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Updated: Apr 29, 2026

Analysis of the c-KIT Ligand Promoter Using Chromatin Immunoprecipitation
Published on: June 27, 2017
Mediator MED18 subunit plays a negative role in transcription via the CDK/cyclin module
Masayuki Kumafuji1, Hiroyasu Umemura, Tadashi Furumoto
1Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan.
Abstract:
The Mediator complex (Mediator) is conserved among eukaryotes and is comprised of head, middle, tail and CDK/cyclin modules. The head module has received the most attention because its interaction with RNA polymerase II (Pol II) and the general transcription factors TFIIH and TBP facilitates phosphorylation of the carboxy-terminal domain (CTD) of the largest subunit of Pol II. We studied the human head module subunit hMED18 to elucidate how Mediator is involved in both transcriptional activation and repression. siRNA-mediated hMED18 depletion augmented transcription, indicating that hMED18 functions in transcriptional repression. Treatment of cells with two histone deacetylase (HDAC) inhibitors, the HDAC inhibitor trichostatin A (TSA) and the SIRT inhibitor nicotinamide showed that this repression was not caused by those HDAC activities. A screen for hMED18-target genes showed that the promoters for cap RNA methyltransferase RNMT-activating mini protein (RAM/FAM103A1) and divalent metal transporter 1 (DMT1/SLC11A2) genes were bound by hMED18. Depletion of hMED18 showed hMED18 and the middle module subunit hMED1 were lost from the promoters of those genes, whereas the CDK/cyclin module subunit hCDK8 remained bound. This indicates a novel transcriptional repression mechanism of hMED18 mediated by hCDK8 and further a novel positive role of free CDK/cyclin module in transcriptional activation. [Correction added on 12 June 2014, after first online publication: SLC11A2 amended from SCL11A2.].
Insights
The human Mediator complex subunit hMED18 represses transcription, independent of HDAC activity. Its depletion releases repression, revealing a novel mechanism involving hCDK8 and a positive role for the CDK/cyclin module in activation.
Area of Science:
- Molecular Biology
- Gene Regulation
- Eukaryotic Transcription
Background:
- The Mediator complex is a conserved eukaryotic transcriptional co-activator.
- The head module, including hMED18, interacts with RNA polymerase II and general transcription factors.
- Understanding hMED18's role is crucial for elucidating Mediator's dual function in transcription.
Purpose of the Study:
- To investigate the function of the human Mediator complex head module subunit, hMED18.
- To determine hMED18's role in transcriptional activation and repression.
- To elucidate the mechanism underlying hMED18-mediated transcriptional regulation.
Main Methods:
- siRNA-mediated depletion of hMED18.
- Treatment with histone deacetylase (HDAC) inhibitors (trichostatin A and nicotinamide).
- Chromatin immunoprecipitation (ChIP) to assess protein binding at target gene promoters (RAM/FAM103A1 and DMT1/SLC11A2).
Main Results:
- hMED18 depletion led to increased transcription, indicating a repressive role for hMED18.
- hMED18-mediated repression was not dependent on HDAC activity.
- hMED18 depletion caused the loss of hMED18 and hMED1 from target gene promoters, while hCDK8 remained bound, suggesting a novel repression mechanism.
- This mechanism involves hMED18, hCDK8, and the middle module subunit hMED1.
Conclusions:
- hMED18 functions as a transcriptional repressor.
- A novel mechanism of transcriptional repression mediated by hMED18 and hCDK8 was identified.
- The study suggests a novel positive role for the free CDK/cyclin module in transcriptional activation.
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