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. 2021 Nov;31(11):2095–2106. doi: 10.1101/gr.271627.120

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© 2021 Zhao et al.; Published by Cold Spring Harbor Laboratory Press

This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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Figure 5. — IPAFinder reveals that intronic polyadenylation can be influenced by factors related to splicing and m⁶A modification. (A,C,E,G) Scatterplot of IPUI values reflecting the relative IpA usage in cells with knockdown (KD) of U2AF1 (A, in HFF cell), U2AF2 (C, in HFF cell), YTHDC1 (E, in HeLa cell), or METTL3 (G, in HEK293T cell). Red and blue dots represent genes with increased and decreased IpA usage upon knockdown of corresponding genes. (B,D,F,H) Representative RNA-seq density plots for genes with significantly increased IpA usage upon knockdown of U2AF1 (B), U2AF2 (D), YTHDC1 (F), or METTL3 (H). Each knockdown condition has two IpA examples: the composite terminal exon IpA (top) and the skipped terminal exon IpA (bottom).