A cookbook for DNase Hi-C

Epigenetics & Chromatin

Viktoria Yu Voinova¹  Maria I. Yablonskaya¹  Maria Gridina²  Evgeniy Mozheiko²  Emil Valeev³  Veniamin Fishman³  Zhanna G. Markova⁴  Nadezhda V. Shilova⁴  Ludmila P. Nazarenko⁵  Maria E. Lopatkina⁵  Igor N. Lebedev⁵ 

[1] Clinical Research Institute of Pediatrics Named After Acad. Y.E. Veltischev, Moscow, Russia;Institute of Cytology and Genetics SB RAS, Lavrentjeva ave 10, Novosibirsk, Russia;Institute of Cytology and Genetics SB RAS, Lavrentjeva ave 10, Novosibirsk, Russia;Novosibirsk State University, Pirogova str., 2, Novosibirsk, Russia;Research Centre for Medical Genetics, Moskvorechie str., 1, Moscow, Russia;Research Institute of Medical Genetics, Tomsk National Research Medical Center, Kooperativny Str, 5, Tomsk, Russia;

关键词: DNAse I;    Hi-C;    Genome organization;    Human peripheral blood;    K562;    LNCaP;    A549;   

DOI  :  10.1186/s13072-021-00389-5

来源: Springer

【 摘 要 】

BackgroundThe Hi-C technique is widely employed to study the 3-dimensional chromatin architecture and to assemble genomes. The conventional in situ Hi-C protocol employs restriction enzymes to digest chromatin, which results in nonuniform genomic coverage. Using sequence-agnostic restriction enzymes, such as DNAse I, could help to overcome this limitation.ResultsIn this study, we compare different DNAse Hi-C protocols and identify the critical steps that significantly affect the efficiency of the protocol. In particular, we show that the SDS quenching strategy strongly affects subsequent chromatin digestion. The presence of biotinylated oligonucleotide adapters may lead to ligase reaction by-products, which can be avoided by rational design of the adapter sequences. Moreover, the use of nucleotide-exchange enzymes for biotin fill-in enables simultaneous labelling and repair of DNA ends, similar to the conventional Hi-C protocol. These improvements simplify the protocol, making it less expensive and time-consuming.ConclusionsWe propose a new robust protocol for the preparation of DNAse Hi-C libraries from cultured human cells and blood samples supplemented with experimental controls and computational tools for the evaluation of library quality.

【 授权许可】

CC BY