Epigenetic regulation and innate Immunity
We are interested in epigenetic gene regulation in innate immunity and study transcription-coupled chromatin exchange. Our current focus is to investigate the activity of three key proteins using newly constructed mouse strains. The proteins we focus are  the replacement histone H3.3, that is incorporated into the genome through transcription.  BRD4, the bromodomain protein that binds to acetylated histones and regulates transcription elongation, and  IRF8, the DNA binding transcription factor that promotes development of the innate immune system and plays a role in anti-microbial defense. We seek to clarify how these factors control transcriptional programs and affect epigenetic memory.
H3.3 is a histone variant present in actively transcribed regions of the genome and is believed to play an important role in epigenetic memory. However, biology of H3.3 has remained elusive for a long time, because of technical difficulties in studying this histone. We have been interested in the role of H3.3 in innate immune responses and showed that stimulation with type I interferons triggers rapid incorporation of H3.3 into interferon stimulated genes (ISGs) in various cells. Surprisingly this deposition continues for several cell generations, eventually leaving a lasting transcriptional mark in activated genes1. To further study transcription-coupled chromatin exchange, we have begun studying a mouse model in which the endogenous H3.3 genes are replaced by the HA-tagged H3.3, which makes it easier to study dynamic H3.3 exchange. With these mice genome-wide H3.3 incorporation is being studied in fibroblasts, macrophages (M¿) and other cells important for innate immunity. Epigenetic memory created by interferon stimulation is being studied in terms of its biology and mechanism.
BRD4 which we first reported in 2000, binds to acetylated histones and recruits the elongation factor, P-TEFb to the transcription start site. BRD4 thus regulates numerous constitutive and inducible genes in tissue culture cells. Today, BRD4 is intensely studied by cancer biologists worldwide, because its inhibitor JQ1/I-BET can interfere with cancer growth. We have previously shown that BRD4 remains bound to chromosomes during mitosis, a feature unusual for transcription factors. We have shown that during mitosis BRD4 specifically binds to genes programmed to be expressed in telophase when post-mitotic transcription resumes. Our current interest is its global role in shaping chromatin-based transcriptional programs. An approach we take is to study Brd4 conditional knock-out (cko) mice. Currently we study how BRD4 regulates the development of immune cells focusing on key lineages as well as how BRD4 controls chromatin environment and genome-wide gene expression during development.
IRF8 is an interferon inducible transcription factor expressed in cells of innate immunity such as M¿, dendritic cells, microglia and is critical for host resistance against various pathogens. SNP based epidemiological studies identified IRF8 as a risk factor for several autoimmune diseases, including multiple sclerosis and SLE. Our analyses indicate that IRF8 directs gene expression programs in M¿s, DCs and microglia that consistently promote proinflammatory pathways promoting autohagy and development of Th1 and Th17 cells. For these analyses we study IRF8-GFP knock-in mice and IRF8 cko mice newly constructed in collaboration with Dr. Herbert Morse in NIAID.