KCNQOT1 ChIRP seq and perturbation epigentic profiles [ChIP-seq]

Transposon (de)repression and heterochromatin reorganization are dynamically regulated during cell fate determination and are hallmarks of cellular senescence. However, whether they are sequence specifically regulated remains unknown. Here, we uncover the KCNQ1OT1 lncRNA, by sequence-specific Hoogsteen base-pairing with double-stranded genomic DNA via its repeat-rich region and binding to heterochromatin protein HP1⍺, guides, induces and maintains epigenetic silencing at specific repetitive DNA elements. Repressing KCNQ1OT1 or deleting its repeat-rich region reduces DNA methylation and H3K9me3 on KCNQ1OT1 targeted transponsons. Engineering a fusion KCNQ1OT1 with an ectopically targeting guiding triplex sequence induces de novo DNA methylation at the target site. Phenotypically, repressing KCNQ1OT1 induces senescence associated heterochromatin foci, transposon activation and retrotransposition, and cellular senescence, demonstrating an essential role of KCNQ1OT1 to safeguard against genome instability and senescence. H3K9me3 modification status was analyzed by ChIP-seq in HEK293TWT, EV and KCNQ1OT1_K KD cells.