Collapse of the hepatic gene regulatory network in the absence of FoxA factors

FoxA transcription factors are critical for liver development through their pioneering activity, which initiates a highly complex network thought to become resistant to the loss of any individual hepatic transcription factor via mutual redundancy. To investigate the dispensability of FoxA factors for this regulatory network, we ablated all FoxA genes in the adult liver. Remarkably, loss of FoxA caused a rapid and massive reduction in the expression of key liver genes back to the low levels of the fetal prehepatic endoderm stage, leading to necrosis and lethality within days. Mechanistically, we found FoxA proteins to be required for maintaining chromatin activity, nucleosome positioning and binding by other hepatic transcription factors. Thus, the hepatic gene regulatory network is dependent on the FoxA proteins throughout life. We depleted all three FoxA genes in 8 week-old mice by injecting adeno-associated virus 8 (AAV8) carrying the gene for Cre recombinase under the control of the hepatocyte-specific thyroid-binding globulin (Tbg) promoter to adult FoxA1L/L/FoxA2 L/L/FoxA3-/- mice and validated FoxA depletion (FoxA triple null). As controls we injected the same transgenes with AAV expressing GFP. FoxA triple nulls were compared also to FoxA1/A2 lox animals, FoxA1/A2 cre alfp and to hepatoblast and new-born RNA-seq data. In addition, RNA-seq was also performed on HNF4a null livers depleted in adult livers.