Genic Position and Methylation Context Shape DNA Methylation-Expression Relationships in Rice Internode Development
Year: 2026
Type: preprint
Abstract: Elongating rice internodes present a developmental gradient from dividing meristem to mature cells, providing an elegant pseudo-time course for study of plant vegetative development. We tested the hypothesis that DNA methylation regulates gene expression during rice internode development by integrating RNA-seq and bisulfite DNA sequencing across eight internode segments. Previously described topologically associated chromatin domain borders aligned with transcription start sites of constitutive expressed genes. CpG and CHG differential methylation was enriched in young segments, consistent with maintenance methylation; whereas CHH methylation showed similar differential abundance in young and old segments. CHH and CHG methylation in upstream regions, CpG methylation within gene bodies, and any methylation in 5′ and 3′ untranslated regions were permissive of moderate to high gene expression. Very low expression was associated with CpG methylation upstream, CHG and CHH methylation within gene bodies, and CpG and CHG methylation downstream. A nonrandom subset of genes, including cell wall-related glycoside hydrolases, lignin and tricin biosynthesis enzymes, and WD40 proteins, showed methylation-expression correlations, with expression changes enriched in triple-marked elements. These results suggest that internode phenotypes of DNA methylation machinery mutants relate to alteration of specific target genes, opening approaches for grass culm improvement for lodging resistance and biomass production. Graphical Abstract Significance statement Stems of cereals and other grasses have an important function in supporting grain production and serving as a source of carbon for the bioeconomy. This study supports methylation of the cytosine bases of DNA as a regulator of chromatin structure and gene expression in the stems of rice. Different methylation contexts are implicated in specific roles in both positive and negative gene expression regulation that might be leveraged to improve stem properties.
Subfield: Molecular Biology
Domain: Life Sciences
SDG: Zero hunger
Open Access status: green
Awards: G1117004060, G1286236842, G155191036, G1863003419, MILK INCOME LOSS CONTRACTS; TO MAINTAIN AND EXPAND EXISTING MARKETS FOR DAIRY WHICH ARE VITAL TO THE WELFARE OF MILK PRODUCERS IN THE UNITED STATES, G235908517, G2573784309, NEW; TITLE: ASSOCIATION MAPPING OF CELL WALL SYNTHESIS REGULATORY GENES AND CELL WALL QUALITY IN SWITCHGRASS; PI: LAURE BARTLEY, G3083819904, G313562941, G419881185, G42916606, TESTING PREDICTIONS OF PLANT-MICROBE-ENVIRONMENT INTERACTIONS TO OPTIMIZE CLIMATE ADAPTATION AND IMPROVE SUSTAINABILITY IN SWITCHGRASS FEEDSTOCKS, G4501827968, G4641531387, G498139845, G4988853999, G5094606986, MRI: Acquisition of High Resolution Exact Mass Liquid Chromatograph Mass Spectrometer (LCMS) to Broaden and Enhance Chemical and Biological Education and Research, EPSCoR Research Infrastructure Improvement Plan "Building Oklahoma's Leadership Role in Cellulosic Bioenergy", G5806063297, G6519249983, G6652958823, G7205239661, Systems analysis of grass secondary cell wall development and regulation for biofuel production, Research PGR: Genome-enabled characterization of orphan receptor-like kinases in plants., TESTING PREDICTIONS OF PLANT-MICROBE-ENVIRONMENT INTERACTIONS TO OPTIMIZE CLIMATE ADAPTATION AND IMPROVE SUSTAINABILITY IN SWITCHGRASS FEEDSTOCKS, G834277795, G8447919883, G876836414, MRI: Acquisition of Thermal Analysis and Calorimetry Equipment for Multiple Applications Emphasizing Research on Sustainable Fuels, G969889393
OpenAlex ID: W7167934589
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