ArticleNature protocols2021
Identifying high-confidence capture Hi-C interactions using CHiCANE.
Article in Nature protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Chromatin-associated intronic RNAs from long genes form introsomes that shape nuclear architecture in neuronal cells.bioRxiv : the preprint server for biology · 2026Article
- Article
- Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).Methods in molecular biology (Clifton, N.J.) · 2026Article
- Techniques to detect physical interactions between genomic regions.Epigenomics · 2025Review
- Read Mapping for Hi-C Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- RADIP technology comprehensively identifies H3K27me3-associated RNA-chromatin interactions.Nucleic acids research · 2024Article
- Using paired-end read orientations to assess technical biases in capture Hi-C.NAR genomics and bioinformatics · 2024Article
- Accelerating 3D genomics data analysis with Microcket.Communications biology · 2024Article
- SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease.Nature communications · 2023Article
- Approaches for Modes of Action Study of Long Non-Coding RNAs: From Single Verification to Genome-Wide Determination.International journal of molecular sciences · 2023Review
- Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters.Genome biology · 2023Article
- Novel biological insights revealed from the investigation of multiscale genome architecture.Computational and structural biotechnology journal · 2023Review
- Long-range chromosomal interactions increase and mark repressed gene expression during adipogenesis.Epigenetics · 2022Article
- Integrating epigenetics and metabolomics to advance treatments for pulmonary arterial hypertension.Biochemical pharmacology · 2022Review
- Comparison of Capture Hi-C Analytical Pipelines.Frontiers in genetics · 2022Article
- 3D genome organization links non-coding disease-associated variants to genes.Frontiers in cell and developmental biology · 2022Review
- Transcriptional enhancers and their communication with gene promoters.Cellular and molecular life sciences : CMLS · 2021Review
- Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools.Nature protocols · 2021Article
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
The ability to identify regulatory interactions that mediate gene expression changes through distal elements, such as risk loci, is transforming our understanding of how genomes are spatially organized and regulated. Capture Hi-C (CHi-C) is a powerful tool to delineate such regulatory interactions. However, primary analysis and downstream interpretation of CHi-C profiles remains challenging and relies on disparate tools with ad-hoc input/output formats and specific assumptions for statistical modeling. Here we present a data processing and interaction calling toolkit (CHiCANE), specialized for the analysis and meaningful interpretation of CHi-C assays. In this protocol, we demonstrate applications of CHiCANE to region capture Hi-C (rCHi-C) and promoter capture Hi-C (pCHi-C) libraries, followed by quality assessment of interaction peaks, as well as downstream analysis specific to rCHi-C and pCHi-C to aid functional interpretation. For a typical rCHi-C/pCHi-C dataset this protocol takes up to 3 d for users with a moderate understanding of R programming and statistical concepts, although this is dependent on dataset size and compute power available. CHiCANE is freely available at https://cran.r-project.org/web/packages/chicane .
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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.