PAS conservation impacts gene expression and APA regulation. (A) Relative abundance of APA isoform versus PAS conservation levels. Relative abundance of APA isoform is based on all isoforms of a gene. (B) Isoform expression breadth versus PAS conservation level. Isoform expression breadth is based on PSE normalized to the maximum PSE of all isoforms of the gene. (C) Median Shannon index for APA isoforms of three types of genes, including genes with no conserved PAS, one conserved PAS, and multiple conserved PASs. Data for testis, heart, and brain are shown. For A–C: (***) P < 0.001 (K-S test). (D) Comparison of gene expression levels between mouse and rat for three types of genes. Gene types and tissue types are as in C. (E) Correlation of APA profiles between mouse and rat for four types of genes. As illustrated, the four types of gene are genes with (1) no conserved APA sites, (2) only proximal PAS conserved, (3) only distal PAS conserved, and (4) both proximal and distal PASs conserved. APA profiles are based on testis versus heart or brain versus heart. (F) As in D, except that data comparing two mouse strains, C57BL/6J (C57) and FVB/JN (FVB), are shown. (G) As in E, except that data comparing two mouse strains (C57 versus FVB) are shown.
