Fig. 6

3’UTR shortening eliminates TEs. a TE contents in 5’UTR, CDS and 3’UTR of all genes. aUTR, alternative 3’UTR; cUTR, common 3’UTR; sUTR, single 3’UTR (gene without APA). The fraction of mRNA sequence related to TEs was based on the number of nucleotides of the TEs annotated by the RepeatMasker track of UCSC Genome Browser (mm9). b Change of TE-containing mRNAs in spermatogenesis. The fraction of the transcripts containing 3’UTR TEs at each time point is plotted. c Gene expression changes for genes with or without 3’UTR TEs. Only genes with a single 3’UTR (sUTR) were used for this analysis. Expression was based on the 3’READS data. P values (K–S test) indicating difference between the two gene groups are shown. d Expression changes of four types of genes. A type 1 gene has 3’UTR shortened and contains TEs only in aUTR; a type 2 gene also has 3’UTR shortened but contains TEs in cUTR only; a type 3 gene has 3’UTR unchanged and contains TEs in aUTR; a type 4 gene has a single 3’UTR (no APA) and there are TEs in the 3’UTR. All APA regulation was based on the 4w vs. 2w comparison. Bottom, gene expression was analyzed using 3’READS data (4w vs. 2w, left), or CDS reads of RNA-seq data (28 dpp vs. 15 dpp, right). P values (K–S test) indicating difference between type 1 genes and others are indicated on the top. e Gene expression difference in Miwi−/− vs. Miwi+/− at the early round spermatid stage for the four gene types described in (d) except that the APA analysis was based on 3w vs. 1w comparison. Gene expression was based on RNA-seq reads mapped to CDS. The type 1 gene set was compared with other types using the K–S test. P values are all significant (<1 × 10⁻³)