ZmDDM1 directs the occurrence of ZmAGO4-dependent RdDM on active chromatin. A, Profile of CHH methylation in the ZmAGO4 peaks summit-centered genomic regions (red line). Profile of CHH methylation at a set of control loci was also shown (blue line). B, Abundance of 21-, 22-, and 24-nt siRNA in the ZmAGO4 peaks summit-centered genomic regions. C, Meta-plots showing average ZmAGO4 ChIP signals across all of annotated protein-coding genes. lgG-ChIP signal was shown in the same plot as a negative control. D, Venn diagram showing the overlap between ZmDDM1 and ZmAGO4 peaks. E, Comparisons of CHH methylation, 24-nt siRNA levels and ZmAGO4 occupancy between types I and II ZmAGO4 peaks. Triple asterisks indicated P < 2.2e−16 (two-sided Kolmogorov–Smirnov test). F, Comparisons of H3K4me3, H3K9ac, H3K9me2, CG, and CHG methylation level between types I and II ZmAGO4 peaks. Triple asterisks indicated P <2.2e−16 (two-sided Kolmogorov–Smirnov test). G, Comparisons of ATAC-seq and DNase-seq abundance between types I and II ZmAGO4-binding sites. Triple asterisks indicated P <2.2e−16 (two-sided Kolmogorov–Smirnov test). H, Comparisons of the GC content between types I and II ZmAGO4-binding sites. Triple asterisks indicated P <2.2e−16 (two-sided Kolmogorov–Smirnov test). I, A diagram depicting the likely existence of two ZmAGO4-involved RdDM pathways in maize. The first pathway is dependent on ZmDDM1 activity and occurs preferentially in active and open chromatin. The second pathway is independent of ZmDDM1 activity and associate with relatively repressive chromatin. It is noted that the other chromatin remodeler involving in the type II pathway remains elusive at this point. RPKM, reads per million per kilobase.