ArticleNucleic acids research2020
Hierarchical chromatin organization detected by TADpole.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 39 citations in OpenAlex.
- TADShop: systematic benchmarking and identification of topologically associating domains.Nature methods · 2026Article
- A comparative analysis of topological domain callers over RNA-associated interactome.BMC bioinformatics · 2026Article
- A polymer physics model of the interphase cell nucleus for radiobiological simulations.Scientific reports · 2026Article
- Deciphering chromatin domain, domain community and chromunity for 3D genome maps with Mactop.Communications biology · 2025Article
- The hierarchical folding dynamics of topologically associating domains during early embryo development.BMC biology · 2025Article
- RobusTAD: reference panel based annotation of nested topologically associating domains.Genome biology · 2025Article
- A comprehensive review and benchmark of differential analysis tools for Hi-C data.Briefings in bioinformatics · 2025Review
- deepTAD: an approach for identifying topologically associated domains based on convolutional neural network and transformer model.Briefings in bioinformatics · 2025Article
- Uncovering topologically associating domains from three-dimensional genome maps with TADGATE.Nucleic acids research · 2025Article
- COCOA: A Framework for Fine-scale Mapping of Cell-type-specific Chromatin Compartments Using Epigenomic Information.Genomics, proteomics & bioinformatics · 2025Article
- Genome structural dynamics: insights from Gaussian network analysis of Hi-C data.Briefings in functional genomics · 2024Article
- A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains.Nature communications · 2024Article
- Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection.Bioinformatics (Oxford, England) · 2024Article
- Hi-C, a chromatin 3D structure technique advancing the functional genomics of immune cells.Frontiers in genetics · 2024Review
- The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data.Briefings in bioinformatics · 2023Review
- DeDoc2 Identifies and Characterizes the Hierarchy and Dynamics of Chromatin TAD-Like Domains in the Single Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Characterization of network hierarchy reflects cell state specificity in genome organization.Genome research · 2023Article
- TOAST: A novel method for identifying topologically associated domains based on graph auto-encoders and clustering.Computational and structural biotechnology journal · 2023Article
- HPTAD: A computational method to identify topologically associating domains from HiChIP and PLAC-seq datasets.Computational and structural biotechnology journal · 2023Article
- Nucleome programming is required for the foundation of totipotency in mammalian germline development.The EMBO journal · 2022Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The rapid development of Chromosome Conformation Capture (3C-based techniques), as well as imaging together with bioinformatics analyses, has been fundamental for unveiling that chromosomes are organized into the so-called topologically associating domains or TADs. While TADs appear as nested patterns in the 3C-based interaction matrices, the vast majority of available TAD callers are based on the hypothesis that TADs are individual and unrelated chromatin structures. Here we introduce TADpole, a computational tool designed to identify and analyze the entire hierarchy of TADs in intra-chromosomal interaction matrices. TADpole combines principal component analysis and constrained hierarchical clustering to provide a set of significant hierarchical chromatin levels in a genomic region of interest. TADpole is robust to data resolution, normalization strategy and sequencing depth. Domain borders defined by TADpole are enriched in main architectural proteins (CTCF and cohesin complex subunits) and in the histone mark H3K4me3, while their domain bodies, depending on their activation-state, are enriched in either H3K36me3 or H3K27me3, highlighting that TADpole is able to distinguish functional TAD units. Additionally, we demonstrate that TADpole's hierarchical annotation, together with the new DiffT score, allows for detecting significant topological differences on Capture Hi-C maps between wild-type and genetically engineered mouse.
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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.