Co-location of chromatin loop anchors with the gene transcription machinery in maize

In this study, various genomic datasets were generated to assess the co-location of chromatin loop anchors with the gene transcription machinery (including expressed genes, promoters and long-range regulatory elements) in maize. Those datasets were all generated from a single tissue type (leaf v04 stage) and a single sample, in the maize B73 genotype. They included mRNA-seq, ATAC-seq and Hi-C datasets to assess gene expression, open chromatin and protein binding to DNA, and chromatin loop structures, respectively. Co-location analysis of those different data, combined with additional public ChIA-PET datasets, indicated that expressed genes and open chromatin regions are largely confined to a limited set of chromatin loop anchors flanking repeat-rich loop interiors regions and organized in a nested manner, revealing the possibility of a phase separation mechanism in maize for the three dimensional regulation of gene expression.