Lineage-specific reorganization of nuclear peripheral heterochromatin and H3K9me2 domains

Dynamic and regulated organization of chromatin within the 3-dimensional space of the nucleus has been postulated to contribute to gene accessibility, gene expression, and cell fate. Here we define the genome-wide lineage-specific reorganization of nuclear peripheral heterochromatin as a multipotent P19 embryocarcinoma cell adopts either a neural or a cardiac fate. We demonstrate that H3K9me2 marked nuclear peripheral heterochromatin undergoes lineage-specific local reorganization during cell fate determination. Lineage-specific loss of H3K9me2 is associated with spatial repositioning of genomic loci away from the nuclear periphery as shown by high-resolution 3D immuno-fluorescence in situ hybridization (3D immuno-FISH). The lineage-specific repositioning of loci away from the nuclear periphery is not always associated with activation of gene expression, but a subset of these genes is transcriptionally activated. Master regulator Mef2c is specifically repositioned from nuclear periphery during early neurogenic differentiation, but not early cardiogenic differentiation, with associated transcript upregulation. Master regulator Myocd is specifically repositioned during early cardiogenic differentiation, but not early neurogenic differentiation, and is transcriptionally upregulated at later stages of cardiac differentiation. These results provide experimental evidence for lineage-specific regulation of nuclear architecture when the same multipotent progenitor cell adopts distinct fates. In this study, we examined the genome wide distribution of nuclear peripheral heterochromatin and global transcriptomic changes in multipotent undifferentiated P19 cells, Day 3 RA-treated and Day 3 DMSO-treated P19 cells. We performed H3K9me2 ChIP-seq to mark nuclear peripheral heterochromatin and H3 ChIP-seq as parallel control with three biological replicates per condition. We performed RNA-seq at day 3 and day 6 of differentiation with three biological replicates per condition to assess transcriptomic changes.