Genome-wide profiling and functional characterization of N4-acetyldeoxycytosine reveals conserved epigenetic roles in rice and Arabidopsis.

BACKGROUND: N4-acetyldeoxycytosine (4acC) is a recently identified DNA modification that has been detected across multiple species. However, previous studies have largely focused on Arabidopsis, and the distribution and function of 4acC in other plant species poorly understood. RESULTS: In this study, we generated a genome-wide map of 4acC in rice and conducted a feature-level comparison with Arabidopsis. Although 4acC in rice shows a more uniform chromosomal distribution and is more frequently located in intergenic regions, it exhibits conserved associations with transcriptional activation in both species. Specifically, 4acC is significantly enriched in open chromatin regions, transcription factor binding sites, and activating histone modifications, and its modification levels are generally independent of 5-methylcytosine (5mC). Functionally, 4acC is associated with alternative splicing, particularly intron retention events. Evolutionary and population genetic analyses show that 12.8% of one-to-one orthologous genes carry 4acC in both species, a proportion significantly higher than expected by chance, and that 4acC is preferentially localized to genomic regions with trait-associated QTLs. CONCLUSIONS: In conclusion, our results reveal that 4acC is a conserved DNA modification with potential roles in plant phenotypic variation, adaptive evolution, and post-transcriptional regulation, providing new insights into its epigenetic function.