EXPERIMENT_TITLE: GSM5930911: 22Rv1_HiC_rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: In situ Hi-C experiments were performed in 22Rv1 cells, using a previously described protocol 25 with minor modifications. Briefly, 1× 107 cells were digested and cross-linked in 1% formaldehyde. Chromatin was digested with 150 U MboⅠ (NEB, R0147) at 37 ℃ with rotation. To fill in restriction fragment overhangs, 50 U DNA Polymerase Ⅰ, Large Fragment (NEB, M0210), combined with dNTPs containing biotin-dATP (Thermofisher, 19524016), were added and incubated at 37℃ for 1 h. For ligation, 4000 U T4 DNA ligase (NEB, M0202) was added and incubated at room temperature for 4 h with slow rotation. To reverse cross-links, 25 μl proteinase K (20 mg/ml) was added and incubated at 65 ℃ overnight. Purified Hi-C samples were sheared to 200-300 bp by sonication. Biotin pull-down was performed using Streptavidin C-1 beads (Life Technologies, 65002) with 2× biotin binding buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA and 2 M NaCl). The Hi-C library was amplified with 8 cycles using Illumina primers.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: To date, genome-wide association studies (GWAS) have revealed over 200 genetic risk loci associated with prostate cancer; yet, true disease-causing variants in gene regulatory regions remain elusive. Identification of causal variants and their targets from association signals relevant to prostate cancer is complicated by high linkage disequilibrium and limited availability of functional genomics data for specific tissue/cell types. Here, we integrated statistical fine-mapping and functional annotation from prostate-specific epigenomic profiles, high resolution 3D genome features, and quantitative trait loci data to distinguish causal variants from associations and identify target genes they regulate. Our fine-mapping analysis yielded 1,892 likely causal variants, and multiscale functional annotation linked them to 406 target genes. We prioritized rs10486567, located in an enhancer, as a genome-wide top-ranked SNP and predicted HOTTIP as its target. Deletion of the rs10486567-associated enhancer in prostate cancer cells decreased their capacity for invasive migration. HOTTIP overexpression in an enhancer-KO cell line rescued defective invasive migration. Furthermore, we found that rs10486567 regulates HOTTIP through allele-specific long- range chromatin interaction. Overall design: HiC experiments of 22Rv1
SAMPLE_TITLE: 22Rv1_HiC_rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Prostate"}, {"TAG": "cell line", "VALUE": "22Rv1"}, {"TAG": "restriction enzyme", "VALUE": "MboI"}]
Pool_Member_@attributes_sample_title: 22Rv1_HiC_rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: 22Rv1_HiC_rep1
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