Fig. 5

Patterns of retroelement RNA localization change during zebrafish embryo development. Retroelement transcript localization during zebrafish development was studied by analyzing RNA-sequencing data from libraries prepared by rRNA depletion (RiboZero) from nuclear (Nuc) and cytoplasmic (Cyt) fractions of 64 cell, 256 cell, 1000 cell, Dome and Shield stage zebrafish embryos. a Retroelement RNAs in zebrafish are relatively equally distributed in the nucleus and cytoplasm in 64 cell and 256 cell stages but are primarily nuclear localized starting at the 1000 cell stage (MWU, ns = p > 0.05, **** = p < 0.0001). RNA from single-copy protein coding genes (scPCGs) do not show preferential localization to any subcellular compartment during any stage of embryogenesis. The graphs show log₂(Nuc/Cyt) ratios plotted for all scPCGs and individual, annotated retroelement types (Retro) which had normalized read count > 20 for each sample. 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 line at the center of the box. Transcripts with log₂(Nuc/Cyt) values greater than 0 are considered nuclear and those less than 0 are considered cytoplasmic. Number of retroelement types and scPCGs analyzed per sample are included in Additional File 9C. b Schematic diagram showing the developmental stages of zebrafish embryos included in this analysis and the overlap of maternal to zygotic transition (MZT) and zygotic genome activation (ZGA) with nuclear localization of retroelement RNAs (hpf = hours post fertilization)