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Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

Figure 4

Evidence of purifying selection in TE–derived DNA transcribed as lncRNAs.

LncRNAs correspond to Gencode v13 (human) and protein coding genes to Refseq 57 (human, 20,848 genes). Boxplots show primate PhyloP scores computed in order to compare the conservation of different sets (see upper panel). Random set is size and number-matched for TE-derived DNA in lncRNA exons. Intronic lncRNA TEs correspond to TE-derived DNA in lncRNA introns that don't overlapp with splicing sites and all annotated chromatin marks were removed (see Methods), in order to obtain a most neutral set [inactive chromatin, see 32]. Statistical test used: permutation test with 1000 permutations were performed in R. Boxplots depicts the median upper (75%) and lower (25%) quantiles. The whiskers extend beyond the upper and lower quantile by 1.5× the inner quartile range. Outliers have been removed for visualization.

Figure 4

doi: https://doi.org/10.1371/journal.pgen.1003470.g004