Two primary bodies of epigenomics literature provide insights into the large-scale folding of eukaryotic chromosomes and their relative locations within the nucleus. First, mapping of genomic regions associated with nuclear landmarks such as the nuclear lamina and nuclear pores provides a perspective on chromosomal territories that contact the nuclear periphery. Key insights from such mapping studies include the finding that active chromatin tends to associate with nuclear pores in yeast (Casolari et al. 2004), while megabase-scale domains of repressive chromatin termed lamina-associated domains (LADs) are intimately associated with the nuclear periphery in many organisms (Pickersgill et al. 2006). LADs are dynamic during development, with changes in lamina association being correlated with gene repression. Perhaps the most dramatic perturbation to LAD structure occurs in several examples of sensory epithelia, where physiological down-regulation of the lamin B receptor results in otherwise lamina-associated heterochromatin moving to the nuclear interior. In the case of the retina, this clump of heterochromatin in the nuclear interior has been proposed to play a role in allowing light to reach photoreceptors (Solovei et al. 2009), while in the
