Suggestive evidence for chromosomal localization of non-coding RNA from imprinted LIT1

The non-coding RNA LIT1/KCNQ1OT1, itself the product of an imprinted gene, is involved in cis-limited silencing within an imprinted cluster on human chromosome 11p15.5. Although the locus serves as an imprinting center, the mechanism of transcriptional regulation is not clear. To help understand the function of the LIT1 non-coding RNA, we used fluorescence in situ hybridization (FISH) to examine the sub-cellular localization of LIT1 RNA molecules. LIT1 RNA signals were observed in most of the interphase human lymphoblast and fibroblast cells. The RNA also appeared to accumulate on neighboring regions of chromatin containing the SLC22A18/IMPT1 and CDKN1C/p57KIP2 genes, as shown by high-resolution fiber RNA FISH and modified RNA TRAP (tagging and recovery of associated proteins) methods. These results suggest that LIT1 RNA stably localizes to a specific chromatin region and plays an important role in the transcriptional silencing of the imprinting domain.