ArticleEpigenetics & chromatin2021
A cookbook for DNase Hi-C.
Article in Epigenetics & chromatin, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- The 3D genomics of lampbrush chromosomes highlights the role of active transcription in chromatin organization.Nucleic acids research · 2026Article
- Review
- Chromatin landscape, transcriptomic and ChIP-seq profiling of Anopheles stephensi MSQ43 cell line.Scientific data · 2025Article
- Direction and modality of transcription changes caused by TAD boundary disruption in Slc29a3/Unc5b locus depends on tissue-specific epigenetic context.Epigenetics & chromatin · 2025Article
- Charm is a flexible pipeline to simulate chromosomal rearrangements on Hi-C-like data.NAR genomics and bioinformatics · 2025Article
- Combining chromosome conformation capture and exome sequencing for simultaneous detection of structural and single-nucleotide variants.Genome medicine · 2025Article
- Read Mapping for Hi-C Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions.Nature communications · 2024Article
- Expanding the list of sequence-agnostic enzymes for chromatin conformation capture assays with S1 nuclease.Epigenetics & chromatin · 2023Article
- Function and Evolution of the Loop Extrusion Machinery in Animals.International journal of molecular sciences · 2023Review
- A Cre-LoxP-based approach for combinatorial chromosome rearrangements in human HAP1 cells.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2023Article
- Article
- Anopheles mosquitoes reveal new principles of 3D genome organization in insects.Nature communications · 2022Article
- Investigation of the Basic Steps in the Chromosome Conformation Capture Procedure.Frontiers in genetics · 2021Article
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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