Mediator is a multi-unit molecular complex that plays a key role in transferring 
signals from transcriptional regulators to RNA polymerase II in eukaryotes. We 
have combined biochemical purification of the Saccharomyces cerevisiae Mediator 
from chromatin with chromatin immunoprecipitation in order to reveal Mediator 
occupancy on DNA genome-wide, and to identify proteins interacting specifically 
with Mediator on the chromatin template. Tandem mass spectrometry of proteins in 
immunoprecipitates of mediator complexes revealed specific interactions between 
Mediator and the RSC, Arp2/Arp3, CPF, CF 1A and Lsm complexes in chromatin. 
These factors are primarily involved in chromatin remodeling, actin assembly, 
mRNA 3'-end processing, gene looping and mRNA decay, but they have also been 
shown to enter the nucleus and participate in Pol II transcription. Moreover, we 
have found that Mediator, in addition to binding Pol II promoters, occupies 
chromosomal interacting domain (CID) boundaries and that Mediator in chromatin 
associates with proteins that have been shown to interact with CID boundaries, 
such as Sth1, Ssu72 and histone H4. This suggests that Mediator plays a 
significant role in higher-order genome organization.