Oncogenic lncRNA transgene transcription modulates epigenetic memory at a naive chromosomal locus.

Maintaining genome integrity is crucial for the proper functioning and development of organisms. One intriguing aspect of genome integrity is the formation and function of neocentromeres at non-centromeric sites. CENP-A, a centromere-specific protein, is essential for centromere identification and function. However, in many cancers, CENP-A is often found to be ectopically misplaced when overexpressed. Moreover, CENP-A deposition at the centromere depends on the transcription of centromeric non-coding RNAs. Consequently, ectopic CENP-A is found at transcriptionally active and frequent breakpoint regions. To further explore ectopic CENP-A localization, we previously engineered a stable ectopic CENP-A site on a naive chromosome by overexpressing a non-centromeric oncogenic lncRNA, PCAT2, which was capable of recruiting CENP-A to its transcription site. In this work, we tracked cells carrying this stable transgene to understand the longevity of the induced ectopic CENP-A site at the chromosome that harbors it. Our findings revealed that the induced epigenetic memory was eventually lost due to the suppression of the transgene through competing epigenetic silencing mechanisms. This epigenetic restoration naturally reversed the ectopic CENP-A level to its previous levels at the engineered site. These data suggest that cells may have evolved failsafe mechanisms to prevent neocentromere formation at ectopic sites by suppressing transcription, unless otherwise favored by selection involving multiple components.