Whole genome nucleosome positioning by MNase-Seq on the mouse tumor line, RMA. Mus musculus

We have employed MNase-Seq technology to determine the nucleosome positioning across the Ly49-expressing RMA cell line. This information was compared to the default nucleosome landscape of these cells as predicted by NuPop computations to identify transcription factor binding site regions that significantly deviate from our predictions, potentially indicating an interfering role for nucleosome binding at these sites. We report that expressed Ly49 genes significantly deviate in their nucleosome coverage at AML-1a sites when compared to other, non-expressed Ly49 genes within the same sample. This information has implications for our understanding of NK cell biology, and also presents the Ly49 family as a convenient model system for discovering how various genetic and epigenetic elements impact expression state, since Ly49 genes are stochastically expressed within a given population, but have similar transcription factor requirements. It is our hope that other work on the epigenetic control of gene expression can benefit from this model system. Overall design: Examination of ten genetic regions in one population