Genome-wide association studies (GWAS) have identified thousands of SNPs that are associated with human traits and diseases. But, because the vast majority of these SNPs are located in non-coding regions of the genome, the mechanisms by which they promote disease risk have remained elusive. Employing a new methodology that combines cistromics, epigenomics and genotype imputation, we annotate the non-coding regions of the genome in breast cancer cells and systematically identify the functional nature of SNPs associated with breast cancer risk. Our results show that breast cancer risk–associated SNPs are enriched in the cistromes of FOXA1 and ESR1 and the epigenome of histone H3 lysine 4 monomethylation (H3K4me1) in a cancer- and cell type–specific manner. Furthermore, the majority of the risk-associated SNPs modulate the affinity of chromatin for FOXA1 at distal regulatory elements, thereby resulting in allele-specific gene expression, which is exemplified by the effect of the rs4784227 SNP on the TOX3 gene within the 16q12.1 risk locus.
Subscribe to Journal
Get full journal access for 1 year
only $18.75 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Gene Expression Omnibus
Frazer, K.A., Murray, S.S., Schork, N.J. & Topol, E.J. Human genetic variation and its contribution to complex traits. Nat. Rev. Genet. 10, 241–251 (2009).
1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010).
Heintzman, N.D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39, 311–318 (2007).
Lupien, M. et al. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell 132, 958–970 (2008).
Heintzman, N.D. et al. Histone modifications at human enhancers reflect global cell type–specific gene expression. Nature 459, 108–112 (2009).
Khalil, A.M. et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA 106, 11667–11672 (2009).
Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43–49 (2011).
Zentner, G.E., Tesar, P.J. & Scacheri, P.C. Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res. 21, 1273–1283 (2011).
Lupien, M. & Brown, M. Cistromics of hormone-dependent cancer. Endocr. Relat. Cancer 16, 381–389 (2009).
Schmidt, D. et al. A CTCF-independent role for cohesin in tissue-specific transcription. Genome Res. 20, 578–588 (2010).
Carroll, J.S. et al. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 122, 33–43 (2005).
Carroll, J.S. et al. Genome-wide analysis of estrogen receptor binding sites. Nat. Genet. 38, 1289–1297 (2006).
Krum, S.A. et al. Unique ERα cistromes control cell type–specific gene regulation. Mol. Endocrinol. 22, 2393–2406 (2008).
Wang, Q. et al. Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell 138, 245–256 (2009).
Grant, S.F. & Hakonarson, H. Microarray technology and applications in the arena of genome-wide association. Clin. Chem. 54, 1116–1124 (2008).
McClellan, J. & King, M.C. Genetic heterogeneity in human disease. Cell 141, 210–217 (2010).
Hindorff, L.A. et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. USA 106, 9362–9367 (2009).
Johnson, W.E. et al. Model-based analysis of tiling-arrays for ChIP-chip. Proc. Natl. Acad. Sci. USA 103, 12457–12462 (2006).
Akhtar-Zaidi, B. et al. Epigenomic enhancer profiling defines a signature of colon cancer. Science 336, 736–739 (2012).
Magnani, L., Eeckhoute, J. & Lupien, M. Pioneer factors: directing transcriptional regulators within the chromatin environment. Trends Genet. 27, 465–474 (2011).
Long, J. et al. Identification of a functional genetic variant at 16q12. 1 for breast cancer risk: results from the Asia Breast Cancer Consortium. PLoS Genet. 6, e1001002 (2010).
Pomerantz, M.M. et al. The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer. Nat. Genet. 41, 882–884 (2009).
Tuupanen, S. et al. The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling. Nat. Genet. 41, 885–890 (2009).
Wright, J.B., Brown, S.J. & Cole, M.D. Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk–associated single-nucleotide polymorphism in colorectal cancer cells. Mol. Cell. Biol. 30, 1411–1420 (2010).
Sekiya, T. & Zaret, K. Repression by Groucho/TLE/Grg proteins: genomic site recruitment generates compacted chromatin in vitro and impairs activator binding in vivo. Mol. Cell 28, 291–303 (2007).
Riaz, M. et al. Correlation of breast cancer susceptibility loci with patient characteristics, metastasis-free survival, and mRNA expression of the nearest genes. Breast Cancer Res. Treat. 133, 843–851 (2012).
De Gobbi, M. et al. A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter. Science 312, 1215–1217 (2006).
Gaulton, K.J. et al. A map of open chromatin in human pancreatic islets. Nat. Genet. 42, 255–259 (2010).
Jia, L. et al. Functional enhancers at the gene-poor 8q24 cancer-linked locus. PLoS Genet. 5, e1000597 (2009).
McDaniell, R. et al. Heritable individual-specific and allele-specific chromatin signatures in humans. Science 328, 235–239 (2010).
Reddy, T.E. et al. Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res. 22, 860–869 (2012).
Eeckhoute, J., Carroll, J.S., Geistlinger, T.R., Torres-Arzayus, M.I. & Brown, M. A cell-type-specific transcriptional network required for estrogen regulation of cyclin D1 and cell cycle progression in breast cancer. Genes Dev. 20, 2513–2526 (2006).
He, H.H. et al. Nucleosome dynamics define transcriptional enhancers. Nat. Genet. 42, 343–347 (2010).
Laganière, J. et al. Location analysis of estrogen receptor α target promoters reveals that FOXA1 defines a domain of the estrogen response. Proc. Natl. Acad. Sci. USA 102, 11651–11656 (2005).
Hurtado, A., Holmes, K.A., Ross-Innes, C.S., Schmidt, D. & Carroll, J.S. FOXA1 is a key determinant of estrogen receptor function and endocrine response. Nat. Genet. 43, 27–33 (2011).
Easton, D.F. et al. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447, 1087–1093 (2007).
Stacey, S.N. et al. Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor–positive breast cancer. Nat. Genet. 39, 865–869 (2007).
Ruiz-Narváez, E.A. et al. Polymorphisms in the TOX3/LOC643714 locus and risk of breast cancer in African-American women. Cancer Epidemiol. Biomarkers Prev. 19, 1320–1327 (2010).
Hutter, C.M. et al. Replication of breast cancer GWAS susceptibility loci in the Women's Health Initiative African American SHARe Study. Cancer Epidemiol. Biomarkers Prev. 20, 1950–1959 (2011).
Udler, M.S. et al. Fine scale mapping of the breast cancer 16q12 locus. Hum. Mol. Genet. 19, 2507–2515 (2010).
O'Flaherty, E. & Kaye, J. TOX defines a conserved subfamily of HMG-box proteins. BMC Genomics 4, 13 (2003).
Dittmer, S. et al. TOX3 is a neuronal survival factor that induces transcription depending on the presence of CITED1 or phosphorylated CREB in the transcriptionally active complex. J. Cell Sci. 124, 252–260 (2011).
Smid, M. et al. Genes associated with breast cancer metastatic to bone. J. Clin. Oncol. 24, 2261–2267 (2006).
Antoniou, A.C. et al. Common breast cancer–predisposition alleles are associated with breast cancer risk in BRCA1 and BRCA2 mutation carriers. Am. J. Hum. Genet. 82, 937–948 (2008).
Freedman, M.L. et al. Principles for the post-GWAS functional characterization of cancer risk loci. Nat. Genet. 43, 513–518 (2011).
Zhang, X. et al. Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus. Genome Res. 22, 1437–1446 (2012).
Park, J.H. et al. Estimation of effect size distribution from genome-wide association studies and implications for future discoveries. Nat. Genet. 42, 570–575 (2010).
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
Li, B., Kadura, I., Fu, D.J. & Watson, D.E. Genotyping with TaqMAMA. Genomics 83, 311–320 (2004).
Hagège, H. et al. Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat. Protoc. 2, 1722–1733 (2007).
Neve, R.M. et al. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell 10, 515–527 (2006).
We thank M. Brown, M.L. Freedman and M. Lemaire for discussions, as well as B.G. Neel and R. Marcotte for technical assistance. We acknowledge support from the US National Cancer Institute (NCI; 2P30CA023108-32), the American Cancer Society (ACS; IRG-82-003-27 to M.L.), the US National Institutes of Health (NIH; R01LM009012 to J.H.M. and R01CA155004 to M.L.) and the Princess Margaret Hospital Foundation (M.L.).
The authors declare no competing financial interests.
Supplementary Figures 1–4 and Supplementary Tables 2–10 and 15–21 (PDF 308 kb)
LDXI: BCa AVS. (XLSX 84 kb)
LDXI: DNase filtered BCa AVS. (XLSX 51 kb)
LDXI: Prostate cancer AVS. (XLSX 87 kb)
LDXI: Bone mineral density AVS. (XLSX 72 kb)
LDXI: Colorectal cancer AVS. (XLSX 67 kb)
About this article
Cite this article
Cowper-Sal·lari, R., Zhang, X., Wright, J. et al. Breast cancer risk–associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression. Nat Genet 44, 1191–1198 (2012). https://doi.org/10.1038/ng.2416
Association of the functional genetic variants of TOX3 gene with breast cancer in Iran: A case-control study
Gene Reports (2020)
Trans-acting non-synonymous variant of FOXA1 predisposes to hepatocellular carcinoma through modulating FOXA1-ERα transcriptional program and may have undergone natural selection
Biochimica et Biophysica Acta (BBA) - Reviews on Cancer (2020)
Transcription Factor Enrichment Analysis in Enhancers Identifies EZH2 as a Susceptibility Gene for Osteoporosis
The Journal of Clinical Endocrinology & Metabolism (2020)
Single‐nucleotide polymorphism rs13426236 contributes to an increased prostate cancer risk via regulating MLPH splicing variant 4
Molecular Carcinogenesis (2020)