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CDK8 and CDK19 regulate intestinal differentiation and homeostasis via the chromatin remodeling complex SWI/SNF
Marius V. Dannappel, Danxi Zhu, Xin Sun, Hui Kheng Chua, Marle Poppelaars, Monica Suehiro, Subash Khadka, Terry C.C. Lim Kam Sian, Dhanya Sooraj, Melissa Loi, Hugh Gao, Daniel Croagh, Roger J. Daly, Pouya Faridi, Thomas G. Boyer, Ron Firestein
Marius V. Dannappel, Danxi Zhu, Xin Sun, Hui Kheng Chua, Marle Poppelaars, Monica Suehiro, Subash Khadka, Terry C.C. Lim Kam Sian, Dhanya Sooraj, Melissa Loi, Hugh Gao, Daniel Croagh, Roger J. Daly, Pouya Faridi, Thomas G. Boyer, Ron Firestein
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Research Article Gastroenterology Genetics

CDK8 and CDK19 regulate intestinal differentiation and homeostasis via the chromatin remodeling complex SWI/SNF

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Abstract

Initiation and maintenance of transcriptional states are critical for controlling normal tissue homeostasis and differentiation. The cyclin dependent kinases CDK8 and CDK19 (Mediator kinases) are regulatory components of Mediator, a highly conserved complex that orchestrates enhancer-mediated transcriptional output. While Mediator kinases have been implicated in the transcription of genes necessary for development and growth, its function in mammals has not been well defined. Using genetically defined models and pharmacological inhibitors, we showed that CDK8 and CDK19 function in a redundant manner to regulate intestinal lineage specification in humans and mice. The Mediator kinase module bound and phosphorylated key components of the chromatin remodeling complex switch/sucrose non-fermentable (SWI/SNF) in intestinal epithelial cells. Concomitantly, SWI/SNF and MED12-Mediator colocalized at distinct lineage-specifying enhancers in a CDK8/19–dependent manner. Thus, these studies reveal a transcriptional mechanism of intestinal cell specification, coordinated by the interaction between the chromatin remodeling complex SWI/SNF and Mediator kinase.

Authors

Marius V. Dannappel, Danxi Zhu, Xin Sun, Hui Kheng Chua, Marle Poppelaars, Monica Suehiro, Subash Khadka, Terry C.C. Lim Kam Sian, Dhanya Sooraj, Melissa Loi, Hugh Gao, Daniel Croagh, Roger J. Daly, Pouya Faridi, Thomas G. Boyer, Ron Firestein

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Figure 5

Phospho-proteomic analysis of MED12-Mediator identifies interactions with the SWI/SNF complex.

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Phospho-proteomic analysis of MED12-Mediator identifies interactions wit...
(A) Quantitative proteomics (liquid chromatography–tandem mass spectrometry [LC-MS/MS]) after isobaric labeling of MED1-coimmunoprecipitated proteins in VillinCreERT2/Cdk8fl/fl/Cdk19–/– intestinal organoids 7 days after EtOH and 4-OHT treatment. Components of the Mediator complex are color-coded as indicated. (B) Quantitative proteomics (LC-MS/MS) after isobaric labeling of MED12-coimmunoprecipitated proteins in VillinCreERT2/Cdk8fl/fl/Cdk19–/– intestinal organoids. Mediator and SWI/SNF complex components are colored as indicated. (C) STRING analysis of MED12 interaction partners in EtOH-treated VillinCreERT2/Cdk8fl/fl/Cdk19–/– organoids and STRING cellular components (Gene Ontology) enrichment analysis. (D) Inset table shows identified phosphorylation sites reduced in 4-OHT–treated VillinCreERT2/Cdk8fl/fl/Cdk19–/– organoids compared with EtOH-treated controls 5 days after treatment (log2FC < –1, FDR < 0.05). (E) Coimmunoprecipitation (co-IP) assay in VillinCreERT2 intestinal organoids. Immunoprecipitation antibody is ARID1A or IgG control; Western blot antibodies are MED12 and ARID1A. Arrow indicates coimmunoprecipitated protein. (F) Co-IP assay in VillinCreERT2 intestinal organoids. Immunoprecipitation antibody is MED12 or IgG control; Western blot antibodies are MED12 and ARID1A. Arrow indicates coimmunoprecipitated protein. (G) Coomassie blue–stained gel shows reconstituted CDK8, MED12, and CCNC. Blot shows 32P-labeled protein in the presence of the kinase complex as indicated. 4x(S-A), ARID1A fragment (aa 659–751) containing S-to-A mutations on Ser696, Ser699, Ser703, and Ser716.

Copyright © 2026 American Society for Clinical Investigation
ISSN: 0021-9738 (print), 1558-8238 (online)

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