An IDR-dependent Mechanism for Nuclear Receptor Control of Mediator Interaction with RNA Polymerase II

Overview

Journal Mol Cell

Publisher Cell Press

Specialty Cell Biology

Date 2024 Jul 2

PMID 38955181

Authors

Haiyan Zhao

Jiaqin Li

Yufei Xiang

Sohail Malik

Supriya V Vartak

Giovana M B Veronezi

Natalie Young

McKayla Riney

Jens Kalchschmidt

Andrea Conte

Seol Kyoung Jung

Srinivas Ramachandran

Robert G Roeder

Yi Shi

Rafael Casellas

Francisco J Asturias

Affiliations

Soon will be listed here.

Abstract

The essential Mediator (MED) coactivator complex plays a well-understood role in regulation of basal transcription in all eukaryotes, but the mechanism underlying its role in activator-dependent transcription remains unknown. We investigated modulation of metazoan MED interaction with RNA polymerase II (RNA Pol II) by antagonistic effects of the MED26 subunit and the CDK8 kinase module (CKM). Biochemical analysis of CKM-MED showed that the CKM blocks binding of the RNA Pol II carboxy-terminal domain (CTD), preventing RNA Pol II interaction. This restriction is eliminated by nuclear receptor (NR) binding to CKM-MED, which enables CTD binding in a MED26-dependent manner. Cryoelectron microscopy (cryo-EM) and crosslinking-mass spectrometry (XL-MS) revealed that the structural basis for modulation of CTD interaction with MED relates to a large intrinsically disordered region (IDR) in CKM subunit MED13 that blocks MED26 and CTD interaction with MED but is repositioned upon NR binding. Hence, NRs can control transcription initiation by priming CKM-MED for MED26-dependent RNA Pol II interaction.

Citing Articles

Mechanisms of synergistic Mediator recruitment in RNA polymerase II transcription activation revealed by single-molecule fluorescence.

Zhou D, Jeon J, Farheen N, Friedman L, Kondev J, Buratowski S bioRxiv. 2024; .

PMID: 39713438 PMC: 11661148. DOI: 10.1101/2024.12.10.627625.

References

Jeronimo C, Robert F . The Mediator Complex: At the Nexus of RNA Polymerase II Transcription. Trends Cell Biol. 2017; 27(10):765-783. DOI: 10.1016/j.tcb.2017.07.001. View

Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O . Highly accurate protein structure prediction with AlphaFold. Nature. 2021; 596(7873):583-589. PMC: 8371605. DOI: 10.1038/s41586-021-03819-2. View

Elmlund H, Baraznenok V, Lindahl M, Samuelsen C, Koeck P, Holmberg S . The cyclin-dependent kinase 8 module sterically blocks Mediator interactions with RNA polymerase II. Proc Natl Acad Sci U S A. 2006; 103(43):15788-93. PMC: 1635081. DOI: 10.1073/pnas.0607483103. View

Jeronimo C, Langelier M, Bataille A, Pascal J, Pugh B, Robert F . Tail and Kinase Modules Differently Regulate Core Mediator Recruitment and Function In Vivo. Mol Cell. 2016; 64(3):455-466. PMC: 5824718. DOI: 10.1016/j.molcel.2016.09.002. View

Scheres S . RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol. 2012; 180(3):519-30. PMC: 3690530. DOI: 10.1016/j.jsb.2012.09.006. View

Soutourina J . Transcription regulation by the Mediator complex. Nat Rev Mol Cell Biol. 2017; 19(4):262-274. DOI: 10.1038/nrm.2017.115. View

Paoletti A, Parmely T, Tomomori-Sato C, Sato S, Zhu D, Conaway R . Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors. Proc Natl Acad Sci U S A. 2006; 103(50):18928-33. PMC: 1672612. DOI: 10.1073/pnas.0606379103. View

Davis J, Takagi Y, Kornberg R, Asturias F . Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interaction. Mol Cell. 2002; 10(2):409-15. DOI: 10.1016/s1097-2765(02)00598-1. View

Schilbach S, Hantsche M, Tegunov D, Dienemann C, Wigge C, Urlaub H . Structures of transcription pre-initiation complex with TFIIH and Mediator. Nature. 2017; 551(7679):204-209. PMC: 6078178. DOI: 10.1038/nature24282. View

10.

Skene P, Henikoff S . An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. Elife. 2017; 6. PMC: 5310842. DOI: 10.7554/eLife.21856. View

11.

Osman S, Mohammad E, Lidschreiber M, Stuetzer A, Bazso F, Maier K . The Cdk8 kinase module regulates interaction of the mediator complex with RNA polymerase II. J Biol Chem. 2021; 296:100734. PMC: 8191332. DOI: 10.1016/j.jbc.2021.100734. View

12.

Vian L, Pekowska A, Rao S, Kieffer-Kwon K, Jung S, Baranello L . The Energetics and Physiological Impact of Cohesin Extrusion. Cell. 2018; 173(5):1165-1178.e20. PMC: 6065110. DOI: 10.1016/j.cell.2018.03.072. View

13.

Zybailov B, Mosley A, Sardiu M, Coleman M, Florens L, Washburn M . Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res. 2006; 5(9):2339-47. DOI: 10.1021/pr060161n. View

14.

Malik S, Baek H, Wu W, Roeder R . Structural and functional characterization of PC2 and RNA polymerase II-associated subpopulations of metazoan Mediator. Mol Cell Biol. 2005; 25(6):2117-29. PMC: 1061600. DOI: 10.1128/MCB.25.6.2117-2129.2005. View

15.

Fondell J, Ge H, Roeder R . Ligand induction of a transcriptionally active thyroid hormone receptor coactivator complex. Proc Natl Acad Sci U S A. 1996; 93(16):8329-33. PMC: 38670. DOI: 10.1073/pnas.93.16.8329. View

16.

Asturias F, Jiang Y, Myers L, Gustafsson C, Kornberg R . Conserved structures of mediator and RNA polymerase II holoenzyme. Science. 1999; 283(5404):985-7. DOI: 10.1126/science.283.5404.985. View

17.

Pettersen E, Goddard T, Huang C, Couch G, Greenblatt D, Meng E . UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004; 25(13):1605-12. DOI: 10.1002/jcc.20084. View

18.

Sabari B, DallAgnese A, Boija A, Klein I, Coffey E, Shrinivas K . Coactivator condensation at super-enhancers links phase separation and gene control. Science. 2018; 361(6400). PMC: 6092193. DOI: 10.1126/science.aar3958. View

19.

Louder R, He Y, Lopez-Blanco J, Fang J, Chacon P, Nogales E . Structure of promoter-bound TFIID and model of human pre-initiation complex assembly. Nature. 2016; 531(7596):604-9. PMC: 4856295. DOI: 10.1038/nature17394. View

20.

Punjani A, Rubinstein J, Fleet D, Brubaker M . cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat Methods. 2017; 14(3):290-296. DOI: 10.1038/nmeth.4169. View