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

Oudelaar AM., Davies JOJ., Downes DJ., Higgs DR., Hughes JR.

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.

DOI

10.1093/nar/gkx1194

Type

Journal article

Journal

Nucleic Acids Res

Publication Date

15/12/2017

Volume

45

Keywords

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

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