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. 2015 Mar;25(3):368–380. doi: 10.1101/gr.180802.114

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© 2015 Watanabe et al.; Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it 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 4. — Retrotransposon sequences are enriched in the up-regulated mRNAs and lncRNAs. (A) Most piRNA-complementary sequences were observed within the 3′ UTR. The average number (RPM) of antisense piRNA matches at each position was calculated using a moving window of 100 bases (step size = 100 bases). (TSS) Transcription start site. (B) Many of the piRNA-complementary sequences in mRNAs were SINE sequences. Each position in piRNA-complementary sequences within the up-regulated mRNAs was annotated. (C,D) The number of matches to repeat-derived piRNAs was correlated with the extent of up-regulation. Box plots analyzing the number of matches to nonrepeat-derived piRNAs (left) and repeat-derived piRNAs (right) are shown. When the RPM value was <0.1, the value was treated as 0.1. (E,F) The up-regulated mRNAs (E) and lncRNAs (F) frequently contain retrotransposon sequences. The number of genes and lncRNAs in each class is shown above the bar on the left graph. P-values between the <1 and >2 groups were calculated by the R function prop.test. (G,H) High density of retrotransposon sequences in the 3′ UTR of the up-regulated mRNAs (G) and across the entire region of the up-regulated lncRNAs (H). Regions examined are divided into 0.1-kb bins (window size = 100 bases, step size = 100 bases).