Fig. 3

Examples of lengthening events detected by QAPA based on updated 3′ UTR isoform annotations. Four examples of 3′ UTR lengthening: a Ssh1, b Sipa1l1, c Hspa4, and d Mecp2. In each example, RNA-seq read coverage of each 3′ UTR at each DIV stage (rows) is displayed (using the first replicate of each stage as a representative example). A schematic from the UCSC Genome Browser (mm10) [82] for each 3′ UTR is shown below. Four annotation tracks are shown. From top to bottom, these tracks are: QAPA-annotated 3′ UTR models, PolyAsite [14] annotations with score ≥ 3, GENCODE [33] gene annotation models, and GENCODE Poly(A) track annotations (except for Sipa1l1, in which no supporting GENCODE Poly(A) data were found). Ssh1, Sipal1l, and Mecp2 are shown in the reverse strand orientation. For Mecp2, although an intermediate GENCODE poly(A) site is present, there was insufficient support from PolyAsite annotations and thus it was not used to define a 3′ UTR model (see “Methods”). The horizontal boxplots to the right show the PPAU values across replicates in each corresponding DIV stage to the row