(A) Scheme of five alternative TSSs (ATSSs) generating isoforms with alternative 5′ UTR regions (Siegel et al., 2019; Sant et al., 2010; Kröber et al., 2002; Zenz et al., 2010; Herling et al., 2006) and modification of the N′ termini for example, new chimeric CDS (Kröber et al., 2002) and N′-terminal truncation (Herling et al., 2006). (B) The frequency and the percentage of uni-TSS genes and multi-TSS genes including only TSS clusters that constitute over 10% of total gene expression. (C) Frequencies of alternative TSSs that were upregulated (orange) and downregulated (gray) in Eµ-Tcl1, grouped by gene-structure locations. (D) Gene track showing differential TSS usage (DTU) in Pdcd1lg2 (PD-L2) in Eµ-Tcl1 and WT mice. Canonical promoter (P3) and intra-genic promoter (P4, located just upstrem to the last CDS of PD-L2) are up- and downregulated in Eµ-Tcl1, respecively. Both, located on the plus strand (blue). Bellow, is a scheme illustrating the P4-induced truncation of PD-L2 lossing most of its functional domains. (E) Chd1 protein truncation in Eµ-Tcl1 resulted by induction of cryptic promoter. In the upper track, two promoters on the plus strand (blue ticks) presented along to a partial gene-structure scheme. While the canonical promoter located upstream to the annotated 5′ UTR is similarly expressed in Eµ-Tcl1 and WT, an Eµ-Tcl1-specific induction of an intra-genic alternative TSS located in the 16th intron resulting in N′ terminus truncation of Chd1 lacking several active domains as illustrated below. (F)Fbxo5 5′ UTR shorthening resulted by DTU in Eµ-Tcl1. On the upper track, two alternative promoters located on the minus strand shown as short red bars with indicator tick of TSS. Coverage peaks in the two lower tracks (WT and Eµ-Tcl1) showing differential expression of the two promoters where the nearest alternative TSS to the ORF is upregulated in Eµ-Tcl1. (G) Dot plot of ORF-retaining alternative TSS (ATSS) in peach and ORF-truncating intra-genic alternative TSS (turquoise) presenting expression (log2 TPM) against ATSS log FC evaluating the degree of promoter shifting (DTU). Positive and negative ATSS log FCs refer to Eµ-Tcl1 up- and downregulated ATSS, respectively. Dot sizes correspond to the FDR statistical significance of the DTU analysis.