Abstract
Targeted chromosome conformation capture (HiCap) is an experimental method for detecting spatial interactions of genomic features such as promoters and/or enhancers. The protocol first describes the design of sequence capture probes. After that, it provides details on the chromosome conformation capture adapted for next-generation sequencing (Hi-C). Finally, the methodology for coupling Hi-C with sequence capture technology is described.
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References
Dekker J, Rippe K, Dekker M et al (2002) Capturing chromosome conformation. Science 295(5558):1306–1311
Lieberman-Aiden E, van Berkum NL, Williams L et al (2009) Comprehensive map** of long-range interactions reveals folding principles of the human genome. Science 326(5950):289–293
Schmitt AD, Hu M, Ren B (2016) Genome-wide map** and analysis of chromosome architecture. Nat Rev Mol Cell Biol 17(12):743–755
Hughes JR, Roberts N, McGowan S et al (2014) Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet 46(2):205–212
Sahlen P, Abdullayev I, Ramskold D et al (2015) Genome-wide map** of promoter-anchored interactions with close to single-enhancer resolution. Genome Biol 16:156
Dryden NH, Broome LR, Dudbridge F et al (2014) Unbiased analysis of potential targets of breast cancer susceptibility loci by capture Hi-C. Genome Res 24(11):1854–1868
Zhao Z, Tavoosidana G, Sjolinder M et al (2006) Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet 38(11):1341–1347
Simonis M, Klous P, Splinter E et al (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38(11):1348–1354
Fullwood MJ, Liu MH, Pan YF et al (2009) An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462(7269):58–64
Javierre BM, Burren OS, Wilder SP et al (2016) Lineage-specific genome architecture links enhancers and non-coding disease variants to target gene promoters. Cell 167(5):1369–84 e19
Sahlen P, Spalinskas R, Asad S et al (2021) Chromatin interactions in differentiating keratinocytes reveal novel atopic dermatitis and psoriasis-associated genes. J Allergy Clin Immunol 147(5):1742–1752
Pradhananga S, Spalinskas R, Poujade FA et al (2020) Promoter anchored interaction landscape of THP-1 macrophages captures early immune response processes. Cell Immunol 355:104148
Akerborg O, Spalinskas R, Pradhananga S et al (2019) High-resolution regulatory maps connect vascular risk variants to disease-related pathways. Circ Genom Precis Med 12(3):e002353
Beesley J, Sivakumaran H, Moradi Marjaneh M et al (2020) Chromatin interactome map** at 139 independent breast cancer risk signals. Genome Biol 21(1):8
Anil A, Spalinskas R, Akerborg O et al (2018) HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications. Bioinformatics 34(4):675–677
Cairns J, Freire-Pritchett P, Wingett SW et al (2016) CHiCAGO: robust detection of DNA loo** interactions in capture Hi-C data. Genome Biol 17(1):127
Yang Y (2011) Thermodynamics of DNA binding and break repair by the Pol I DNA polymerases from Escherichia coli and Thermus aquaticus
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Zhigulev, A., Sahlén, P. (2022). Targeted Chromosome Conformation Capture (HiCap). In: Sexton, T. (eds) Spatial Genome Organization. Methods in Molecular Biology, vol 2532. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2497-5_5
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DOI: https://doi.org/10.1007/978-1-0716-2497-5_5
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Publisher Name: Humana, New York, NY
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Online ISBN: 978-1-0716-2497-5
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