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Description: We examined the subcellular location of a number of well-known lncRNAs (Fig. 8D). Unsurprisingly, the X-chromosome inactivating transcript XIST was extremely highly enriched in the nucleus for all cells we examined (with a maximum enrichment of 273-fold in the nucleus of GM12878 cells) (Fig. 8D). Other regulatory lncRNAs such as GAS5, LINC00568 (also known as ncRNA-a1), CYP4A22-AS1 (also known as ncRNA-a3), MIAT, and MEG3 were nuclear enriched in at least two different cell types, consistent with their reported roles in gene regulation. Other transcripts, including the bifunctional transcript SRA1, which acts as both a regulatory RNA and a protein-coding sequence, have more variable subcellular location depending on cell type. As reported previously, the H19 transcript is consistently enriched in the cytoplasm, especially when comparing with the chromatin fraction (cytoplasmic/chromatin enrichment 167-fold).
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