X-Chromosome Targeting and Chromosome-Wide Transcriptional Repression by the Caenorhabditis elegans Dosage Compensation Complex

In organisms that determine sex using specialized sex chromosomes, chromosome-wide dosage compensation is required to equalize gene expression between the sexes. In each well-studied dosage compensation system, factors are targeted to the sex chromosomes of only one sex to modulate sex-chromosome expression. In the nematode Caenorhabditis elegans, the dosage compensation complex (DCC) binds both X chromosomes of XX hermaphrodites and reduces X-linked transcript levels by approximately half to equal those of the XO male. My research addresses the mechanisms by which the DCC recognizes X chromosomes and controls transcription once bound. Previous studies determined that the DCC is recruited to the X chromosomes through rex sites that recruit the DCC autonomously. rex sites contain high-scoring matches to several DNA sequence elements that are required for full binding of the DCC, including the motif enriched on X (MEX). In addition to binding to rex sites, the DCC binds to dox sites that reside in the promoters of active genes and are bound only when attached to the X chromosome. In this dissertation, I report advances in understanding how the DCC is targeted to the X chromosome and how it regulates transcription of X-linked genes once it is bound. In chapter 2, I describe experiments that redefine our understanding of DCC composition, binding and function, performed in collaboration with another graduate student. The protein DPY-30 is shown to be a component of both the repressive DCC and the activating MLL/COMPASS complex. We define fundamental differences in the molecular requirements for DCC binding to rex and dox sites, and describe the relationship between DCC binding at these two classes of sites. Finally, we show that C. elegans dosage compensation controls X-linked transcript levels by regulating transcription. In chapter 3, I describe work performed in collaboration with John Lis's laboratory at Cornell University using Global Run-On Sequencing (GRO-seq) to