ArticleNature protocols2016
Mapping 3D genome architecture through in situ DNase Hi-C.
Article in Nature protocols, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
87 citing papers in PubMed, 137 citations in OpenAlex.
- A Mid-Atlantic Brook Trout (Salvelinus fontinalis) genome to advance conservation and comparative genomics.G3 (Bethesda, Md.) · 2026Article
- LAWS-HiC: A Locally Adaptive Weighting and Screening (LAWS) Approach to Improve Detection of Long-Range Chromatin Interactions from Hi-C Data.Methods and protocols · 2026Article
- Mapping 3D genome organization at nucleosome-scale with Micro-C and Region Capture Micro-C (RCMC).Nature protocols · 2026Review
- A generalizable Hi-C foundation model for chromatin architecture, single-cell and multiomics analysis across species.Nature methods · 2026Article
- The genome of the medicinal plant Uncaria rhynchophylla provides new insights into monoterpenoid indole alkaloid metabolism and its molecular regulatory mechanism.Molecular horticulture · 2026Article
- CiFi: accurate long-read chromosome conformation capture with low-input requirements.Nature communications · 2025Article
- The inner nuclear membrane protein LEMD3 organizes the 3D chromatin architecture to maintain vascular smooth muscle cell identity.Nature communications · 2025Article
- The Biological Function of Genome Organization.International journal of molecular sciences · 2025Review
- Review
- StripePy: fast and robust characterization of architectural stripes.Bioinformatics (Oxford, England) · 2025Article
- Polymer model integrates imaging and sequencing to reveal how nanoscale heterochromatin domains influence gene expression.Nature communications · 2025Article
- Comparative genomics provides insights into the biogeographic and biochemical diversity of meliaceous species.Nature communications · 2025Article
- Predicting chromatin conformation contact maps.PloS one · 2025Article
- CWL-Based Analysis Pipeline for Hi-C Data: From FASTQ Files to Matrices.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Memory CD4+ T cells sequentially restructure their 3D genome during stepwise activation.Frontiers in cell and developmental biology · 2025Article
- A method for chromatin domain partitioning based on hypergraph clustering.Computational and structural biotechnology journal · 2024Article
- Multiscale 3D genome rewiring during PTF1A-mediated somatic cell reprogramming into neural stem cells.Communications biology · 2024Article
- Sex and neo-sex chromosome evolution in beetles.PLoS genetics · 2024Article
- DiffGR: Detecting Differentially Interacting Genomic Regions from Hi-C Contact Maps.Genomics, proteomics & bioinformatics · 2024Article
- 3D epigenomics and 3D epigenopathies.BMB reports · 2024Review
27 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 2 institutions in 1 country.
Funding
Abstract
With the advent of massively parallel sequencing, considerable work has gone into adapting chromosome conformation capture (3C) techniques to study chromosomal architecture at a genome-wide scale. We recently demonstrated that the inactive murine X chromosome adopts a bipartite structure using a novel 3C protocol, termed in situ DNase Hi-C. Like traditional Hi-C protocols, in situ DNase Hi-C requires that chromatin be chemically cross-linked, digested, end-repaired, and proximity-ligated with a biotinylated bridge adaptor. The resulting ligation products are optionally sheared, affinity-purified via streptavidin bead immobilization, and subjected to traditional next-generation library preparation for Illumina paired-end sequencing. Importantly, in situ DNase Hi-C obviates the dependence on a restriction enzyme to digest chromatin, instead relying on the endonuclease DNase I. Libraries generated by in situ DNase Hi-C have a higher effective resolution than traditional Hi-C libraries, which makes them valuable in cases in which high sequencing depth is allowed for, or when hybrid capture technologies are expected to be used. The protocol described here, which involves ∼4 d of bench work, is optimized for the study of mammalian cells, but it can be broadly applicable to any cell or tissue of interest, given experimental parameter optimization.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.