Differential nuclease sensitivity profiling of chromatin in diploid and allopolyploid cotton

To investigate differential regulatory control of duplicated genes (aka homoeologs) in allopolyploid cotton, we initiated a collaborative project in 2016 with Dr. Daniel L. Vera and Professor Hank W. Bass (Florida State University, USA) to explore the role of chromatin accessibility and nucleosome position on duplicated gene expression in allopolyploid cotton. Nucleosome formation is known to directly regulate the access of regulatory proteins to DNA sequences, and strongly associated with gene expression and other features of epigenetic modifications. Using a technique based on chromatin digestion by micrococcal nuclease followed by illumine sequencing (MNase-seq), we prepared mono-nucleosomal DNAs from four Gossypium species (both diploid parents, their F1 hybrid, and the natural allopolyploid cotton) using two different levels of MNase digestion.