Zinc finger protein SALL4 functions through an AT-rich motif to regulate heterochromatin formation

The zinc finger transcription factor SALL4 is highly expressed in embryonic stem cells, down-regulated in most adult tissues, but reactivated in many aggressive cancers. This unique expression pattern makes SALL4 an attractive target for designing therapeutic strategies. However, whether SALL4 binds DNA directly to regulate gene expression is unclear and many of its targets in cancer cells remain elusive. Here, through an unbiased screen and Cleavage Under Targets and Release Using Nuclease (CUT&RUN) experiments, we identified and validated the DNA binding domain of SALL4 and its consensus binding sequence. Combined with RNA-seq analyses after SALL4 knockdown, we discovered hundreds of SALL4 target genes that it directly regulates in aggressive liver cancer cells. Our genomic studies uncovered a novel epigenetic regulatory mechanism by which SALL4 promotes heterochromatin formation in cancer cells via repressing genes that encode a family of histone 3 lysine 9-specific demethylases (KDMs). Taken together, these results elucidated the mechanism of SALL4 DNA binding and suggest a previously unknown mechanism for its regulation of chromatin landscape of cancer cells, thus present novel pathways and molecules to target in SALL4-dependent tumors.