Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq

Despite the ever-growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is transcription factors (TFs) binding to specific DNA loci across the genome. Given that the DNA is packed to chromatin, the accessibility of these loci for TF binding is highly regulated and determines where and when TFs bind. To uncover global accessible regulatory sites (AREs) in Arabidopsis, we coupled the INTACT method for nuclei isolation with ATAC-seq. We revealed 41,419 AREs in roots, of which approximately half are found in gene promoters and contain the H3K4me3 active histone mark. Interestingly, most of the root-unique AREs are found in nongenic regions but are correlated with root-specific expression of distant genes. Importantly, these gene-distant sites are enriched for binding motifs of TFs important for root development as well as motifs for TFs that may play a role as novel transcriptional regulators in roots, suggesting that these AREs are functional novel gene-distant regulatory elements.

We present a feasible pipeline to profile accessible chromatin in plants. Our results suggest predominance of intergenic sites in defining organ identity possibly via long-range chromatin interactions. This workflow can be rapidly applied to study the regulatory landscape in other cell types, plant species and conditions.