Understanding ETS1 expression and function in B cells
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Ets1 is a transcription factor that is highly expressed in lymphocytes, and is required for proper lymphocyte responses. Ets1 deficient mice develop an autoimmune syndrome and the human ETS1 gene has been identified as a susceptibility locus for multiple autoimmune diseases. B cells from Ets1 -/- mice are hyper-responsive to Toll-like receptor stimuli and undergo enhanced differentiation to antibody-secreting plasma cells. These phenotypes indicate that Ets1 has an important role in preventing the development of autoimmune diseases, potentially by regulating B cell responses. The expression of Ets1 is high in naive B cells, but reduced upon activation and low in plasma cells. Ets1 might transcriptionally regulate the expression of key B cell-specific genes that regulate B cell differentiation. I identified genome-wide targets of Ets1 using ChIP-sequencing to show that Ets1 binds near many genes involved in B cell activation and differentiation. I further analyzed Ets1 function by identifying gene expression changes in Ets1 -/- B cells compared to wild-type B cells. I found that Ets1 represses genes are associated with nucleosome organization and activates genes are associated with the immune response. By comparing ChIP-seq and RNA-seq data, I identified only 323 genes that harbor a nearby Ets1 binding site and show altered expression in Ets1 -/- B cells. Among this subset of 323 genes, Ets1 activates genes that are associated with immune function and glycobiology, while it represses genes involved in cell homeostasis. Interestingly, a number of the Ets1-regulated genes are implicated in autoimmune disease and/or plasma cell differentiation, including Ptpn22, Stat4, Prdm1 and Egr1. However, restoring normal expression of these genes individually did not reverse excessive plasma cell formation by Ets1 -/- B cells. This suggests that these genes are not independently responsible for the hyper-responsiveness of Ets1 -/- B cells. I also performed studies to identify the enhancer sequences that regulate the expression of Ets1 in B cells. I first identified seven potential lymphocyte-specific enhancers of mouse Ets1 using epigenetic marks and chromatin accessibility. Three of these sites (Sites 1-3) were lymphocyte-specific, since the epigenetic marks were enriched in B and T cell lines, but not non-lymphoid cells. Generating BAC transgenic mice carrying these seven potential enhancer sites and a GFP marker resulted in reporter gene expression similar to endogenous Ets1 in lymphoid tissue, lymphocytes, and stimulated B cells. Individual sites resulted in weak or no activity in transient transfection, but Site 2 had the best activity in transfected B cells. Overall, my studies have helped define downstream target genes regulated by Ets1 in B cells as well as upstream enhancers that control expression of Ets1 itself. This information may prove important in understanding the function of Ets1 in autoimmune diseases.