Fig. 2

Transcripts from different classes of retroelements are enriched in the nucleus in human cell lines. RNA-sequencing data from nuclear (Nuc) and cytoplasmic (Cyt) fractions of A549, HUVEC, IMR90, K562, MCF7 and SK-N-SH cells was analyzed to study localization of retroelement RNAs. In (a) A549, (b) HUVEC, (c) IMR90, (d) K562, (e) MCF7 and (f) SK-N-SH cell lines, all classes of retroelements are highly enriched in the nucleus (heatmaps on the left for each pair) compared to single-copy protein coding genes (scPCGs) (heatmaps on the right for each pair). Each row in the heatmaps presents the log₂ ratio of nuclear to cytoplasmic expression of a specific type of retroelement or a unique scPCG. Please note that ratios were calculated from consolidated signals summarizing the expression of individual copies of each element type. In all heatmaps, log₂(Nuc/Cyt) values greater than 0 are represented as green and indicate nuclear localization, log₂(Nuc/Cyt) values less than 0 are represented as red and indicate cytoplasmic localization whereas log₂(Nuc/Cyt) values equal to 0 are represented as black and indicate no preferential localization. Retroelement and scPCG expression values were normalized to spike-in count (see Methods). Number of rows in each heatmap (n) is indicated. Please note that the group of scPCGs and individual retroelement types analyzed for each cell line may differ (see Methods for inclusion criteria)