| dc.description.abstract | Sex chromosome constitution is the largest and oldest source of genetic variation in the human population. One sex chromosome—the “active X” (Xa)—is present in all individuals. The second sex chromosome differs between sexes; most males have a Y while most females have a second X, which adopts a distinct conformation from Xa and is termed the “inactive X” (Xi). Despite its name, the human Xi expresses ~20% of its genes. Xi-expressed genes and their Y homologs play critical gene regulatory roles. Examining mechanisms and effects of Xi gene expression is essential to understanding these functions. In this thesis, I investigate chromatin landscape across the human Xi to identify features of Xi-expressed and Xi-silent genes; I also interrogate the role of an Xi-expressed gene and its Y homolog in regulating chromatin genome-wide. To examine chromatin state differences between Xi-expressed and Xi-silent genes, we quantified H3K4me3, H3K27me3, and CTCF along Xi by linear modeling in cells of individuals with zero to three Xis. We demonstrate that Xi-expressed genes are enriched for H3K4me3 compared to Xi-silent genes. Moreover, Xi-silent genes near strongly Xi-expressed genes have higher H3K27me3 than other Xi-silent genes. CTCF shields strongly Xi-expressed gene promoters from surrounding heterochromatin. We propose a framework associating combinations of chromatin marks with subcategories of Xi-expressed and Xi-silent genes. A key Xi-expressed gene, KDM6A, encodes an H3K27me3 demethylase—enabling Xi to impact chromatin structure genome-wide. Its Y homolog, UTY, is thought to encode a catalytically dead enzyme. However, we demonstrate that Xi and Y copy number-dependent changes to H3K27me3 across autosomes are strongly correlated. Moreover, KDM6A knockdown results in increased H3K27me3 at similar genomic regions as UTY knockdown. We posit that KDM6A and UTY share demethylase-dependent functions. Deciphering features and genome-wide effects of Xi expression is essential to understanding fundamental mechanisms of gene regulation and the shared and differential roles of the sex chromosomes outside the reproductive tract. This work highlights critical chromatin-level differences between Xi-silent and Xi-expressed genes, the effects of an Xi-expressed gene on chromatin structure genome-wide, and striking similarities between Xi and Y in modulating autosomal chromatin structure and gene expression. | |
