Epigenetic and Transcriptional Functions of Nuclear Receptors and Chromatin Remodeling Proteins in Stem and Cancer Cells

National Institute Of Environmental Health Sciences

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Abstract

The elegant organization of nucleic acids, predominantly DNA, into chromatin serves essential structural and regulatory roles in eukaryotic cells. This beautiful architecture allows for an expansion of the underlying genetic information by overlaying a spectrum of epigenetic controls. The interplay between genome accessibility, chromatin posttranslational modifications and transcriptional activity is a critical hub of gene expression regulation. Fundamental to many disease processes is a dysregulation of transcription that underlies the critical role regulated gene transcription plays in normal development physiology and homeostasis. A major focus, of the Archer group has been an understanding of how epigenetic enzymes, including chromatin remodeling proteins such as the SWI/SNF complex, work with transcription factors, such as the glucocorticoid receptor, to respond to environmental cues, both internal and external. Many of our studies have utilize the glucocorticoid receptor, a ligand-activated transcription factor that has important functions in many aspects of mammalian physiology including development, reproduction, immune response, cardiac function, and energy metabolism. Consistent with the broad physiological functions, dysregulation of GR activity is a major factor in health and disease. In this way we hope to understand the function of both the receptor and the requirement for chromatin remodeling and other epigenetic enzymes in these processes. The organization of DNA as chromatin, and its assembly around four core histones, as well as a linker histone, H1, provides a platform for studying mechanisms of gene transcription that relate to environmental responses as well as developmental cues important in determining prepotency of embryonic stem cells. The advent of both embryonic stem cells as well as induced pluripotency stem cells (iPSCs) have opened a significant avenue of experimental approaches to understand both normal and disease states in humans. Many of the studies with pluripotent stem cells have affirmed a major determinant of a role for epigenetics as a mechanism by which the DNA residing in all cells can have specific features of pluripotency. Research pursued in the chromatin and gene expression group within the ESCBL aligns with the NIEHS strategic plan themes one, two and three and multiple goals within those three themes particularly with respect to basic biological research, outreach communications and engagement, environmental health disparities and environmental justice, the professional pipeline, and greater workforce diversity and training in capacity building in global health. Together these studies allow us to fulfill the mission of the NIEHS to improve an understanding of environmental impact on human health and development. A major focus, our research program has been our attempts to understand how chromatin remodeling proteins such as the SWI/SNF complex work with transcription factors, such as the glucocorticoid receptor, to respond to environmental cues, both internal and external. Many of our previous studies made use of the MMTV model promoter which was crucial in demonstrating that the chromatin remodeler BRG1 was critical for GR transcriptional activity. However, subsequent studies demonstrated that GR binds to thousands of sites scattered throughout the genome, representing diverse chromatin landscapes that elicit the hormone response. To expand our studies, Dr. Jackson Hoffman, and Mr. Kevin Trotter, utilized a variety of genome-scale experiments (ChIP-seq, ATAC-seq, RNA-seq, and Start-seq) in human breast cancer cells to identify GR and BRG1 binding sites or peaks throughout the genome and to interrogate the characteristics of the underlying chromatin. Our study reveals that the pattern of BRG1 interaction at GR peaks defines three distinct classes of GR binding site. In contrast to models based on binding sites in at a restricted number of well-established model hormone responsive genes, BRG1 interacts with a significant subset of GR prior to hormone exposure. GR peaks that are pre-occupied by BRG1 are uniquely enriched for active chromatin and are associated with active enhancers and TSSs. The peak classes we define also have distinct patterns of transcription factor motif enrichment and pioneer factor binding. Importantly, BRG1 binding prior to hormone exposure was predictive of GR interaction with pioneer factors. Furthermore, reduction of BRG1 expression blocked hormone-dependent recruitment of pioneer factors to GR binding sites. Finally, we show that BRG1 is required for a robust and proper hormone-induced transcriptional response. Taken together, these findings demonstrate that BRG1 is critical to both pre-pattern GR binding sites and to facilitate hormone-dependent chromatin and transcription factor dynamics. (Hoffman et al., 2018 https://elifesciences.org/articles/35073)