Characterization of distinct types of open chromatin and their impacts on gene transcription in maize [MNase-seq]

Open chromatin plays key roles in regulating gene expression in eukaryotic genomes. However, functional implications of fragile nucleosome overlapping open chromatin are still largely unknown, especially in plants. Here, through simultaneous measurement of MHSs and nucleosomes, we detected two distinct types of open chromatin, one with nucleosome-free (type-I MHSs) and the other with fragile nucleosomes (type-II MHSs) in maize and Arabidopsis. Both types of MHSs can function as cis-regulatory elements and have similar TF binding motifs. Furthermore, fragile nucleosomes with MHSs have unique DNA sequence features with less AT and more GC dinucleotides, whereas other fragile nucleosomes without overlapping MHSs have more AT and less GC dinucleotides. In particular, we observed distinct fragile nucleosome positioning patterns occurred around the summit of type-I and type-II MHSs, phased fragile nucleosome arrays and only two well-phased fragile nucleosomes surrounding the summit of type-I and type-II MHSs, respectively. We finally found that type-II MHS-related genes with BCTSS or SCTSS express more than type-I-related genes with the corresponding CTSS, which is mediated by combined actions of MHSs with TFs, fragile nucleosomes, Pol II and epigenetic marks. Overall design: Low-MNase-seq, High-MNase-seq.