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

Oudelaar, A. M.; Davies, J. O. J.; Downes, D. J.; Higgs, D. R.; Hughes, J. R.

doi:10.1093/nar/gkx1194

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

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Oudelaar, A. M.
Lise Meitner Group Genome Organization and Regulation, MPI for Biophysical Chemistry, Max Planck Society;

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Citation

Oudelaar, A. M., Davies, J. O. J., Downes, D. J., Higgs, D. R., & Hughes, J. R. (2017). Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C. Nucleic Acids Research, 45(22): e184. doi:10.1093/nar/gkx1194.

Cite as: https://hdl.handle.net/21.11116/0000-0007-6159-8

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.