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Nucleic Acids Res. 2017 Dec 15;45(22):e184. doi: 10.1093/nar/gkx1194.

Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C.

Author information

1
Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.

Abstract

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.

PMID:
29186505
PMCID:
PMC5728395
DOI:
10.1093/nar/gkx1194
[Indexed for MEDLINE]
Free PMC Article

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