LAUSR

BACKGROUND & AIMS Hepatoblastoma (HB) is the most common primary liver malignancy in childhood, and lacks targeted therapeutic options. We previously engineered the first Yes Associated Protein 1 (YAP1S127A )-inducible mouse model of HB, demonstrating tumor regression and re-differentiation after YAP1 withdrawal through genome-wide enhancer modulation. Probing accessibility, transcription, and YAP1 binding at regulatory elements in HB tumors may provide more insight into YAP1-driven tumorigenesis and expose exploitable vulnerabilities in HB. APPROACH & RESULTS Using a multi-omics approach, we integrated high-throughput transcriome and chromatin profiling of our murine HB model to identify dynamic activity at candidate cis-regulatory elements (cCREs). We observed that 1,301 of 305,596 cCREs exhibit "Tumor-modified" (TM) accessibility in HB. We mapped 241 TM enhancers to corresponding genes using accessibility and H3K27Ac profiles. Anti-YAP1 Cleavage under targets and tagmentation (CUT&Tag) in tumors revealed 66 YAP1-bound TM cCRE/gene pairs, 31 of which decrease expression after YAP1 withdrawal. We validated the YAP1-dependent expression of a putative YAP1 target, Jun Dimerization Protein 2 (JDP2), in human HB cell lines using YAP1 and LATS1/2 siRNA knockdown. We also confirmed YAP1-induced activity of the Jdp2 TM enhancer in vitro, and discovered an analogous human enhancer in silico. Finally, we used transcription factor (TF) footprinting to identify putative YAP1 co-factors and characterize HB-specific TF activity, genome-wide. CONCLUSIONS Our chromatin profiling techniques define the regulatory frameworks underlying HB and identify novel, YAP1-regulated gene/enhancer pairs. JDP2 is an extensively validated target with YAP1-dependent expression in human HB cell lines and hepatic malignancies.