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Chromosome conformation capture (3C) techniques are crucial to understanding tissue-specific regulation of gene expression, but current methods generally require large numbers of cells. This hampers the investigation of chromatin architecture in rare cell populations. We present a new low-input Capture-C approach that can generate high-quality 3C interaction profiles from 10 000-20 000 cells, depending on the resolution used for analysis. We also present a PCR-free, sequencing-free 3C technique based on NanoString technology called C-String. By comparing C-String and Capture-C interaction profiles we show that the latter are not skewed by PCR amplification. Furthermore, we demonstrate that chromatin interactions detected by Capture-C do not depend on the degree of cross-linking by performing experiments with varying formaldehyde concentrations.

Original publication




Journal article


Nucleic Acids Res

Publication Date





Animals, Cell Count, Cells, Cultured, Chromatin, Chromosomes, Female, Formaldehyde, Gene Expression Regulation, Genetic Techniques, Mice, Inbred C57BL, Molecular Conformation, Nanotechnology