Imprinted gene expression at theDlk1-Dio3cluster is controlled by both maternal and paternalIG-DMRs in a tissue-specific fashion

Imprinting at theDlk1-Dio3cluster is controlled by theIG-DMR, an imprinting control region differentially methylated between maternal and paternal chromosomes. The maternalIG-DMRis essential for imprinting control, functioning as acisenhancer element. Meanwhile, DNA methylation at the paternalIG-DMRis thought to prevent enhancer activity. To explore whether suppression of enhancer activity at the methylatedIG-DMRrequires the transcriptional repressor TRIM28, we analyzedTrim28chatwoembryos and performed epistatic experiments withIG-DMRdeletion mutants. We found that while TRIM28 regulates the enhancer properties of the paternalIG-DMR, it also controls imprinting through other mechanisms. Additionally, we found that the paternalIG-DMR, previously deemed dispensable for imprinting, is required in certain tissues, demonstrating that imprinting is regulated in a tissue-specific manner. Using PRO-seq to analyze nascent transcription, we identified 30 novel transcribed regulatory elements, including 23 that are tissue-specific. These results demonstrate that different tissues have a distinctive regulatory landscape at theDlk1-Dio3cluster and provide insight into potential mechanisms of tissue-specific imprinting control. Together, our findings challenge the premise thatDlk1-Dio3imprinting is regulated through a single mechanism and demonstrate that different tissues use distinct strategies to accomplish imprinted gene expression.