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

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 7

Genomic mapping of a Mediator/SWI-SNF–co-defined enhancer element critical for secretory cell lineage specification.

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Genomic mapping of a Mediator/SWI-SNF–co-defined enhancer element critic...
(A) Genome tracks for H3K27ac, MED1, MED12, ARID1A, and RNA polymerase II (RNA Pol II) ChIP-Seq signals in the vicinity of the Atoh1 locus in VillinCreERT2/Cdk8fl/fl/Cdk19–/– organoids 7 days after EtOH or 4-OHT treatment. Pooled input is shown as a control. Locations of the 4 super-enhancer defined peaks are marked. Gray-shaded areas depict ATOH1-associated super-enhancer peaks. (B) Atoh1 qRT-PCR in C57BL/6 small intestinal organoids harboring nuclease-dead dCas9-KRAB and transduced with the indicated guide RNAs (gRNAs). gRNA-targeted regions are marked as NTC, nontargeting control; Peaks 1–4, the Atoh1 super-enhancer peaks shown in A above. One-way ANOVA with Dunnett’s multiple-comparison test. (C) Bar plot shows organoid number of C57BL/6 organoids expressing dCas9-KRAB transduced with gRNAs targeting the indicated regions (Peak 3, Atoh1 super-enhancer peak 3). Images show organoids from the indicated conditions. One-way ANOVA with Dunnett’s multiple-comparison test. Scale bars: 100 μm. (D) Atoh1 qRT-PCR in VillinCreERT2/Cdk8fl/fl/Cdk19–/– organoids expressing dCas9-VP64 72 hours after transduction with gRNAs targeting ATOH1 promoter, ATOH1 super-enhancer peak 3, and NTC control. Representative data from 3 independent experiments. One-way ANOVA with Dunnett’s multiple-comparison test. (E) ChIP-qPCR for Atoh1 super-enhancer peak 3 after ARID1A or IgG immunoprecipitation in primary IECs from VillinCreERT2 and CDK8iIEC-KO/Cdk19–/– mice 21 days after the first tamoxifen injection. P1, primer 1; P2, primer 2; Peak 3, Atoh1 super-enhancer peak 3. (F) ChIP-qPCR for Atoh1 super-enhancer peak 3 after MED12 or IgG immunoprecipitation in primary IECs from VillinCreERT2 and CDK8iIEC-KO/Cdk19–/– mice 21 days after the first tamoxifen injection. Data represent mean ± SEM. *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.005, ****P ≤ 0.001.