Fat cadherin cleavage releases a transcriptionally active nuclear fragment to regulate target gene expression

The conserved atypical cadherin fat (ft) controls cellular processes such as growth, planar cell polarity, and mitochondrial function, in organisms ranging from fruit flies to mammals. Working at the apical-junctional plasma membrane the intracellular domain of the Ft protein, FtICD, binds to and regulates components of the Hippo and PCP pathways. Unexpectedly, we show that FtICD is present in the nucleus in cultured cells as well as in embryonic and larval tissues, and identify nuclear localization and nuclear export signals in FtICD required for this localization. We show that membrane-bound FtICD is cleaved and enters nuclei in vivo. Using endogenously tagged Ft as well as overexpressed FtICD we conducted ChIP-seq experiments and identified putative Ft targets including genes involved in signaling pathways, chromatin organization, pattern formation, and neural development. RNAseq demonstrates that some of these genes are differentially regulated in ft mutants. We observe strong correlations of Ft binding regions with peaks for other factors such as DREF and BEAF-32, as well as the Hpo pathway components Yorkie (Yki) and Scalloped (Sd), suggesting that Ft may act in conjunction with these factors to regulate gene expression. Supporting this hypothesis, we found that Ft can physically interact with both Yki and Sd in co-immunoprecipitation experiments in S2 cells. We propose that the modulation of Hippo pathway activity constitutes one of the nuclear functions of Ft, complementing its established function as an upstream regulator of Hippo signaling.