Fig. 3

Identification of tapRNAs. a The proportion of pcRNAs, pcRNA-associated coding genes, Gencode lncRNAs and Gencode coding genes with a CTCF peak (based on Encode ChIP-Seq data) overlapping their promoter. The p values reported were calculated with hypergeometric tests. Right: CTCF peak coverage of loci of pcRNAs, pcRNA-associated coding genes, Gencode lncRNAs and Gencode coding genes. The plots report the loci from 20 kb upstream of the transcription start site (TSS) to 20 kb downstream of the transcription end site (TES). For visualization purposes these profiles show the coverage of a random sample of 5000 Gencode lncRNAs and 5000 random Gencode coding genes. b, c Aggregation density plots showing the distribution of the TSS of pcRNAs (red) and lncRNAs (orange) relative to chromatin topological domains (b) and chromatin loop anchor points (c). Domains and loop anchor points were defined based on HiC data. d Venn diagram showing the number of pcRNAs whose promoters overlap a loop anchor point (purple) or a domain boundary (green). e The HOXD locus showing the tapRNAs and chromatin loops defined by HiC data [43]. Modified from a screenshot of the UCSC genome browser. f The proportion of pcRNAs, pcRNA-associated coding genes, Gencode lncRNAs and Gencode coding genes with a HiC loop overlapping their promoter. The p values reported were calculated with hypergeometric tests. Right: HiC loop coverage of loci of pcRNAs, pcRNA-associated coding genes, Gencode lncRNAs and Gencode coding genes. The plotted genomic regions encompass the loci from 20 kb upstream of the TSS to 20 kb downstream of the TES. For visualization purposes these profiles show the coverage of a random sample of 5000 Gencode lncRNAs and 5000 random Gencode coding genes. g Cumulative distribution plot showing the percentage of distal genomic regions in contact with pcRNA promoters (y-axis) as a function of the fraction of length of loop-end annotated as enhancer (left) or promoter (right). For example, the “≥ 0.4” point (x-axis) of the red line in the first plot indicates that ~ 37 % (y-axis) of the distal genomic regions in contact with pcRNA promoters are annotated as enhancer for 40 % or more of their length. Promoters of pcRNAs are significantly more often in contact through loops with enhancer elements compared to generic Gencode lncRNAs (p value 2.85 × 10⁻⁶). The indicated p values were calculated using the Kolmogorov-Smirnov test