ArticleCurrent protocols2021
In situ Chromatin Interaction Analysis Using Paired-End Tag Sequencing.
Article in Current protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- The Encyclopedia of DNA Elements.bioRxiv : the preprint server for biology · 2026Article
- Cohesin extrudes chromatin loop unidirectionally through two modes of mechanisms in human cells.bioRxiv : the preprint server for biology · 2026Article
- HiChIA-Rep quantifies the similarity between enrichment-based chromatin interactions datasets.bioRxiv : the preprint server for biology · 2026Article
- Interplay between cohesin and RNA polymerase II in regulating chromatin interactions and gene transcription.Nature structural & molecular biology · 2026Article
- Extrachromosomal DNA associates with nuclear condensates and reorganizes chromatin structures to enhance oncogenic transcription.Cancer cell · 2025Article
- Genetics-nutrition interactions control diurnal enhancer-promoter dynamics and liver lipid metabolism.Cell metabolism · 2025Article
- Review
- Chromatin landscape alteration uncovers multiple transcriptional circuits during memory CD8+ T-cell differentiation.Protein & cell · 2025Article
- Evolutionary divergence in CTCF-mediated chromatin topology drives transcriptional innovation in humans.Nature communications · 2025Article
- Chromatin structure and gene transcription of recombinant p53 adenovirus vector within host.Frontiers in molecular biosciences · 2025Article
- Epigenetic Explorations of Neurological Disorders, the Identification Methods, and Therapeutic Avenues.International journal of molecular sciences · 2024Review
- 3D chromatin structures associated with ncRNAScience advances · 2024Article
- Advances in the multimodal analysis of the 3D chromatin structure and gene regulation.Experimental & molecular medicine · 2024Review
- Kdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neurons.Nature communications · 2024Article
- BRD9-SMAD2/3 Orchestrates Stemness and Tumorigenesis in Pancreatic Ductal Adenocarcinoma.Gastroenterology · 2024Article
- An intrinsically disordered region controlling condensation of a circadian clock component and rhythmic transcription in the liver.Molecular cell · 2023Article
- Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.Molecular cell · 2023Review
- 3D-GNOME 3.0: a three-dimensional genome modelling engine for analysing changes of promoter-enhancer contacts in the human genome.Nucleic acids research · 2023Article
- Capturing Chromosome Conformation Across Length Scales.Journal of visualized experiments : JoVE · 2023Article
- ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs.Nature communications · 2023Article
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
Chromatin Interaction Analysis Using Paired-End Tag Sequencing (ChIA-PET) is an established method to map protein-mediated chromatin interactions. A limitation, however, is that it requires a hundred million cells per experiment, which hampers its broad application in biomedical research, particularly in studies in which it is impractical to obtain a large number of cells from rare samples. To reduce the required input cell number while retaining high data quality, we developed an in situ ChIA-PET protocol, which requires as few as 1 million cells. Here, we describe detailed step-by-step procedures for performing in situ ChIA-PET from cultured cells, including both an experimental protocol for sample preparation and data generation and a computational protocol for data processing and visualization using the ChIA-PIPE pipeline. As the protocol significantly simplifies the experimental procedure, reduces ligation noise, and decreases the required input of cells compared to previous versions of ChIA-PET protocols, it can be applied to generate high-resolution chromatin contact maps mediated by various protein factors for a wide range of human and mouse primary cells. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Sample preparation and data generation Support Protocol: Bridge linker preparation Basic Protocol 2: Data processing and visualization.
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