Mediator binds to boundaries of chromosomally interacting domains and to proteins involved in DNA looping

We have combined biochemical purification of Mediator from chromatin with ChIP-sequencing to reveal Mediator occupupancy to DNA globally and to identify proteins interacting specifically with Mediator in chromatin. We find that Mediator occupy strong chromosomally interacting domain (CID) boundaries and nearly all tRNA genes. Purification of Mediator from chromatin shows that it interacts with proteins and protein complexes that have been shown to interact with CID boundaries such as RSC, Ssu72 and histone H4. We also show specific interaction between Mediator and the Arp2/Arp3, CPF, CF 1A and LSm, complexes in chromatin. These factors are involved in mRNA 3''-end processing, gene looping, actin assembly and mRNA decay. Overall design: We assesed binding of Mediator to chromatin by ChIP-Seq. We sequenced ChIP DNA libraries prepared from Myc- and TAP-tagged Med3, Med7, Med14, Med15, Med17, Med19 and CycC strains.