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The cellular genome is packaged as nucleosomes in the nucleus to form chromatin. Different forms of chromatin can be identified by specific modifications of the histones that make up the nucleosome, or by replacing canonical histones in the nucleosome with a histone variant. A specific type of chromatin, heterochromatin, is responsible for permanently silencing large swaths of the genome in a sequence-independent manner, and a wide variety of proteins have been implicated in regulating heterochromatin establishment, spread, and maintenance. This dissertation describes work that elucidates the molecular mechanisms of two such heterochromatin regulators: macroH2A, a histone variant, and HP1/Swi6, a non-histone protein which recognizes covalent methylation of Lysine 9 the histone H3 tail (H3K9). The variant macroH2A is enriched on the silenced X chromosome in mammals and is thought to play a role in maintaining X silencing. My work shows that macroH2A selectively prevents binding by SWI/SNF family complexes, a class of ATP-dependent chromatin remodeling complexes that is associated with gene activation. In contrast, HP1 is involved in the establishment and spread of H3K9-associated heterochromatin and is enriched in centromeric heterochromatin on all chromosomes. Work in the Narlikar laboratory has shown that the S. pombe homologue of HP1, Swi6, forms tetramers on individual nucleosomes in vitro, suggesting that the Swi6 complex is able to bind to nearby nucleosomes. However, it remains unknown how such Swi6 bridging occurs across multiple nucleosomes, or how such bridging affects heterochromatin structure. My work with Swi6 suggests that Swi6 spread across chromatin does not occur linearly, but may rather bind across alternate nucleosomes, supporting the "two-start" model of chromatin folding.