ArticlePLoS genetics2022
HiCuT: An efficient and low input method to identify protein-directed chromatin interactions.
Article in PLoS genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 30 citations in OpenAlex.
- p-LoopF is associated with chromatin looping in large introns of Ginkgo biloba.Cell research · 2026Article
- Truncated Life History Underlies Rapid Local Adaptation in Island Rattlesnake Venom Expression.Genome biology and evolution · 2026Article
- PATTY corrects open-chromatin bias for improved bulk and single-cell CUT&Tag profiling.Nature communications · 2026Article
- Highly efficient chromatin conformation capture with post-enrichment in single cells by HiChew.Genome biology · 2026Article
- Trimodal single-cell profiling of transcriptome, epigenome and 3D genome in complex tissues with scHiCAR.Nature biotechnology · 2026Article
- An integrated multi-omics and network analysis of neutrophil differentiation from initial- to late-stage.Genome biology · 2026Article
- PATTY corrects open-chromatin bias for improved bulk and single-cell CUT&Tag profiling.Research square · 2025Article
- Nuclear FGF2 orchestrates phase separation-mediated rDNA chromatin architecture to control BMSCs cell fate.Bone research · 2025Article
- PATTY corrects open chromatin bias for improved bulk and single-cell CUT&Tag profiling.bioRxiv : the preprint server for biology · 2025Article
- Techniques to detect physical interactions between genomic regions.Epigenomics · 2025Review
- The Lyn/RUVBL1 Complex Promotes Colorectal Cancer Liver Metastasis by Regulating Arachidonic Acid Metabolism Through Chromatin Remodeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Active enhancers: recent research advances and insights into disease.Biology direct · 2024Review
- Improved simultaneous mapping of epigenetic features and 3D chromatin structure via ViCAR.Genome biology · 2024Article
- Hi-Tag: a simple and efficient method for identifying protein-mediated long-range chromatin interactions with low cell numbers.Science China. Life sciences · 2024Article
- BL-Hi-C reveals the 3D genome structure ofHorticulture research · 2024Article
- Technological advances in probing 4D genome organization.Current opinion in cell biology · 2023Review
- Tn5 DNA Transposase in Multi-Omics Research.Methods and protocols · 2023Review
- Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution.Nature communications · 2023Article
- ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms.Nucleic acids research · 2023Article
- Transcriptional regulation of innate lymphoid cells and T cells by aryl hydrocarbon receptor.Frontiers in immunology · 2023Review
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
3D genome organization regulates gene expression, and disruption of these long-range (>20kB) DNA-protein interactions results in pathogenic phenotypes. Chromosome conformation methods in conjunction with chromatin immunoprecipitation were used to decipher protein-directed chromatin interactions. However, these methods required abundant starting material (>500,000 cells), sizable number of sequencing reads (>100 million reads), and elaborate data processing methods to reduce background noise, which limited their use in primary cells. Hi-C Coupled chromatin cleavage and Tagmentation (HiCuT) is a new transposase-assisted tagmentation method that generates high-resolution protein directed long-range chromatin interactions as efficiently as existing methods, HiChIP and ChIA-PET, despite using 100,000 cells (5-fold less) and 12 million sequencing reads (8-fold fewer). Moreover, HiCuT generates high resolution fragment libraries with low background signal that are easily interpreted with minimal computational processing. We used HiCuT in human primary skin cells to link previously identified single nucleotide polymorphisms (SNPs) in skin disease to candidate genes and to identify functionally relevant transcription factors in an unbiased manner. HiCuT broadens the capacity for genomic profiling in systems previously unmeasurable, including primary cells, human tissue samples, and rare cell populations, and may be a useful tool for all investigators studying human genetics and personalized epigenomics.
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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.