Chromosome conformation capture (3C) and its derivatives (e.g., 4C, 5Cand Hi-C) are used to analyze the 3D organization of genomes. We recently developed targeted chromatin capture (T2C), an inexpensive method for studying the 3D organization of genomes, interactomes and structural changes associated with gene regulation, the cell cycle, and cell survival and development. Here, we present the protocol for T2Cbased on capture, describing all experimental steps and bio-informatic tools in full detail. T2Coffers high resolution, a large dynamic interaction frequency range and a high signal-to-noise ratio. Its resolution is determined by the resulting fragment size of the chosen restriction enzyme, which can lead to sub-kilobase-pair resolution. T2C's high coverage allows the identification of the interactome of each individual DNAfragment, which makes binning of reads (often used in other methods) basically unnecessary. Notably, T2Crequires low sequencing efforts. T2Calso allows multiplexing of samples for the direct comparison of multiple samples. It can be used to study topologically associating domains (TADs), determining their position, shape, boundaries, and intra- And inter-domain interactions, as well as the composition of aggregated loops, interactions between nucleosomes, individual transcription factor binding sites, and promoters and enhancers. T2Ccan be performed by any investigator with basic skills in molecular biology techniques in ∼7-8 d. Data analysis requires basic expertise in bioinformatics and in Linux and Python environments.

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Kolovos, P, Brouwer, R.W.W, Kockx, C, Lesnussa, M, Kepper, F.N, Zuin, J, … Grosveld, F. (Frank). (2018). Investigation of the spatial structure and interactions of the genome at sub-kilobase-pair resolution using T2C. Nature Protocols, 13(3), 459–477. doi:10.1038/nprot.2017.132