| In eukaryotic organisms, DNA is packaged into chromatin, which consists of repeating nucleosome units that can restrict access to the underlying DNA sequence. ATP-dependent chromatin remodeling proteins catalyze the repositioning of nucleosomes along DNA fragments thereby altering the accessibility of the DNA. Because their catalytic activity can affect high-fidelity processes that require access to DNA sequence, chromatin remodeling proteins need to be regulated. Here I describe the regulation and targeting of the S. cerevisiae Chd1 chromatin remodeling protein by the non-ATPase domains. I show that the N-terminal chromodomains possess a conserved acidic helical element that restricts access to the ATPase motor through an autoinhibitory interaction. This autoregulation allows for selective activation of the ATPase on canonical nucleosome substrates. Additionally, I provide evidence that the C-terminal DNA binding domain of Chd1 targets remodeling activity by providing a high affinity interaction with extranucleosomal DNA. Replacement of the endogenous DNA binding domain with foreign, sequence-specific DNA binding domains allows for directional nucleosome sliding toward the DNA recruitment sequence. Finally, targeting of Chd1 activity to specific promoters can be achieved by introducing Chd1-AraC or Chd1-Ume6 fusion proteins to their DNA recognition elements in vivo. This targeting allows for selective repression of RNA expression at both the REC104 and INO1 promoters. This work demonstrates how auxiliary domains can modulate the activity of the catalytic ATPase domain in chromatin remodeling proteins, and provides the initial characterization of a new tool for creating chromatin rearrangements in vivo.. |
