PT  - JOURNAL ARTICLE
AU  - Damien J. Downes
AU  - Matthew E. Gosden
AU  - Jelena Telenius
AU  - Stephanie J. Carpenter
AU  - Lea Nussbaum
AU  - Sara De Ornellas
AU  - Martin Sergeant
AU  - Chris Q. Eijsbouts
AU  - Ron Schwessinger
AU  - Jon Kerry
AU  - Nigel Roberts
AU  - Arun Shivalingam
AU  - Afaf El-Sagheer
AU  - A. Marieke Oudelaar
AU  - Tom Brown
AU  - Veronica J. Buckle
AU  - James O.J. Davies
AU  - Jim R. Hughes
TI  - Targeted high-resolution chromosome conformation capture at genome-wide scale
AID  - 10.1101/2020.03.02.953745
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.03.02.953745
4099  - http://biorxiv.org/content/early/2020/03/02/2020.03.02.953745.short
4100  - http://biorxiv.org/content/early/2020/03/02/2020.03.02.953745.full
AB  - Chromosome conformation capture (3C) provides an adaptable tool for studying diverse biological questions. Current 3C methods provide either low-resolution interaction profiles across the entire genome, or high-resolution interaction profiles at up to several hundred loci. All 3C methods are affected to varying degrees by inefficiency, bias and noise. As such, generation of reproducible high-resolution interaction profiles has not been achieved at scale. To overcome this barrier, we systematically tested and improved upon current methods. We show that isolation of 3C libraries from intact nuclei, as well as shortening and titration of enrichment oligonucleotides used in high-resolution methods reduces noise and increases on-target sequencing. We combined these technical modifications into a new method Nuclear-Titrated (NuTi) Capture-C, which provides a >3-fold increase in informative sequencing content over current Capture-C protocols. Using NuTi Capture-C we target 8,061 promoters in triplicate, demonstrating that this method generates reproducible high-resolution genome-wide 3C interaction profiles at scale.