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Breast cancer risk is strongly associated with an intergenic region on 11q13. We have previously shown that the strongest risk-associated SNPs fall within a distal enhancer that regulates CCND1. Here, we report that, in addition to regulating CCND1, this enhancer regulates two estrogen-regulated long noncoding RNAs, CUPID1 and CUPID2. We provide evidence that the risk-associated SNPs are associated with reduced chromatin looping between the enhancer and the CUPID1 and CUPID2 bidirectional promoter. We further show that CUPID1 and CUPID2 are predominantly expressed in hormone-receptor-positive breast tumors and play a role in modulating pathway choice for the repair of double-strand breaks. These data reveal a mechanism for the involvement of this region in breast cancer.

Original publication




Journal article


American Journal of Human Genetics

Publication Date





255 - 266


Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia.


Cell Line, Tumor, Chromosomes, Human, Pair 11, Chromatin, Humans, Breast Neoplasms, DNA Damage, Genetic Predisposition to Disease, Cyclin D1, RNA, Small Interfering, RNA, Guide, Estrogens, DNA Repair, Gene Expression Regulation, Neoplastic, RNA Interference, Polymorphism, Single Nucleotide, Female, DNA Breaks, Double-Stranded, Enhancer Elements, Genetic, Promoter Regions, Genetic, MCF-7 Cells, RNA, Long Noncoding