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CDK8 and CDK19 regulate intestinal differentiation and homeostasis via the chromatin remodeling complex SWI/SNF
Marius V. Dannappel, … , Thomas G. Boyer, Ron Firestein
Marius V. Dannappel, … , Thomas G. Boyer, Ron Firestein
Published August 25, 2022
Citation Information: J Clin Invest. 2022;132(20):e158593. https://doi.org/10.1172/JCI158593.
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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 6

Integrated genomic-transcriptomic profiling identifies lineage-specifying transcription factors directly regulated by Mediator kinase.

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Integrated genomic-transcriptomic profiling identifies lineage-specifyin...
(A) Pie chart showing ARID1A binding distribution and violin plot for ARID1A peak intensity in VillinCreERT2/Cdk8fl/fl/Cdk19–/– organoids 7 days after EtOH or 4-OHT treatment. Total number of peaks for each condition is indicated. Mann-Whitney test. (B) Heatmap for ARID1A binding regions and average ChIP peak intensity plots at MED1/MED12/H3K27ac enhancers in EtOH- and 4-OHT–treated VillinCreERT2/Cdk8fl/fl/Cdk19–/– organoids. Immunoblot for total ARID1A protein in VillinCreERT2/Cdk8fl/fl/Cdk19–/– organoids 7 days after EtOH (E) or 4-OHT (T) treatment. (C) Hockey stick plot showing MED12-associated enhancers and super-enhancers and Venn diagram of super-enhancers in EtOH- and 4-OHT–treated VillinCreERT2/Cdk8fl/fl/Cdk19–/– organoids. (D) Gene expression as fold change of genes associated with MED1/MED12-associated super-enhancers lost after ablation of CDK8/19. Mean point represents average fold change across all MED1/MED12-associated SE-associated genes. (E) qRT-PCR for Atoh1 in VillinCreERT2/Cdk8fl/fl/Cdk19–/– organoids 7 days after EtOH and 4-OHT treatment and IECs with the indicated genotypes. Unpaired 2-tailed t test. (F) GSEA for small intestinal ATOH1 target genes in VillinCreERT2/Cdk8fl/fl/Cdk19–/– organoids 7 days after EtOH and 4-OHT treatment and IECs with the indicated genotypes. (G) Relative organoid numbers at passage 3 after EtOH and 4-OHT treatment of parental VillinCreERT2/Cdk8fl/fl/Cdk19–/– organoids and VillinCreERT2/Cdk8fl/fl/Cdk19–/– organoids containing a doxycycline-inducible (Dox-inducible) ATOH1 overexpression construct after Dox pulsing for 24 hours following 48 hours in the absence of Dox. Representative data from 3 independent experiments. ATOH1OE, ATOH1 overexpression construct. One-way ANOVA with Tukey’s multiple-comparison test. (H) qRT-PCR for Lyz after Dox pulsing for 24 hours followed by 48 hours without Dox of EtOH- and 4-OHT–treated parental and ATOH1-overexpression VillinCreERT2/Cdk8fl/fl/Cdk19–/– organoids. Representative data from 2 independent experiments. ATOH1OE, ATOH1 overexpression construct. One-way ANOVA with Tukey’s multiple-comparison test. Data represent mean ± SEM. **P ≤ 0.01, ***P ≤ 0.005, ****P ≤ 0.001.

Copyright © 2023 American Society for Clinical Investigation
ISSN: 0021-9738 (print), 1558-8238 (online)

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