Dynamic DNA methylation changes reveal tissue-specific gene expression in sugarcane

Abstract

DNA methylation is an important mechanism for the dynamic regulation of gene expression and silencing of transposons during plant developmental processes. Here, we analyzed genome-wide methylation patterns in sugarcane (Saccharum officinarum) leaves, roots, rinds, and piths at single-base resolution. DNA methylation patterns were similar among the different sugarcane tissues, whereas DNA methylation levels differed. We also found that DNA methylation in different genic regions or sequence contexts plays different roles in gene expression. Differences in methylation among tissues resulted in many differentially methylated regions (DMRs) between tissues, particularly CHH DMRs. Genes overlapping with DMRs tended to be differentially expressed (DEGs) between tissues, and these DMR-associated DEGs were enriched in biological pathways related to tissue function, such as photosynthesis, sucrose synthesis, stress response, transport, and metabolism. Moreover, we observed many DNA methylation valleys (DMVs), which always overlapped with transcription factors (TFs) and sucrose-related genes, such as WRKY, bZIP, WOX, SPS, and FBPase. Collectively, these findings provide significant insights into the complicated interplay between DNA methylation and gene expression and shed light on the epigenetic regulation of sucrose-related genes in sugarcane.

The lemon genome and DNA methylome unveil epigenetic regulation of citric acid biosynthesis during fruit development

“…S5 , see online supplementary material) demonstrated high consistency among replicates. In conclusion, the quality and depth of our sequencing data were excellent compared to other experiments [ 26 , 27 ] and can be used for subsequent studies.…”

Haplotype‐resolved genome assembly of Phanera championii reveals molecular mechanisms of flavonoid synthesis and adaptive evolution

“…Allele‐specific DNA methylation was found to cause differential expression of alleles during maize endosperm development (Xu et al., 2022). Additionally, DNA methylation (Wang et al., 2015, 2018; Xu et al., 2022; Xue et al., 2022), histone modifications (Guo et al., 2015), non‐coding RNAs function (O'Neill, 2005; Rong et al., 2005), and cis ‐ or trans ‐regulation (Zhang & Borevitz, 2009) are also involved in the ASEs, and further studies are needed to investigate these mechanisms in P. championii .…”

The Sink-Source Relationship in Cucumber (Cucumis sativus L.) Is Modulated by DNA Methylation

“…Whereas the present study found that under conditions of varying sink strengths (removing all fruits or retaining one fruit on a plant), it was also able to alter the DNA methylation pattern in cucumber source leaves. Moreover, DNA methylation has been studied in more detail in sucrose-transporting plants [ 30 , 31 ], but very little in RFO-transporting plants. Meanwhile, we externally applied 5-Aza-dC, a widespread DNA methylation inhibitor, on FNLs, and found that it could increase stachyose synthase ( CsSTS ) gene expression, enzyme activity and stachyose content in the RFO synthesis pathway of source leaves and increase fruit length and dry weight, which further verified that DNA methylation promotes fruit enlargement by regulating RFO synthesis.…”

“…It has been widely reported that DNA methylation modulates gene expression in the pre- and post-transcriptional regulation of several biological processes, including the vernalization response, defense against parasitic elements, and stress responses [ 25 , 26 , 27 , 28 , 29 ]. Recent research has shown that DNA methylation affects the expression of genes related to starch and sucrose metabolism, photosynthesis, and plant hormone signal transduction, as well as stress response in sucrose-transporting crops, such as apple and sugarcane [ 30 , 31 ]. However, the role of DNA methylation in sink-source regulation in crops that rely on RFOs as the major transport form of photoassimilates in vivo has not been reported.…”