Heterochromatin remains a mysterious component of eukaryotic genomes. The amounts and kinds of repetitive elements within heterochromatin of a focal segment have emerged as potential determinants of gene expression across the genome (trans-regulation). Highly repetitive segments of heterochromatin represent one of the last frontiers of eukaryotic genomes and the mechanisms by which heterochromatin dosage exert their effects across the genome have remained elusive. Here we report two sets of results. First, we describe our efforts constructing a whole Y-chromosome dosage series with polymorphic Y chromosomes (XY, XYY, XX, XXY) in a homogeneous background of a autosomes and X chromosomes. Second, we report novel functional genome analyses across a number of attributes in these genotypes that help illuminate the impact of perturbing the nuclear environment with extra Y chromosomes. We discuss the results in view of several proposed models for heterochromatin action in trans, including a classical hypothesis known as the heterochromatin sink as well as others.