title: Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C.
abstract: Genome-wide association studies have identified more than 70 common variants that are associated with breast cancer risk. Most of these variants map to non-protein-coding regions and several map to gene deserts, regions of several hundred kilobases lacking protein-coding genes. We hypothesized that gene deserts harbor long-range regulatory elements that can physically interact with target genes to influence their expression. To test this, we developed Capture Hi-C (CHi-C), which, by incorporating a sequence capture step into a Hi-C protocol, allows high-resolution analysis of targeted regions of the genome. We used CHi-C to investigate long-range interactions at three breast cancer gene deserts mapping to 2q35, 8q24.21, and 9q31.2. We identified interaction peaks between putative regulatory elements ("bait fragments") within the captured regions and "targets" that included both protein-coding genes and long noncoding (lnc) RNAs over distances of 6.6 kb to 2.6 Mb. Target protein-coding genes were IGFBP5, KLF4, NSMCE2, and MYC; and target lncRNAs included DIRC3, PVT1, and CCDC26. For one gene desert, we were able to define two SNPs (rs12613955 and rs4442975) that were highly correlated with the published risk variant and that mapped within the bait end of an interaction peak. In vivo ChIP-qPCR data show that one of these, rs4442975, affects the binding of FOXA1 and implicate this SNP as a putative functional variant.
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom;
authors.forename: Nicola H
authors.initials: NH
authors.lastname: Dryden
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom;
authors.forename: Laura R
authors.initials: LR
authors.lastname: Broome
authors.affiliation: Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom;
authors.forename: Frank
authors.initials: F
authors.lastname: Dudbridge
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom;
authors.forename: Nichola
authors.initials: N
authors.lastname: Johnson
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom;
authors.forename: Nick
authors.initials: N
authors.lastname: Orr
authors.affiliation: Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom;
authors.forename: Stefan
authors.initials: S
authors.lastname: Schoenfelder
authors.affiliation: Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom;
authors.forename: Takashi
authors.initials: T
authors.lastname: Nagano
authors.affiliation: Babraham Bioinformatics, The Babraham Institute, Cambridge CB22 3AT, United Kingdom.
authors.forename: Simon
authors.initials: S
authors.lastname: Andrews
authors.affiliation: Babraham Bioinformatics, The Babraham Institute, Cambridge CB22 3AT, United Kingdom.
authors.forename: Steven
authors.initials: S
authors.lastname: Wingett
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom;
authors.forename: Iwanka
authors.initials: I
authors.lastname: Kozarewa
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom;
authors.forename: Ioannis
authors.initials: I
authors.lastname: Assiotis
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom;
authors.forename: Kerry
authors.initials: K
authors.lastname: Fenwick
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom;
authors.forename: Sarah L
authors.initials: SL
authors.lastname: Maguire
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom;
authors.forename: James
authors.initials: J
authors.lastname: Campbell
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom;
authors.forename: Rachael
authors.initials: R
authors.lastname: Natrajan
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom;
authors.forename: Maryou
authors.initials: M
authors.lastname: Lambros
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom;
authors.forename: Eleni
authors.initials: E
authors.lastname: Perrakis
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom;
authors.forename: Alan
authors.initials: A
authors.lastname: Ashworth
authors.affiliation: Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom;
authors.forename: Peter
authors.initials: P
authors.lastname: Fraser
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, United Kingdom; Olivia.Fletcher@icr.ac.uk.
authors.forename: Olivia
authors.initials: O
authors.lastname: Fletcher
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation; D002874:Chromosome Mapping; D002889:Chromosomes, Human, Pair 2 / Q000235:genetics; D002898:Chromosomes, Human, Pair 8 / Q000235:genetics; D002899:Chromosomes, Human, Pair 9 / Q000235:genetics; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics; D055106:Genome-Wide Association Study / Q000379:methods*; D051541:Hepatocyte Nuclear Factor 3-alpha / Q000235:genetics / Q000378:metabolism; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D006801:Humans; D000090062:Kruppel-Like Factor 4; D061986:MCF-7 Cells; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D011485:Protein Binding; D025941:Protein Interaction Mapping; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
chemical_list: C496499:FOXA1 protein, human; C484414:HOXB13 protein, human; D051541:Hepatocyte Nuclear Factor 3-alpha; D018398:Homeodomain Proteins; C000715467:KLF4 protein, human; D000090062:Kruppel-Like Factor 4; D062085:RNA, Long Noncoding