Fig. 4: Analysis of subcellular localization of TE-alone loci.
From: Zygotic activation of transposable elements during zebrafish early embryogenesis
a A chart to illustrate how to calculate the relative N/C proportion for TE-alone, TE-gene and gene transcripts. TN/C, TgN/C and GN/C are total TPMs for TE-alone, TE-gene and gene transcripts in the nucleus and cytoplasm, respectively. b Comparison of relative N/C proportion among TE-alone, TE-gene and gene at indicated stages. The red dash line indicates the relative N/C proportion as 1. The outliers and data points with the relative N/C proportion >20 are not shown. The total number of transcripts at each stage is 9302, 10,455, 10,207 (Gene) and 9503, 11,437 and 11,037 (TE-gene). The number of TE subfamilies is 45, 147 and 180. c The linear relationship between relative N/C proportion and fractions of TE sequences in TE-gene chimeric transcripts at indicated stages. d Comparison of relative N/C proportion among TE subfamilies at indicated stages. Wilcoxon rank sum test, two-sided is applied to statistical significance. The number of DNA transposon, LINE and LTR subfamilies is 11, 9 and 25; 32, 24 and 91; and 38, 34 and 108 for the 1k-cell, dome and shield stages. e–g FISH experiments showing the subcellular distribution of transcripts from the three selected TE subfamilies at indicated stages (n = 3 independent experiments; 30 embryos were used in total). Green, β-Catenin staining for cell membrane; Blue, DAPI staining for nucleus; Red, specific probes against indicated TE-alone transcripts. Scale bar = 10 μm.
