Extended Data Fig. 4: EPRI features.
From: Complementary Alu sequences mediate enhancer–promoter selectivity
a, Enhancer-regulated genes tend to be functionally related compared with randomly selected genes. n = 7 cell lines. The center line of the box plot represents the median, the box borders represent the first (Q1) and third (Q3) quartiles, and the whiskers are the most extreme data points within 1.5× the interquartile range (from Q1 to Q3). Two-tailed unpaired Student’s t-test. b, Enhancers-regulated functional clusters. Orange dots, enhancers; outside dots, target genes. c, qPCR showing reduced transcription of target genes linked to TE19551 after eRNA knockdown using the mixture of two independent LNA ASOs. Non-target gene HLA-DQA1 serves as a negative control. Data are the mean ± s.d.; n = 3 biological replicates, two-tailed unpaired Student’s t-test. d–e, Pairwise interacting RNA fragments from enhancers (d) and promoters (e) enrich motifs (red bars) that can cover the most consensus sequence of the Alu element. The color scale indicates E-value for each motif calculated by MEME. f–j, The relative distribution of LINE/L1 (f), LINE/L2 (g), SINE/MIR (h), LTR/ERV1 (i), and LTR/ERVL-MaLR (j) repeat elements around pairwise interacting RNA fragments in enhancers (left) and promoters (right). k, The relative distribution of mouse B1 elements around EPRIs in MEF cells. l, Bar graph showing the percentage of Hi-C and HiChIP detected enhancer-promoter loops that contained at least one Alu element. m–n, Enhancer-gene pairs supported by EPRIs (red line, n = 58,594) have higher nascent RNA levels than that supported by Hi-C (m, blue line, n = 3,749) or HiChIP (n, blue line, n = 300,734). Two-tailed Kolmogorov–Smirnov test. o–q, EPRI chimeric reads overlapped Alu elements tend to have higher ATAC-seq (o), DNase-seq (p), and GRO-seq signals (q) than other Alu elements from the same enhancer-promoter pairs. Data are the mean ± s.e.m., two-tailed unpaired Student’s t-test.
