The role of the pioneer transcription factor PU.1
The lineage-specific transcription factor PU.1 is bound to the enhancers of many pro-inflammatory cytokines, including those of IL12B and IL1A, in resting macrophages, and our studies show that PU.1 binding keeps these enhancers accessible and associated with intermediate levels of nucleosomes, which allows their induction in response to LPS (Tagore et al., 2015). For these studies we used a tamoxifen inducible cell-line that was derived from a PU.1-/- mouse and contains a PU.1-estrogen receptor (PUER) fusion (Walsh et al., 2002). PU.1 is essential, but hematopoietic progenitors can be derived from fetal livers, and reintroduction of PUER allows differentiation of these cells into macrophage-like cells in the presence of tamoxifen and IL3. We demonstrated that in this cell-line a fraction of macrophage-specific enhancers is able to bind PUER in the presence of tamoxifen, while another is not. PUER binding leads to decreased nucleosome occupancy at PU.1-sites and allows induction of the associated genes in the presence of LPS.
In contrast, enhancers that fail to bind PUER, become associated with the polycomb repression complex PRC2 as cells differentiate and cannot be induced in response to LPS in mature cells. PRC2 binding leads to wrapping of the whole gene locus into heterochromatin, which is associated with increased levels of nucleosome occupancy and H3K27me3, a mark of facultative heterochromatin placed by PRC2. We hypothesize that one role of lineage-specific or pioneer transcription factors is to prevent binding of PRC2 to cell-type specific genes and to keep chromatin at their regulatory sites accessible to the transcriptional machinery.