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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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Analysis of APA in LTP. (a) Experimental design. RNAs from chemical LTP (cLTP)-induced and time-matched control hippocampal slices were subjected to 3′READS+ analysis to examine APA, or RNA-seq for gene expression. (b) Distribution of the A[A/U]UAA element in identified poly(A) sites (PASs). Percentage of PASs associated with either AAUAAA, AUUAAA, other variants of A[A/U]UAAA, or not associated with any A[A/U]UAAA element are shown for each sample group. (c) Number of PASs identified per gene. Genes with only one PAS have the highest frequency and the majority of genes displayed APA in the hippocampal samples analyzed. (d) Diagram showing 3′UTR APA (top) and intronic APA (bottom). 3′UTR APA isoforms have alternative 3′ UTRs resulting from the choice of different PASs in the 3′UTR. Two PASs are shown, i.e., proximal PAS and distal PAS. Intronic APA isoforms have different 3′UTRs as well as coding sequences (CDS). (e) Distribution of PASs in different regions of the mRNA: 3′UTR (in 3′-most exon only) vs. upstream intron. Change of PAS distribution during LTP is observed 3 hr post LTP induction. Number of PAS in each region is specified in each bar. P-values (Binomial test) indicate difference in fractions of 3′UTR PASs and intronic PASs in LTP vs. control samples.