This application addresses broad Challenge Area (14) Stem Cells, and the specific Challenge topic, 14-AG-104: Delineate factors that control the differentiation of pluripotent stem cells. The ability to convert adult somatic cells into induced pluripotent stem (iPS) cells with properties indistinguishable from human embryonic stem (hES) cells represents a major advance in regenerative medicine. In the proposed studies, we will examine the fidelity of (re-)programming in iPS and hES cells that is linked to epigenetic mechanisms controlling pluripotency during self-renewal (Aim 1) and cell fate determination during differentiation (Aim 2). We will characterize architectural epigenetics as the inheritance of chromatin structural information by progeny cells during mitosis that includes the association of (i) lineage-specific and pluripotency-related gene regulatory factors, (ii) variant core (H2A, H2B, H3 and H4) histone proteins, as well as (iii) variant linker histone (H1) proteins with specific target gene promoters during mitosis. We will experimentally address the central hypothesis that the complement of proteins associated with genes in mitotic chromosomes is fundamental to the pluripotency of both iPS and hES cells and that modifications in this mitotic protein/DNA interactome are critical for lineage commitment and are mechanistically coupled with loss of pluripotency. Also, the post-mitotic organization of chromatin micro-environments during interphase will be functionally analyzed to diagnose fidelity of self-renewal and cell cycle progression in pluripotent and lineage-committed cells. Our approach will establish the fundamental basis of pluripotency and (re-)programming from the perspective of architectural epigenetics. We will thus identify principal gene regulatory proteins that influence gene expression following completion of mitotic cell division and define the ability of stem cells for self-renewal and lineage-specific programming. The regulatory parameters and factors identified in the proposed studies can be targeted for biological strategies supporting tissueengineering and regenerative medicine in elderly patients. PUBLIC HEALTH RELEVANCE: Many age-related diseases may be curable by converting normal cells from patients into cells that have the potential to become any other cell type to regenerate a deteriorating tissue or organ (e.g., bone, brain, muscle or cardiovascular cells). It is possible to induce cells to reach this so-called 'pluripotent state', but the fidelity by which this process produces genuine stem cells remains undefined. Our laboratory has shown that transcription factors can remain bound to mitotic chromosomes to define a novel mechanism that can transmit heritable regulatory information ('architectural epigenetics') to progeny after cell division. We will use sophisticated and state-of-the art biochemical, molecular and cellular approaches to define the mechanistic roles of regulatory proteins that are bound to mitotic chromosomes during the cell cycle in na[unreadable]ve and programmed stem cells. In addition, we will investigate how these factors contribute to the formation of microscopic domains within the nucleus that mediate gene expression. Our studies will establish how cells can stay pluripotent or become specialized cells from the perspective of architectural epigenetics. Our approaches will identify major factors that control how genes are used immediately after cells complete a round of cell division. Because these factors regulate instructions for cell multiplication through self-renewal or for conversion into specialized cells, they may be particularly suitable for biological strategies supporting tissue-engineering and regenerative medicine in elderly patients.