UC Berkeley

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.