Extended Data Fig. 9: The distribution and characterization of U1 sites in the human genome.
From: Transcription directionality is licensed by Integrator at active human promoters
a. Density of predicted 5’ U1 splice sites within a 1-kb region flanking gene TSS. Strong and medium sites are defined in the Methods. b. Definition of U1 sites and distance with TSS. The red bar shows the predicted U1 sites. The green box shows the analyzed region. c. Quantitative boxplots of PROMPTs categorized by SOM using predicted U1 site parameters (details in Methods). Left, reads count from the CTRL sample. Right, PROMPT fold change after INTS11 depletion. P values were calculated by two-sided Mann-Whitney test. See Extended Data Fig. 1 for description of boxplots. d. IGV examples of an enhancer locus with a low U1 score together with ChromRNA-seq, TT-seq, RNAPII ChIP-seq, and predicted U1 site results. e. Schematic diagram of the endogenous 3 x U1 sequence in the CTTN gene PROMPT region. f. The sequence of the artificial 3xU1 site sequence. Predicted U1 sites are shown as green boxes below. g. The sequence of the first predicted U1 site sequence in the CTTN gene PROMPT region. The sequence was removed by homologous recombination. h. Boxplots representing the change in transcription levels of PROMPTs (left) and pre-mRNA (right) after blocking U1 snRNA using fully modified ASO. P values were calculated by two-sided Mann-Whitney test. See Extended Data Fig. 1 for description of boxplots.
