maize DDM1 targets RNA-directed DNA methylation on active chromatin

In this work, we used chromatin immunoprecipitation coupled with high throughput sequencing (ChIP-seq) to ascertain the genome-wide occupancy of ZmDDM1 in maize genome. The results revealed that ZmDDM1 recognized an 8-bp-long GC-rich degenerate DNA sequence motif, which is enriched in transcription start sites (TSSs) and other euchromatic regions. Meanwhile, 24-nucleotide siRNAs and CHH methylation were delineated at the edge of ZmDDM1-occupied sites. ZmDDM1 could be co-purified with ZmAGO4 proteins, providing further evidence that ZmDDM1 is a component of RdDM complex in planta. ZmDDM1 and ZmAGO4 ChIP-seq in maize developing embryo