Specifically expressed Alu elements may function as cell-type–specific enhancers. (A) Genes within 10 kb of Alu elements expressed in a biosample tend to be more highly expressed in the same biosample than genes within 10 kb of Alu elements expressed in other biosamples. Only biosamples with more than 50 expressed Alu elements were included in this analysis. Wilcoxon rank-sum test FDR-adjusted P-values are reported. (B) Gene Ontology (GO) terms enriched in genes near tissue-specific expressed Alu elements are shown with color intensities corresponding to their FDR values. (C) Compared with unexpressed Alu elements annotated in the human genome (dashed line), expressed and robustly expressed Alu elements showed significant enrichments in cCREs (left; P-value < 2.2 × 10−16, chi-squared test) and cCREs-ELS (right; P-value < 2.2 × 10−16). (D) Alu elements expressed in K562 or GM12878 cells were enriched in K562-specific (top; P-value = 8.05 × 10−96, chi-squared test) or GM12878-specific (bottom; P-value = 4.27 × 10−81) cCREs-ELS, respectively. (E) K562 (top) and GM12878 (bottom) cCREs-ELS Alu elements were enriched in the strong enhancer chromatin state annotated by ChromHMM in the respective cell types (K562, P-value = 1.89 × 10−67; GM12878, P-value = 2.69 × 10−32, chi-squared tests). (F) cCREs-ELS Alu elements expressed in K562 or GM12878 cells were more frequently linked to nearby promoters in the corresponding biosample than non-cCREs-ELS Alu elements expressed in the corresponding biosample (P-values ≤ 7.17 × 10−2, chi-squared test), Alu elements expressed in other biosamples (P-values ≤ 3.40 × 10−7), and unexpressed Alu elements (P-values ≤ 1.61 × 10−15), with links measured by Pol II ChIA-PET interactions.
