Fig. 3: Various pre-mRNA processing factors have distinct impacts on full-length and cleaved readthrough transcripts.

a Schematic shows the independent analysis for full-length readthrough transcripts and 3’ cleavage products. Full-length readthrough transcripts are shown in blue, and 3’ cleavage products are shown in orange. b Example with RBCS1A (AT1G67090). Displays various transcription intermediates, including full-length readthrough transcripts, 5’ cleavage products, 3’ cleavage products, and poly(A) transcripts in WT and mutants. Box plots show the distribution of distances from the 3’ end of reads to the gene’s poly(A) site for full-length readthrough transcripts (blue) and 3’ cleavage products (orange). The box plots display the median (central line), second to third quartiles (box), and whiskers extending to the minima and maxima. Outliers are indicated as individual points. The significance of the change in readthrough between each mutant and WT was assessed using a two-sided Mann-Whitney U test. For full-length transcripts, the resulting p-values were 1.5 × 10⁻⁴ (fpa) and 0.90 (xrn3); for 3’ cleavage products, the p-values were 0.44 (fpa) and 1.5 × 10⁻¹² (xrn3). Source data are provided as a Source Data file. c Meta-profile of 3’ end distribution. Presents the 3’ end distribution of all readthrough transcripts, full-length readthrough transcripts, and 3’ cleavage products at downstream of the poly(A) site in mutants and corresponding WT. Position 0 on the x-axis represents the poly(A) site. The WT are shown in blue, and mutants in red. The significance of the difference between WT and mutant distributions was determined by a two-sided K-S test. Source data are provided as a Source Data file.