ArticleNucleic acids research2017
Computational characterization of chromatin domain boundary-associated genomic elements.
Article in Nucleic acids research, 2017. 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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Who cites it
31 citing papers in PubMed.
- Integrating heterogeneity into topologically associating domain boundary prediction in large genomic context in human.NAR genomics and bioinformatics · 2026Article
- Systematic evaluation of the heterogeneity of topologically associating domain boundaries in a large genomic context in humans.NAR genomics and bioinformatics · 2026Article
- Chromatin accessibility classification of TAD boundaries discloses new architectural proteins.Nucleic acids research · 2026Article
- A functional overlap between actively transcribed genes and chromatin insulator elements.The EMBO journal · 2026Article
- The Many Faces of SetDB1.Epigenomes · 2026Review
- TPST2-mediated tyrosine sulfation orchestrates porcine preimplantation development.BMC biology · 2026Article
- Exploring the Shared Diagnostic Biomarkers and Molecular Mechanisms Related to Mitochondrial Dysfunction in Inflammatory Bowel Disease and Rheumatoid Arthritis.Current issues in molecular biology · 2026Article
- EmbedTAD Using Graph Embedding and Unsupervised Learning to Identify TADs from High-Resolution Hi-C Data.Communications biology · 2025Article
- A long noncoding RNA with enhancer-like function in pig zygotic genome activation.Journal of molecular cell biology · 2025Article
- Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function.Molecular cell · 2025Article
- ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF.Molecular cell · 2025Article
- Machine and Deep Learning Methods for Predicting 3D Genome Organization.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Clusters of lineage-specific genes are anchored by ZNF274 in repressive perinucleolar compartments.Science advances · 2024Article
- Article
- TAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function.Nature communications · 2023Article
- SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells.Nature communications · 2023Article
- Article
- TADfit is a multivariate linear regression model for profiling hierarchical chromatin domains on replicate Hi-C data.Communications biology · 2022Article
- SBTD: A Novel Method for Detecting Topological Associated Domains from Hi-C Data.Interdisciplinary sciences, computational life sciences · 2021Article
- Computational methods for the prediction of chromatin interaction and organization using sequence and epigenomic profiles.Briefings in bioinformatics · 2021Article
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Topologically associated domains (TADs) are 3D genomic structures with high internal interactions that play important roles in genome compaction and gene regulation. Their genomic locations and their association with CCCTC-binding factor (CTCF)-binding sites and transcription start sites (TSSs) were recently reported. However, the relationship between TADs and other genomic elements has not been systematically evaluated. This was addressed in the present study, with a focus on the enrichment of these genomic elements and their ability to predict the TAD boundary region. We found that consensus CTCF-binding sites were strongly associated with TAD boundaries as well as with the transcription factors (TFs) Zinc finger protein (ZNF)143 and Yin Yang (YY)1. TAD boundary-associated genomic elements include DNase I-hypersensitive sites, H3K36 trimethylation, TSSs, RNA polymerase II, and TFs such as Specificity protein 1, ZNF274 and SIX homeobox 5. Computational modeling with these genomic elements suggests that they have distinct roles in TAD boundary formation. We propose a structural model of TAD boundaries based on these findings that provides a basis for studying the mechanism of chromatin structure formation and gene regulation.
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