ArticleNucleic acids research2016
De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles.
Article in Nucleic acids research, 2016. 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, 50 citations in OpenAlex.
- Single-Cell Hi-C Technologies and Computational Data Analysis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- Machine and Deep Learning Methods for Predicting 3D Genome Organization.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Article
- Summary of ChIP-Seq Methods and Description of an Optimized ChIP-Seq Protocol.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Article
- Computational methods for the prediction of chromatin interaction and organization using sequence and epigenomic profiles.Briefings in bioinformatics · 2021Article
- DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell.Genome biology · 2021Article
- Deciphering hierarchical organization of topologically associated domains through change-point testing.BMC bioinformatics · 2021Article
- Histone modifications form a cell-type-specific chromosomal bar code that persists through the cell cycle.Scientific reports · 2021Article
- Quantitative prediction of enhancer-promoter interactions.Genome research · 2020Article
- A computational method to predict topologically associating domain boundaries combining histone Marks and sequence information.BMC genomics · 2019Article
- 7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs.BMC genomics · 2019Article
- Predicting three-dimensional genome organization with chromatin states.PLoS computational biology · 2019Article
- TADKB: Family classification and a knowledge base of topologically associating domains.BMC genomics · 2019Article
- Revealing Gene Function and Transcription Relationship by Reconstructing Gene-Level Chromatin Interaction.Computational and structural biotechnology journal · 2019Article
- Characteristic arrangement of nucleosomes is predictive of chromatin interactions at kilobase resolution.Nucleic acids research · 2017Article
- Sparse conserved under-methylated CpGs are associated with high-order chromatin structure.Genome biology · 2017Article
- A critical assessment of topologically associating domain prediction tools.Nucleic acids research · 2017Article
- Inference of cell type specific regulatory networks on mammalian lineages.Current opinion in systems biology · 2017Article
- 3DSNP: a database for linking human noncoding SNPs to their three-dimensional interacting genes.Nucleic acids research · 2017Article
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Authors and funding
5 authors at 1 institution in 2 countries.
Funding
Abstract
Defining chromatin interaction frequencies and topological domains is a great challenge for the annotations of genome structures. Although the chromosome conformation capture (3C) and its derivative methods have been developed for exploring the global interactome, they are limited by high experimental complexity and costs. Here we describe a novel computational method, called CITD, for de novo prediction of the chromatin interaction map by integrating histone modification data. We used the public epigenomic data from human fibroblast IMR90 cell and embryonic stem cell (H1) to develop and test CITD, which can not only successfully reconstruct the chromatin interaction frequencies discovered by the Hi-C technology, but also provide additional novel details of chromosomal organizations. We predicted the chromatin interaction frequencies, topological domains and their states (e.g. active or repressive) for 98 additional cell types from Roadmap Epigenomics and ENCODE projects. A total of 131 protein-coding genes located near 78 preserved boundaries among 100 cell types are found to be significantly enriched in functional categories of the nucleosome organization and chromatin assembly. CITD and its predicted results can be used for complementing the topological domains derived from limited Hi-C data and facilitating the understanding of spatial principles underlying the chromosomal organization.
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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.