GSE168538
N4-acetyldeoxycytosine DNA modification marks euchromatin regions in Arabidopsis thaliana.
We report the application of Next-generation sequencing (NGS) for high-throughput profiling of N4-acetylcytosine (4acC) DNA modification in Arabidopsis thaliana. We find  that 4acC  peaks mostly distribute in the euchromatin regions and are present in nearly half of the protein-coding genes in Arabidopsis.  4acC mainly locates around transcription start sites (TSSs) of protein-coding genes and positively correlates with gene expression level . Compared to non-4acC marked genes, 4acC marked genes display a higher methylation level of 5mC in the CG context within coding regions, but a lower methylation level of 5mC in the CHG and CHH contexts. In addition, 4acC peaks showed higher overlaps with active histone modification marks than by chance, but similar overlaps with repressive histone modification marks.  We observed complex cooperative interactions among 4acC, 5mC, and histone modifications on gene transcription.  4acC containing genes with low level of mCG, or active histone modification marks displayed a higher expression. In sum, we have uncovered 4acC as a hitherto unknown epigenetic DNA mark that is associated with gene expression in Arabidopsis, and suggest potential cross-talks  among epigenetic marks for gene expression. Overall design: Examination of 4acC DNA modification in Arabidopsis thaliana.