Fig. 4

Retroelement RNAs localize to the nucleus in vivo. RNA-sequencing data from libraries prepared by rRNA depletion (RiboZero) from nuclear (Nuc) and cytoplasmic (Cyt) fractions of human brain tissue was analyzed to study retroelement RNA localization in vivo. Retroelement RNAs are significantly nuclear localized (MWU, p < 0.0001) unlike single-copy protein coding genes (scPCGs) in a Pre-natal prefrontal cortex (Br5339, Br5340, Br5341), b Adult dorsolateral prefrontal cortex (Br2046, Br2074) c Fetal frontal cortex (Sample 1–3), d Fetal cerebellum (Sample 1–3) and e Adult frontal cortex tissue (Sample 1–6). For each brain sample, the graphs in (a-e) plot log₂(Nuc/Cyt) ratios plotted for all scPCGs and individual, annotated retroelement types (Retro) which had normalized read count > 10. Please note that ratios were calculated from consolidated signals summarizing expression of individual copies of each element type. The boundaries of the boxes denote 25th and 75th percentile and the whiskers mark the minimum and maximum values. The median log₂(Nuc/Cyt) ratios are represented by the solid line at the center of the box. RNAs with log₂(Nuc/Cyt) values greater than and less than 0 are considered nuclear and cytoplasmic transcripts respectively. Number of retroelements and scPCGs analyzed per sample are included in Additional File 9A and 9B