Fig. 1

Quantification of Pol II pausing at gene 3’ end. a Metagene plot showing Pol II profile across protein-coding genes based on Ser2P Pol II pNET-seq data obtained with 3E10 antibody. Only the expressed protein-coding genes (TPM ≥ 1 based on the Ser2P Pol II pNET-seq data) are used for analysis. TSS, transcription start site. PAS, polyadenylation site. b Diagram showing the definition of the 3’ end pause index (3’PI). c Metagene profile of Ser2P Pol II at paused, non-paused, and inactive genes. Paused and non-paused genes were defined by 3’PI, and inactive genes were determined based on pNET-seq data (TPM < 1 at the gene region). d Scatter plot indicating the relationship between 3’PI and the distance to downstream gene. Only 3’ paused genes that does not overlap with other genes are used for this analysis. e Scatter plot showing the relationship between termination window size and the distance from 3’ end peak to PAS. f Scatter plot showing the relationship between 3’PI and the termination window size. For e and f, only genes with known termination window size and also 3’PI are used for the analysis. For d to f, the Spearman correlation coefficient is shown above the plot. The orange line indicates the trendline fitted based on the least squares method