Mediator, a large (25 polypeptides, MW ~1 MDa) multi-protein complex conserved throughout eukaryotes is the key coactivator responsible for conveying regulatory signals to RNA polymerase II (RNAPII) during transcription initiation. Mediator has essentially no enzymatic activity and it is generally agreed that its mechanism must be based on modulation of molecular interactions and conformational rearrangements. Therefore, a structural understanding of Mediator and its interaction with RNAPII is essential to elucidate how Mediator's role during initiation ultimately influences cell differentiation, development, and homeostasis. Macromolecular electron microscopy (EM) is the technique of choice for characterization of large, dynamic macromolecular assemblies because it is uniquely suited to provide information about their structure, conformational changes, and interactions. EM studies of Mediator supported by this grant have set the stage to achieve a molecular understanding of the complex and here we describe further EM, biochemical, and functional analyses of yeast and human Mediators that build on our previous work and will provide a detailed understanding of the structure, subunit organization, and regulation of Mediator conformation and interactions, and reveal the mechanism of regulation by Mediator across eukaryotes.
In Aim 1 we will pursue EM analysis of yeast Mediator (yMED) at subnanometer resolution and investigate subunit interfaces critical for yMED assembly, conformational variability, and function.
In Aim 2 we will study how different factors control Mediator conformation and interactions to modulate RNAPII engagement and transcription initiation, and obtain detailed structural information about the Mediator-RNAPII holoenzyme.
In Aim 3 we will leverage the experience gained from EM analysis of yMED to pursue EM studies of the structure, subunit organization, and interactions of human Mediator (hMED). Parallel analysis of yeast and human Mediators will reveal fundamental aspects of the regulation mechanism related to structural conservation of Mediator across eukaryotes, while highlight aspects of regulation specific to the more intricate human complex. Our results will provide a molecular understanding of the way in which Mediator enables regulation of transcription initiation, and help us understand the direct connection between dysregulation of gene expression and oncogenesis. The work we propose continues our strategy of combining structural analysis with biochemical and functional studies, and will depend critically on 1) application of novel EM image analysis approaches developed in collaboration with the group of Pawel Penczek (UT Houston) specifically tailored to study the structure of dynamic complexes;2) a strong, ongoing collaboration with the group led by Joan and Ron Conaway (Stowers Institute), leaders in biochemical and functional studies of human Mediator.

Public Health Relevance

We will use macromolecular electron microscopy, advanced image analysis techniques, and biochemistry, to study the way in which Mediator, a dynamic multiprotein complex, influences cellular differentiation, development, and homeostasis by regulating gene expression. The results of our studies are critical to public health because deregulation of gene expression is directly connected to cancer and other important diseases.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Macromolecular Structure and Function C Study Section (MSFC)
Program Officer
Flicker, Paula F
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Scripps Research Institute
La Jolla
United States
Zip Code
Ando, Nozomi; Li, Haoran; Brignole, Edward J et al. (2016) Allosteric Inhibition of Human Ribonucleotide Reductase by dATP Entails the Stabilization of a Hexamer. Biochemistry 55:373-81
Murakami, Kenji; Tsai, Kuang-Lei; Kalisman, Nir et al. (2015) Structure of an RNA polymerase II preinitiation complex. Proc Natl Acad Sci U S A 112:13543-8
Lai, Yen-Ting; Reading, Eamonn; Hura, Greg L et al. (2014) Structure of a designed protein cage that self-assembles into a highly porous cube. Nat Chem 6:1065-71
Tsai, Kuang-Lei; Tomomori-Sato, Chieri; Sato, Shigeo et al. (2014) Subunit architecture and functional modular rearrangements of the transcriptional mediator complex. Cell 157:1430-44
Tsai, Kuang-Lei; Sato, Shigeo; Tomomori-Sato, Chieri et al. (2013) A conserved Mediator-CDK8 kinase module association regulates Mediator-RNA polymerase II interaction. Nat Struct Mol Biol 20:611-9
Lai, Yen-Ting; Tsai, Kuang-Lei; Sawaya, Michael R et al. (2013) Structure and flexibility of nanoscale protein cages designed by symmetric self-assembly. J Am Chem Soc 135:7738-43
Minnihan, Ellen C; Ando, Nozomi; Brignole, Edward J et al. (2013) Generation of a stable, aminotyrosyl radical-induced α2β2 complex of Escherichia coli class Ia ribonucleotide reductase. Proc Natl Acad Sci U S A 110:3835-40
Gibbons, Brian J; Brignole, Edward J; Azubel, Maia et al. (2012) Subunit architecture of general transcription factor TFIIH. Proc Natl Acad Sci U S A 109:1949-54
Zimanyi, Christina M; Ando, Nozomi; Brignole, Edward J et al. (2012) Tangled up in knots: structures of inactivated forms of E. coli class Ia ribonucleotide reductase. Structure 20:1374-83
Cai, Gang; Chaban, Yuriy L; Imasaki, Tsuyoshi et al. (2012) Interaction of the mediator head module with RNA polymerase II. Structure 20:899-910

Showing the most recent 10 out of 24 publications