Dear Editor,
Members of Foxa transcription factor family, namely Foxa1, Foxa2, and Foxa3, play crucial roles in guiding hepatic differentiation and hepatic homeostatic maintenance (Le Lay and Kaestner, 2010; Zaret and Carroll, 2011). They act at several critical time points to regulate hepatic differentiation as early as embryonic definitive endoderm (DE) stage (Gualdi et al., 1996). Combination of both Foxa1 and Foxa2 was required for the formation of foregut DE cells and the further liver bud differentiation during embryonic hepatic development (Lee et al., 2005). Foxa proteins can bind the condensed chromatin of Alb1 enhancer and induce local chromatin relaxation prior to the initiation of transcription (Cirillo et al., 2002). The binding of Foxa on Alb1 enhancer before transcription activation determined the developmental competence by pre-marking the chromatin. Thus, Foxa proteins were proposed to behave as pioneer factors in DE to prime hepatic genes prior to their actual transcription activation in nascent liver (Zaret and Carroll, 2011).
Although Foxa2 binding profiles were extensively mapped in adult liver cells using ChIP-sequencing (ChIP-seq) technology (Wederell et al., 2008; Tuteja et al., 2009; Wallerman et al., 2009; Hoffman et al., 2010), binding profile of Foxa proteins at the embryonic DE stage has not been obtained yet. Functions of Foxa family have been known with significant differences between embryonic hepatic developing stage and post-developing stage (Cirillo et al., 2002; Li et al., 2011). Therefore, a systematic analysis of Foxa binding at the DE stage will help elucidate its functions at early hepatogenesis stage.
We first established a protocol to efficiently differentiate ES cells to DE cells and then early hepatic cells. DE cell fate commitment was confirmed by qPCR and FACS assays and in vitro hepatic differentiation analysis (Supplementary Figure S1).
The obtained DE cells were used …