Posttranslational histone modifications and histone variants form a unique epigenetic landscape on mammalian chromosomes where the principal epigenetic heterochromatin markers, trimethylated histone H3(K9) and the histone H2A.Z, are inversely localized in relation to each other. Trimethylated H3(K9) marks pericentromeric constitutive heterochromatin and the male Y chromosome, while H2A.Z is dramatically reduced at these chromosomal locations. Inactivation of a lysosomal and nuclear protease, cathepsin L, causes a global redistribution of epigenetic markers. In cathepsin L knockout cells, the levels of trimethylated H3(K9) decrease dramatically, concomitant with its relocation away from heterochromatin, and H2A.Z becomes enriched at pericentromeric heterochromatin and the Y chromosome. This change is also associated with global relocation of heterochromatin protein HP1 and histone H3 methyltransferase Suv39h1 away from constitutive heterochromatin; however, it does not affect DNA methylation or chromosome segregation, phenotypes commonly associated with impaired histone H3(K9) methylation. Therefore, the key constitutive heterochromatin determinants can dynamically redistribute depending on physiological context but still maintain the essential function(s) of chromosomes. Thus, our data show that cathepsin L stabilizes epigenetic heterochromatin markers on pericentromeric heterochromatin and the Y chromosome through a novel mechanism that does not involve DNA methylation or affect heterochromatin structure and operates on both somatic and sex chromosomes.In eukaryotic cells, pericentromeric chromosomal regions do not completely decondense in the interphase and form heterochromatin, a more condensed and transcriptionally repressed type of chromatin morphologically distinct from decondensed and transcriptionally active euchromatin (17,21,55). Previous molecular and genetic studies had established a set of epigenetic mechanisms such as a special set of histone modifications also referred to as "histone code" (24) and DNA methylation (26) that demarcate silent heterochromatin and transcriptionally active euchromatin, separating one from the other. A key regulatory mechanism that controls heterochromatin formation is the positive feedback loop by which histone H3 trimethylated at lysine 9 (H3me3K9) recruits heterochromatin protein 1 (HP1) through direct interaction with the HP1 chromodomain (2, 27, 30). HP1, in turn, recruits histone H3(K9) methyltransferase Suv39h (24, 54) to methylate adjacent H3(K9). In addition to H3me3K9, other factors can contribute to the stable association of HP1 with chromatin (10, 59). The presence of HP1 at chromosomal loci is sufficient to induce chromatin condensation and gene repression (64). The highest concentration of HP1 and H3me3K9 is found at simple repeats in the vicinity of centromeric regions forming the largest blocks of heterochromatin, also known as pericentromeric constitutive heterochromatin. In addition, H3me3K9 is localized on chromatin clusters associated with certain ty...