants and mediate the circadian regulation of clock output genes (Farre and Liu, 2013), including genes involved in the regulation of growth, flowering, abiotic stress, and yieldrelated traits (Li C. et al, 2020; Li N. et al, 2020; Sun et al, 2020; Wei et al, 2020; Liang et al, 2021). The regulation of circadian-regulated genes by DNA methylation in Populus trichocarpa suggested that DNA methylation contributes to the expression levels of clock output genes (Liang et al, 2019) Based on these results, we hypothesize that OsPRR37 uses DNA methylation as a pathway to regulate the transcription of its output genes. Our results revealed that DNA methylation was an alternative medium for OsPRR37 to regulate the output genes and plant growth
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
