FoxA pioneer factor: Genetic competence, and epigenetic restriction

The transcription factor FoxA is necessary for endoderm development and endoderm differentiation into liver and other tissues. Previously, we showed that FoxA sites are occupied in the albumin gene enhancer in undifferentiated endoderm cells, prior to hepatic specification and albumin expression. Loss of FoxA occupancy correlated with a loss of the ability to induce albumin expression; we thus hypothesized FoxA occupancy on chromatin is an initiator of competence for gene activation. Here we show ectopic expression of FoxA in 3T3 cells, where it is not endogenously expressed, confers competence to induce a subset of silent genes in response to signaling (Chapter 4). To better understand how FoxA occupancy of silent genes may endow competence for expression in differentiated cells, we performed genomic location analysis of FoxA in the adult liver. By partitioning our analysis of FoxA occupancy at active versus silent genes, we found that FoxA can mark silent genes, such as the intestinal transcription factor Cdx2, at regulatory elements that are repressed by other factors (Chapter 2). Furthermore, our in vivo genome location studies demonstrate that FoxA does not engage most of its potential binding sites in the genome. We were interested to determine what histone modifications enable or inhibit FoxA binding to chromatin. At genes in adult liver and liver cell lines we found a strong inverse correlation between FoxA binding and the presence of a mark of repressed chromatin, H3K27me3. Furthermore, comparing ES cells and their decedents differentiated to endoderm and liver progenitor cells, we see a switch from an H3K27me3-positive state to a negative state precisely when FoxA engages target chromatin (Chapter 3). Together our results suggest that FoxA-mediated genetic competence can be restricted by locally binding repressors and epigenetic restriction of chromatin occupancy. In addition, we observe another forkhead transcription factor, FoxD3, may be able to substitute for FoxA activity in a population of liver progenitor cells and contribute to their differentiation potential (Appendix). Through studying competence for silent gene activation, we gain a deeper understanding of the cellular mechanisms controlling differentiation potential and the stability of cellular identity