Tian Chi, PhD, MD

Research focus: epigenetics in the immune system.

Chromatin is a focal point of gene regulation. Alterations in chromatin structure in response to external signals are often reversible, but the altered chromatin states can sometimes be maintained and propagated to daughter cells and even to the future generations of an animal after the cessation of the signaling event. This latter effect enables transient signals to heritably or "epigenetically" modify gene function without altering DNA sequences, thus providing a molecular basis for cellular memory and transgenerational inheritance of acquired traits. On the other hand, misdirected epigenetic controls, or "epimutations," underlie many human diseases. Epimutations also explain phenotypic differences between identical twins, between cloned and original animals, and explain the high incidents of birth defects in "test tube babies". Epigenetics has emerged as a new frontier in biology, with far-reaching implications. Our long-term goals are to reveal fundamental principles in epigenetics and to define how such principles underpin the development and function of the immune system.

Specialized Terms: Epigenetic memory; Transgenerational inheritance; Chromatin biology

• Chromatin structure dictates whether a DNA template is accessible to nuclear proteins, and is thus a focal point of gene regulation by signaling pathways. External signals often mobilize "chromatin remodeling complexes (CRC)" and histone modifying enzymes to reversibly reconfigure chromatin, but the altered chromatin states can sometimes be maintained and propagated to daughter cells after the cessation of the signaling event. This latter effect enables transient signals to heritably or "epigenetically" modify gene function without altering DNA sequences, thus providing a molecular basis for cellular memory and lineage differentiation. On the other hand, misdirected epigenetic controls are now recognized to underlie many human diseases. For example, during cancer development, tumor suppressor genes often become inactivated by "epimutations" characterized by aberrant chromatin rather than by classic DNA mutations. Epimutations also explain phenotypic differences between genetically identical twins, between cloned and original animals, and explain the high incidents of birth defects in "test tube babies". Epimutations that occur in the germline can be transmitted across generations, which has been inferred from epidemiological studies of human diseases and directly demonstrated in animal models. Epigenetics has thus emerged as a new frontier in biology, with far-reaching implications. Our long-term goals are to reveal fundamental principles in chromatin biology and epigenetics, and to define how such principles underpin the development and function of the immune system. Below are some of the problems we are tackling:
• How do external signals mobilize CRC? The current dogma is that signaling pathways impinge on CRC indirectly, by controlling transcription factors which then recruit CRC to target genes via physical interactions. Our recent data indicate that the Swi/Snf-like BAF complex, the prototypical mammalian CRC, is subject to a novel mode of regulation. Specifically, Toll-like receptor (TLR) signaling in macrophages is found to activate the ubiquitous signaling molecule calmodulin (CaM), which then directly binds the BAF complex and stimulates BAF-dependent remodeling and expression of target genes essential for the innate immune response. Given that both CaM and BAF complex are ubiquitously expressed, this novel pathway, connecting cell surface receptors to chromatin, should operate in diverse tissues beyond macrophages and thus be of general importance. We have also developed cell permeable peptides that can effectively disrupt CaM-BAF interaction and block the innate immune response in animal models. These inhibitors provide a powerful means for dissecting and manipulating this novel signaling pathway, with important implications in basic and clinical research.
• Novel functions of the BAF complex. Although called "CRC", the BAF complex, like other CRC, carries multiple subunits totally dispensable for remodeling in vitro. Our hypothesis is that the BAF complex has novel functions in gene regulation unrelated to remodeling. To test this, we have developed a general strategy to engineer tissue-specific point mutations in mice. Our data confirm our hypothesis. So far, we have found that the complex uses ATPase-independent activities to stimulate CD4 expression and promote the survival of regulatory T cells. We are studying the molecular basis of such mysterious functions.
• How do transient signals trigger heritable changes in gene function? The signals are thought to imprint on histones certain posttranslational modifications or "epigenetic tags" which are subsequently maintained and transmitted to daughter cells independently of the initial signals. However, the identity of the tags and the mechanisms of their self-perpetuation are poorly understood. We have generated an animal model where transient exposure of mice to a drug (doxycycline) triggers irreversible changes in the expression pattern of a target gene that can be transmitted to future generation. We have thus established the first animal model for transgenerational inheritance of a well-defined gene. Preliminary experiments already reveal an unexpected mechanism underlying such a mode of inheritance.

• Roles of BAF complex in T cell development
• Mechanisms of epigenetic memory and transgenerational inheritance