Tissue-specific restriction of transposon-derived regulatory elements safeguards cell-type identity

Transposable elements (TEs) reshape mammalian cis-regulatory landscapes, but the mechanisms controlling their context-specific activity remain unclear. KRAB zinc finger proteins (KZFPs) typically repress TE-derived regulatory activity via TRIM28-mediated H3K9me3 deposition. We expand this paradigm by uncovering non-canonical KZFP-TE relationships. Through comprehensive epigenomic mapping of KZFP-bound TEs, we show that ancient mammalian L2/MIR elements' regulatory activity is delineated by KZFP binding despite low H3K9me3 enrichment. We dissect this relationship by focusing on ZNF436, a non-canonical KZFP highly expressed in the developing human heart. We find that ZNF436 preserves cardiomyocyte function by promoting cardiac gene expression while restricting alternative lineage programs. Mechanistically, ZNF436 associates with the SWI/SNF remodeling complex to limit the accessibility of L2/MIR-derived CREs, otherwise active in non-cardiac tissues. Our findings reveal a TRIM28-independent role for KZFPs in shaping cell-type-specific regulatory landscapes and emphasize the importance of repressing alternative lineage programs while activating lineage-specific ones to safeguard cell identity.