Title

Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture.

Document Type

Article

Publication Date

5-2018

JAX Source

Nat Genet 2018 May; 50(5):754-763.

PMID

29700467

DOI

https://doi.org/10.1038/s41588-018-0111-2

Abstract

Chromosome conformation capture (3C) technologies can be used to investigate 3D genomic structures. However, high background noise, high costs, and a lack of straightforward noise evaluation in current methods impede the advancement of 3D genomic research. Here we developed a simple digestion-ligation-only Hi-C (DLO Hi-C) technology to explore the 3D landscape of the genome. This method requires only two rounds of digestion and ligation, without the need for biotin labeling and pulldown. Non-ligated DNA was efficiently removed in a cost-effective step by purifying specific linker-ligated DNA fragments. Notably, random ligation could be quickly evaluated in an early quality-control step before sequencing. Moreover, an in situ version of DLO Hi-C using a four-cutter restriction enzyme has been developed. We applied DLO Hi-C to delineate the genomic architecture of THP-1 and K562 cells and uncovered chromosomal translocations. This technology may facilitate investigation of genomic organization, gene regulation, and (meta)genome assembly. Nat Genet 2018 May; 50(5):754-763.

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