Robust detection of chromosomal contacts from small cell numbers using low-input Capture-C

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 structure in rare cell populations. We present two new low-input Capture-C protocols that generate high-quality, reproducible interaction profiles from fewer than 20,000 cells, and show that these are not biased by PCR amplification or the degree of formaldehyde fixation. Overall design: The Capture-C technologies combine 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. In this case, the promoters of alpha-globin, beta-globin and Slc25a37 were used as viewpoints. To optimise Capture-C technology for small cell numbers, we developed Low-Input (LI) Capture-C and Tag-Capture-C, and performed experiments with both protocols using 200 ng, 100 ng and 50 ng mouse erythroid 3C libraries, all in triplicates. In the reduced cross-linking experiments, we compared NG Capture-C interactions profiles generated from primary mouse erythroid cells fixed with 5%, 4%, 3%, 2%, 1%, 0.5% or 0% formaldehyde. Experiments were performed in technical duplicates.