In species that use chromosome-based sex determination, the copy number of sex
chromosomes differs between the two sexes. Multiple different molecular mechanisms have
evolved independently in diverse animal taxa to compensate for this imbalance in sex
chromosome dose. In Drosophila species, gene expression from the single X in males is
upregulated twofold. In Caenorhabditis species, genes from the two hermaphrodite Xs are
downregulated by half. In mammals, one of the two X chromosomes is inactivated in females.
In Chapter 1, I use these three dosage compensation strategies to illustrate the variety of ways
in which gene expression can be coordinately regulated across an entire chromosome. The
proteins and non-coding RNAs that enact dosage compensation also change histone marks over
broad domains, compact chromosomes, restructure higher-order domain organization, and
reposition X chromosomes within the nucleus, providing valuable models to dissect how
chromosomes are organized at multiple scales.
In Chapter 2, I use the process of Caenorhabditis elegans X-chromosome dosage compensation
to investigate how chromosome architecture is established and its relationship to gene
expression. In C. elegans, a dosage compensation complex (DCC) equalizes X expression
between sexes by repressing transcription from the two hermaphrodite Xs by half while also
establishing a unique structure composed of megabase-scale topologically associating domains
(TADs). DCC-dependent TAD boundaries all contain a strong DCC binding site (rex site). By
making a series of rex site deletions and insertions and measuring the resulting chromosome
structure, I determined that DCC binding at a strong rex site is necessary and sufficient for
boundary formation. Deleting all eight of the rex sites at DCC-dependent boundaries
recapitulated the TAD structure of a DCC mutant. When TAD structure was disrupted but most
DCC binding was retained, X chromosome expression was not changed, indicating that TADs are
neither a cause nor consequence of X repression. However, the worms showed increased
thermosensitivity, accelerated aging, and shortened lifespan, suggesting a role for chromosome
structure in regulating stress and aging programs.