Silencing of the somatic cell type-specific genes is a critical yet poorly understood step in reprogramming. To uncover pathways that maintain cell identity, we performed a reprogramming screen using inhibitors of chromatin factors. Here, we identify acetyl-lysine competitive inhibitors targeting the bromodomains of coactivators CREB (cyclic-AMP response element binding protein) binding protein (CBP) and E1A binding protein of 300 kDa (EP300) as potent enhancers of reprogramming. These inhibitors accelerate reprogramming, are critical during its early stages and, when combined with DOT1L inhibition, enable efficient derivation of human induced pluripotent stem cells (iPSCs) with OCT4 and SOX2. In contrast, catalytic inhibition of CBP/EP300 prevents iPSC formation, suggesting distinct functions for different coactivator domains in reprogramming. CBP/EP300 bromodomain inhibition decreases somatic-specific gene expression, histone H3 lysine 27 acetylation (H3K27Ac) and chromatin accessibility at target promoters and enhancers. The master mesenchymal transcription factor PRRX1 is one such functionally important target of CBP/EP300 bromodomain inhibition. Collectively, these results show that CBP/EP300 bromodomains sustain cell-type-specific gene expression and maintain cell identity.
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RNA-sequencing, ChIP-sequencing and ATAC-sequencing data are deposited to the NCBI GEO database with the accession number GSE118220.
The custom pipeline for ChIP-seq analysis can be found at: https://github.com/Acribbs/cribbslab/blob/master/Pipelines/pipeline_quantchip.py.
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We would like to thank A. Kocabay and A.C. Taşkın for help with mouse experiments, A. Ruacan (Koç University, School of Medicine, Department of Pathology) for examination of histological sections and E. Hookway as well as T. Seker, E. Kavak (Genomize Inc.) for help with the initial generation and analyses of the RNA-seq data. The authors gratefully acknowledge use of the services and facilities of the Koç University Research Center for Translational Medicine (KUTTAM), funded by the Republic of Turkey Ministry of Development. The content is solely the responsibility of the authors and does not necessarily represent the official views of the Ministry of Development. K.S. was supported by a TUBITAK BIDEB Scholarship. Work in the U.O. laboratory was supported by Arthritis Research UK (program grant no. 20522), Cancer Research UK and the Rosetrees Foundation. The Structural Genomics Consortium is a registered charity (no. 1097737) that receives funds from AbbVie, Bayer Pharma AG, Boehringer Ingelheim, Canada Foundation for Innovation, Eshelman Institute for Innovation, Genome Canada, Innovative Medicines Initiative (EU/EFPIA) (ULTRA-DD grant no. 115766), Janssen, Merck KGaA Darmstadt Germany, MSD, Novartis Pharma AG, Ontario Ministry of Economic Development and Innovation, Pfizer, São Paulo Research Foundation-FAPESP, Takeda, and Wellcome (106169/ZZ14/Z). The research has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 609305. This work was supported by an EMBO Installation Grant (T.T.O.), a Newton Advanced Fellowship (U.O. and T.T.O.) and TUBITAK Project 213S182 (T.T.O.).
The authors declare no competing interests.
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Ebrahimi, A., Sevinç, K., Gürhan Sevinç, G. et al. Bromodomain inhibition of the coactivators CBP/EP300 facilitate cellular reprogramming. Nat Chem Biol 15, 519–528 (2019). https://doi.org/10.1038/s41589-019-0264-z
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