TE amounts and types in human lncRNA and their surrounding regions.

Regions are genome, intergenic regions and exons. In the case of protein coding genes, exons include UTR exons as well as coding exons. 1 or 10 kb up and dw = intergenic regions up to 1 or 10 kb upstream of the TSS and downstream of the polyA respectively. Any annotated exons (RefSeq and Gencode v13 lncRNAs) have been subtracted from intergenic and intronic regions. A. Coverage of all TEs. LncRNA set corresponds to Gencode v13, separated in lincRNA transcripts (intergenic) and genic transcripts. Coverage is calculated as described for Figure 2 and in Methods and is shown per TE class (LTR/ERV, nonLTR/LINE, nonLTR/SINE, DNA) with an additional separation between ERVs (LTR/LTR) and internal parts (LTR/int) of ERV elements. B. Same as A, except that only TEs that overlap with DNaseI hypersensitive sites (‘TE-DHS’) are considered (see Methods). C. Heatmap of distance between LTR and lincRNA (left) and protein-coding genes (right) aggregated for all chromosomes (Jaccard test see Methods). The x-axis is the alignment of all reference features (protein coding exons and lncRNAs). The line depicts the total percentage of TEs found along the reference feature. The color quantifies the departure from null distribution generated from permutation. “Hot” (red) and “cool” (blue) colors mean that there was more or less TEs observed at a given position than by chance, respectively. All p–value <0.001.