Fig. 3

Evolutionarily young and old retroelements are enriched in the nucleus. a Transcripts from evolutionarily young and retrotransposition competent L1-HS are significantly nuclear enriched in multiple cell lines. (A’-A”’) Older LINE-1 subfamilies L1 PA and L1 PB found across primates and L1 MA found across mammals produce transcripts that are also significantly nuclear localized in all cell lines tested. (B-B″) Transcripts from elements in the three Alu subfamilies, AluY, AluS and AluJ, are present at significantly higher levels in the nucleus across all cell lines except in IMR90. (C-C″) Transcripts from elements belonging to the ERVK, ERVL and ERV1 families are significantly enriched in the nucleus as compared to the cytoplasm in all cell lines except in IMR90. For graphs in (A-C″), data points represent normalized read counts from two biological replicates and error bars indicate standard deviation. (ns = FDR > 0.05, * = FDR < 0.05, ** = FDR < 0.01, *** = FDR < 0.001, **** = FDR < 0.0001). FDR values reported here were direct outputs of EdgeR differential gene expression analysis