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.
Volume
50
Issue
5
First Page
754
Last Page
763
ISSN
1546-1718
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.
Recommended Citation
Lin D,
Hong P,
Zhang S,
Xu W,
Jamal M,
Yan K,
Lei Y,
Li L,
Ruan Y,
Fu Z,
Li G,
Cao G.
Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture. Nat Genet 2018 May; 50(5):754-763.