The development of complex multicellular organisms involves hierarchically organized progenitor cells that ultimately give rise to terminally differentiated cell types with specialized functions. Cell fates are specified by lineage-determining transcription factors whose expression is often not limited to a single cell type (Tronche and Yaniv, 1992). Comparisons of the genome-wide binding patterns of different transcription factors in a variety of species and cell types have generated two major insights regarding transcription factor binding patterns: 1. Different factors in the same cell type tend to co-localize on a genome-wide scale (Chen et al., 2008; MacArthur et al., 2009). 2. The same factor in different cell types or at different stages of development exhibits different genome-wide binding patterns (Lupien et al., 2008; Odom et al., 2004; Sandmann et al., 2006).
