BRCA1-associated R-loop affects transcription and differentiation in breast luminal epithelial cells

• Published in: Nucleic acids research Vol. 47; no. 10; pp. 5086 - 5099
• Main Authors: Chiang, Huai-Chin, Zhang, Xiaowen, Li, Jingwei, Zhao, Xiayan, Chen, Jerry, Wang, Howard T-H, Jatoi, Ismail, Brenner, Andrew, Hu, Yanfen, Li, Rong
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 04.06.2019
• Subjects: BRCA1 Protein - genetics; BRCA1 Protein - metabolism; Breast - metabolism; Carcinogenesis; Cell Differentiation; CRISPR-Cas Systems; Enhancer Elements, Genetic; Epithelial Cells - metabolism; Estrogen Receptor alpha - genetics; Female; Gene Deletion; Gene Expression Regulation, Neoplastic; Gene regulation, Chromatin and Epigenetics; Genes, BRCA1; HEK293 Cells; Heterozygote; Humans; MCF-7 Cells; Mutation; Transcription, Genetic
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkz262

BRCA1-associated basal-like breast cancer originates from luminal progenitor cells. Breast epithelial cells from cancer-free BRCA1 mutation carriers are defective in luminal differentiation. However, how BRCA1 deficiency leads to lineage-specific differentiation defect is not clear. BRCA1 is implicated in resolving R-loops, DNA-RNA hybrid structures associated with genome instability and transcriptional regulation. We recently showed that R-loops are preferentially accumulated in breast luminal epithelial cells of BRCA1 mutation carriers. Here, we interrogate the impact of a BRCA1 mutation-associated R-loop located in a putative transcriptional enhancer upstream of the ERα-encoding ESR1 gene. Genetic ablation confirms the relevance of this R-loop-containing region to enhancer-promoter interactions and transcriptional activation of the corresponding neighboring genes, including ESR1, CCDC170 and RMND1. BRCA1 knockdown in ERα+ luminal breast cancer cells increases intensity of this R-loop and reduces transcription of its neighboring genes. The deleterious effect of BRCA1 depletion on transcription is mitigated by ectopic expression of R-loop-removing RNase H1. Furthermore, RNase H1 overexpression in primary breast cells from BRCA1 mutation carriers results in a shift from luminal progenitor cells to mature luminal cells. Our findings suggest that BRCA1-dependent R-loop mitigation contributes to luminal cell-specific transcription and differentiation, which could in turn suppress BRCA1-associated tumorigenesis.