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. 2017 Dec 12;7:17377. doi: 10.1038/s41598-017-17407-w

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© The Author(s) 2017

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Regulation of intronic APA after LTP induction. (a) Schematic of intronic APA analysis. Intronic PASs were compared with 3′UTR-PASs. (b) and (c) Left, scatterplot comparing expression change (LTP vs. control) of intronic PASs (x-axis) and 3′UTR PASs (y-axis). Genes with significantly activated intronic PAS usage are shown in blue (Act) and those with significantly repressed intronic PAS usage in red (Rep) (p < 0.05, DEXSeq and relative abundance change >5%). Grey dots represent genes without significant regulation (Nc). Right, bar graph showing the number of genes with activated or repressed intronic APA. (d) Venn diagram comparing genes with CDS-APA regulation at 1 hr post LTP and 3 hr post LTP. Genes correspond to those in (b) and (c). (e) and (f), Box plot showing the log₂ratio (LTP/Ctrl) of genes with intronic PAS activation or intronic PAS repression, 1 hr (e) or 3 hr (f) post LTP induction. Genes with significant intronic APA regulation are those from (b) or (c). P-values (Wilcoxon rank sum test) indicate the difference between groups. (g) Scatterplot comparing 3′UTR APA regulation (x-axis) and intronic APA regulation (y-axis) at 3 hr post LTP induction. Δ relative abundance for 3′UTR APA is based on the two 3′UTR PASs with most reads, as in Fig. 2, and Δ relative abundance for intronic APA is based on all intronic PAS reads vs. all 3′UTR PAS reads. Genes with intronic APA and/or 3′UTR APA change (>5% relative abundance) are highlighted with different colors based on the type of change.