ArticleNucleic acids research2022
Detecting TAD-like domains from RNA-associated interactions.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 10 citations in OpenAlex.
- InteRRact: a web server for the interactive exploration and comparison of transcriptome-wide RNA-RNA interactions.NAR genomics and bioinformatics · 2026Article
- A comparative analysis of topological domain callers over RNA-associated interactome.BMC bioinformatics · 2026Article
- RADIP technology comprehensively identifies H3K27me3-associated RNA-chromatin interactions.Nucleic acids research · 2024Article
- Role of condensates in modulating DNA repair pathways and its implication for chemoresistance.The Journal of biological chemistry · 2023Review
- The 3D genome and its impacts on human health and disease.Life medicine · 2023Review
- Incorporating cell hierarchy to decipher the functional diversity of single cells.Nucleic acids research · 2023Article
- AP-2δ Is the Most Relevant Target of AP-2 Family-Focused Cancer Therapy and Affects Genome Organization.Cells · 2022Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Topologically associated domains (TADs) are crucial chromatin structural units. Evidence has illustrated that RNA-chromatin and RNA-RNA spatial interactions, so-called RNA-associated interactions (RAIs), may be associated with TAD-like domains (TLDs). To decode hierarchical TLDs from RAIs, we proposed SuperTLD, a domain detection algorithm incorporating imputation. We applied SuperTLD on four RAI data sets and compared TLDs with the TADs identified from the corresponding Hi-C datasets. The TLDs and TADs share a moderate similarity of hierarchies ≥ 0.5312 and the finest structures ≥ 0.8295. Comparison between boundaries and domains further demonstrated the novelty of TLDs. Enrichment analysis of epigenetic characteristics illustrated that the novel TLDs exhibit an enriched CTCF by 0.6245 fold change and H3 histone marks enriched within domains. GO analysis on the TLD novel boundaries exhibited enriched diverse terms, revealing TLDs' formation mechanism related closely to gene regulation.
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