Genetic, Epigenetic and Chromosomal Domain Influences on Gene Expression from the Inactive X Chromosome
Open Access
- Author:
- Stahl, Jill
- Graduate Program:
- Genetics
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- April 19, 2013
- Committee Members:
- Laura Carrel, Dissertation Advisor/Co-Advisor
Laura Carrel, Committee Chair/Co-Chair
Edward Joseph Gunther, Committee Member
Kristin Ann Eckert, Committee Member
Kent Eugene Vrana, Committee Member - Keywords:
- X chromosome inactivation
X chromosome
gene expression
DNA methylation - Abstract:
- X chromosome inactivation (XCI) silences one X chromosome in females to equalize expression between males and females. Despite the chromosome-wide nature of XCI, ~15% of genes escape inactivation. Escapees are frequently found as clusters, suggesting coordinate regulation. Intriguingly, 10% of genes show variable escape and are expressed from the inactive X (Xi) in a subset of women. Variably expressed loci may contribute to normal trait variation amongst females. The goal of this thesis is to better understand regulation of Xi gene expression by evaluating variable genes in an effort to reveal genetic and epigenetic influences. To evaluate variable Xi expression, I isolated a large number of clonal cell lines from both related and unrelated individuals and scored transcribed polymorphisms to quantitatively measure allele-specific expression. The basis of variability due to cell-to-cell differences was examined by testing Xi gene expression in multiple independent clonal lines, and showed that despite inter-individual variation, intra-individual expression is remarkably stable. Strikingly, Xi levels are inherent to a given X as expression can differ even between maternal and paternal Xi clones derived from a single individual. Nonetheless, these results also exclude trans-acting influences for two genes (HCFC1 and NAA10) as the isogenic lines share an autosomal background. Xi heritability was also assessed. For NAA10, divergent Xi expression of the same X in related females excludes heritability, yet similar analysis of HCFC1 is consistent with cis-acting influences. To assess regional influences associated with coordinate regulation of escape, variable genes from two escape domains were examined. Remarkably, clustered genes show extensive Xi variability, prompting redefinition of these domains as ‘escape-prone.’ Within domains Xi levels correlated for most genes, suggesting coordinate regulation of expression within a cluster. Lastly, epigenetic analysis showed promoter hypomethylation for three variable genes independent of Xi expression level, whereas NAA10 methylation was inversely correlated, suggesting hypomethylation contributes to a poised state for some genes. Such results reveal complex regulation on the Xi, and altogether indicate multiple mechanisms of gene regulation. Given that earlier analysis revealed consistent Xi levels for a given X, we propose that additional epigenetic features are essential during establishment of Xi levels.