In this paper, we provided expertise help with analysis of large data sets for a collaborative project. This study used state-of-the-art technology to identify and to compare protein complexes that are critical for gene expression in cancer and embryonic stem cells. We found that these protein complexes are made up of nearly identical members in both cell types and interact in ways that may help establish the very first steps of gene expression. This study adds detailed information on a fundamental biological process that aid in understanding of how cells regulate their gene expression program that determines their identity.
A key feature of RNA polymerase II (Pol II) preinitiation complexes (PICs) is their ability to coordinate transcription initiation with chromatin modification and remodeling. To understand how this coordination is achieved, we employed extensive proteomic and mechanistic analyses to study the composition and assembly of PICs in HeLa cell and mouse embryonic stem cell (ESC) nuclear extracts. Strikingly, most of the machinery that is necessary for transcription initiation on chromatin is part of the PIC. The PIC is nearly identical between ESCs and HeLa cells and contains two major coactivator complexes: Mediator and SAGA. Genome-wide analysis of Mediator reveals that it has a close correlation with Pol II, TATA-binding protein, and messenger RNA levels and thus may play a major role in PIC assembly. Moreover, Mediator coordinates assembly of the Pol II initiation factors and chromatin machinery into a PIC in vitro, whereas SAGA acts after PIC assembly to allow transcription on chromatin.