Using native nucleosome arrays to study OCT4 and SOX2 pioneer activity

Abstract

Cell identity is the control of gene transcription by Transcription Factors (TF) and chromatin. The extent to which human cell identity can be recapitulated outside of the cell using TFs and nucleosomes in unknown. I investigate if hESC-like nucleosome positioning, MNase-sensitivity and OCT4 and SOX2 (OS) binding can be recapitulated in vitro. Nucleosomes reconstitute well into cell-like positions upon human DNA sequences in vitro as determined by MNase-seq. These in vitro nucleosomes display fragility, but these nucleosomes are not fragile in hESCs. A sub-population of 110bp nucleosomes are reconstituted, which demonstrate similar MNase-resistance as the 150bp population of nucleosomes. The addition of OS to the reconstituted nucleosomes reveals SOX2-lead binding to MNase-sensitive 110bp nucleosomes, recapitulating OS binding to MNase-sensitive nucleosomes in hESCs. However, binding locations and hESC motifs are not recapitulated in vitro. These results contribute to the understanding of human nucleosome properties, and pioneer factor targeting of chromatin.