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

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.

SUBMITTER: Oudelaar AM

PROVIDER: S-EPMC5728395 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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

Oudelaar A Marieke AM Davies James O J JOJ Downes Damien J DJ Higgs Douglas R DR Hughes Jim R JR

Nucleic acids research 20171201 22

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 ...[more]

PMID: 29186505

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