Histone H3K4 methylation regulation and three-dimensional aggregating distribution of a subset of genomic loci mediated by CHD3 homolog PKL in Arabidopsis
Arabidopsis PICKLE (PKL) is a putative CHD3-type chromatin remodeling factor. Despite its importance in environmental stimulus responses and plant development, how PKL is recruited to target gene loci and its detailed regulatory role in controlling target gene chromatin states is not fully understood. Here, we report genome-wide evidence for the recruitment of PKL by specific transcription factors, establish the molecular connection between PKL and H3K4me2/3, and demonstrate PKL is essential for the space-clustering distribution of its target genes. We captured the genome-wide binding sites of PKL by ChIP-seq using endogenous antibody. Further analyses gave evidence that plant-specific transcriptional factors containing TCPs, PIFs, and HY5, play dominant role in recruiting PKL to its target gene loci in Arabidopsis thaliana. The chromatin of PKL target genes showed significantly enriched depositions of H3K4me2 and H3K4me3. PKL directly interacted with the COMPASS complex scaffold protein WDR5A. It seems that PKL acts through WDR5A to stabilize the highly accumulated levels of H3K4me2 at specific euchromatic loci. Strikingly, PKL-bound genes distributed space-contiguously, the manner of which is dependent on PKL and PKL-interacted TFs. Moreover, the working model of PKL we proposed in this study is likely conserved in liverwort and rice. PKL associates with specific gene loci by interacting with specific transcription factors and promotes H3K4me2 depositions locally. Meanwhile, PKL acts as a hub mediating its target gene loci spatial-aggregation. PKL and its homologs in rice and liverwort might display similar molecular functions Overall design: Three biological replicates of each genotype were used for high-throughput sequencing analysis. All experiments wer conducted using  9-day-old seedlings grown in continuous white light.