FOXO3 Selectively Amplifies Enhancer Activity to Establish Target Gene Regulation

Forkhead box O (FOXO) transcription factors regulate diverse cellular processes, affecting tumorigenesis, metabolism, stem cell maintenance, and lifespan. We show that FOXO3 transcription regulation mainly proceeds through the most active subset of enhancers. In addition to the general distinction between “open” and “closed” chromatin, we show that the level of activity marks (H3K27ac, RNAPII, enhancer RNAs) of these open chromatin regions prior to FOXO3 activation largely determines FOXO3 DNA binding. Consequently, FOXO3 amplifies the levels of these activity marks and their absolute rather than relative changes associate best with FOXO3 target gene regulation. The importance of preexisting chromatin state in directing FOXO3 gene regulation, as shown here, provides a mechanism whereby FOXO3 can regulate cell-specific homeostasis. Genetic variation is reported to affect these chromatin signatures in a quantitative manner, and, in agreement, we observe a correlation between cancer-associated genetic variations and the amplitude of FOXO3 enhancer binding. [Display omitted] •FOXO3 preferentially binds the most active subset of enhancers•FOXO3 amplifies initial levels of H3K27ac, RNAPII, and enhancer RNA transcription•Absolute changes in enhancers’ activity marks correlate best with gene induction•Transcriptional regulation occurs mainly through the most active subset of enhancers FOXO transcriptional output is highly variable and context dependent, affecting tumorigenesis, metabolism, stem cell maintenance, homeostasis, and lifespan. To elucidate the underlying mechanism of this variability, Burgering and colleagues use integrative analysis by combining genome-wide enhancer profiling and FOXO3-induced gene expression changes. This reveals that, besides the discrimination between “open” and “closed” chromatin, the preexisting level of enhancer activity is a major determinant of FOXO3-DNA binding and transcriptional output. This provides an explanation for the diversity of FOXO functions.