ArticleNucleic acids research2015
Structural heterogeneity and functional diversity of topologically associating domains in mammalian genomes.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Integrating heterogeneity into topologically associating domain boundary prediction in large genomic context in human.NAR genomics and bioinformatics · 2026Article
- Mapping early PRC2 nucleation sites upon Suz12 reintroduction reveals features ofbioRxiv : the preprint server for biology · 2025Article
- LDB1 establishes multi-enhancer networks to regulate gene expression.Molecular cell · 2025Article
- LDB1 establishes multi-enhancer networks to regulate gene expression.bioRxiv : the preprint server for biology · 2024Article
- A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains.Nature communications · 2024Article
- Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single-cell transcriptome analysis.Frontiers in molecular biosciences · 2024Article
- Decoding the spatial chromatin organization and dynamic epigenetic landscapes of macrophage cells during differentiation and immune activation.Nature communications · 2022Article
- TADfit is a multivariate linear regression model for profiling hierarchical chromatin domains on replicate Hi-C data.Communications biology · 2022Article
- Cotton D genome assemblies built with long-read data unveil mechanisms of centromere evolution and stress tolerance divergence.BMC biology · 2021Article
- Spatial density of open chromatin: an effective metric for the functional characterization of topologically associated domains.Briefings in bioinformatics · 2021Article
- Methods for mapping 3D chromosome architecture.Nature reviews. Genetics · 2020Review
- HiTAD: detecting the structural and functional hierarchies of topologically associating domains from chromatin interactions.Nucleic acids research · 2017Article
- Developmentally regulated higher-order chromatin interactions orchestrate B cell fate commitment.Nucleic acids research · 2017Article
- The TAD-pathway for GWAS signals.European journal of human genetics : EJHG · 2017Article
- Topologically-associating domains: gene warehouses adapted to serve transcriptional regulation.Transcription · 2016Review
- 4D nucleomes in single cells: what can computational modeling reveal about spatial chromatin conformation?Genome biology · 2016Review
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4 authors.
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Abstract
Recent chromosome conformation capture (3C) derived techniques have revealed that topologically associating domain (TAD) is a pervasive element in chromatin three-dimensional (3D) organization. However, there is currently no parameter to quantitatively measure the structural characteristics of TADs, thus obscuring our understanding on the structural and functional differences among TADs. Based on our finding that there exist intrinsic chromatin interaction patterns in TADs, we define a theoretical parameter, called aggregation preference (AP), to characterize TAD structures by capturing the interaction aggregation degree. Applying this defined parameter to 11 Hi-C data sets generated by both traditional and in situ Hi-C experimental pipelines, our analyses reveal that heterogeneous structures exist among TADs, and this structural heterogeneity is significantly correlated to DNA sequences, epigenomic signals and gene expressions. Although TADs can be stable in genomic positions across cell lines, structural comparisons show that a considerable number of stable TADs undergo significantly structural rearrangements during cell changes. Moreover, the structural change of TAD is tightly associated with its transcription remodeling. Altogether, the theoretical parameter defined in this work provides a quantitative method to link structural characteristics and biological functions of TADs, and this linkage implies that chromatin interaction pattern has the potential to mark transcription activity in TADs.
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