Complementary Alu sequences mediate enhancer-promoter selectivity

Nature. 2023 Jul;619(7971):868-875. doi: 10.1038/s41586-023-06323-x. Epub 2023 Jul 12.


Enhancers determine spatiotemporal gene expression programs by engaging with long-range promoters1-4. However, it remains unknown how enhancers find their cognate promoters. We recently developed a RNA in situ conformation sequencing technology to identify enhancer-promoter connectivity using pairwise interacting enhancer RNAs and promoter-derived noncoding RNAs5,6. Here we apply this technology to generate high-confidence enhancer-promoter RNA interaction maps in six additional cell lines. Using these maps, we discover that 37.9% of the enhancer-promoter RNA interaction sites are overlapped with Alu sequences. These pairwise interacting Alu and non-Alu RNA sequences tend to be complementary and potentially form duplexes. Knockout of Alu elements compromises enhancer-promoter looping, whereas Alu insertion or CRISPR-dCasRx-mediated Alu tethering to unregulated promoter RNAs can create new loops to homologous enhancers. Mapping 535,404 noncoding risk variants back to the enhancer-promoter RNA interaction maps enabled us to construct variant-to-function maps for interpreting their molecular functions, including 15,318 deletions or insertions in 11,677 Alu elements that affect 6,497 protein-coding genes. We further demonstrate that polymorphic Alu insertion at the PTK2 enhancer can promote tumorigenesis. Our study uncovers a principle for determining enhancer-promoter pairing specificity and provides a framework to link noncoding risk variants to their molecular functions.

MeSH terms

  • Alu Elements* / genetics
  • Cell Line
  • Enhancer Elements, Genetic* / genetics
  • Focal Adhesion Kinase 1 / genetics
  • Gene Expression Regulation
  • Nucleic Acid Conformation
  • Nucleic Acid Heteroduplexes
  • Promoter Regions, Genetic* / genetics
  • RNA* / chemistry
  • RNA* / genetics
  • RNA* / metabolism
  • Sequence Deletion


  • Focal Adhesion Kinase 1
  • Nucleic Acid Heteroduplexes
  • RNA