Maize earshoot MOA-seq; open chromatin profiling using micrococcal nuclease with formaldehyde-crosslinked nuclei.

Developmental processes mediated through changes in gene expression from the nuclear genome are regulated at the level of local chromatin structure. Increased accessibility of gene-proximal DNA to diffusible nucleases has previously been shown to correlate with increased gene expression defined as increased steady-state levels of polyadenylated mRNAs relative to control. Here we present a cost-efficient strategy to identify these nuclease hypersensitive loci called MNase Open and Accessible chromatin mapping, abbreviated MOA-seq in this study. Briefly, MOA-seq is based on isolation and sequencing of only small, subnucleosomal-sized fragments from light MNase digests of chromatin. In this study, size selected NGS libraries (~50-130 bp genomic fragments) were prepared from a developmental series of field-grown ear shoots of Zea mays L. staged by size as 0-1 cm, 1-2 cm, 2-3 cm, 3-5 cm. These libraries, sequenced at ~20 million reads per sample, efficiently capture open chromatin regions during this developmental time course.