ArticleScientific reports2019
DNA sequence-dependent chromatin architecture and nuclear hubs formation.
Article in Scientific reports, 2019. 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, 44 citations in OpenAlex.
- Multiscale physical effects of CpG methylation on DNA mechanics, nucleosome wrapping, and chromatin condensates.EMBO reports · 2026Article
- Prediction and functional interpretation of inter-chromosomal genome architecture from DNA sequence with TwinC.Nature communications · 2026Article
- The Fluid Mosaic Model of chromatin organization: integrating dynamics, conformational heterogeneity and multiscale organization.Communications biology · 2026Review
- Superabundant microRNAs are transcribed from human rDNA spacer promoters insulated by CTCF.Science advances · 2026Article
- The emerging sequence grammar of 3D genome organisation.Human genetics · 2025Review
- Article
- Small RNA Toxin-Assisted Evolution of GC-Preferred ErCas12a for Enhanced Genome Targeting Range.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Prediction and functional interpretation of inter-chromosomal genome architecture from DNA sequence with TwinC.bioRxiv : the preprint server for biology · 2025Article
- Employing bimodal representations to predict DNA bendability within a self-supervised pre-trained framework.Nucleic acids research · 2024Article
- Characterization of H3K9me3 and DNA methylation co-marked CpG-rich regions during mouse development.BMC genomics · 2023Article
- Combined SPT and FCS methods reveal a mechanism of RNAP II oversampling in cell nuclei.Scientific reports · 2023Article
- Emergence and influence of sequence bias in evolutionarily malleable, mammalian tandem arrays.BMC biology · 2023Article
- Mammalian nuclear speckles exhibit stable association with chromatin: a biochemical study.Nucleus (Austin, Tex.) · 2022Article
- Contribution of CRISPRable DNA to human complex traits.Communications biology · 2022Review
- Reconstruct high-resolution 3D genome structures for diverse cell-types using FLAMINGO.Nature communications · 2022Article
- The "Genomic Code": DNA Pervasively Moulds Chromatin Structures Leaving no Room for "Junk".Life (Basel, Switzerland) · 2021Review
- Phase separation of DNA: From past to present.Biophysical journal · 2021Review
- Histone modifications form a cell-type-specific chromosomal bar code that persists through the cell cycle.Scientific reports · 2021Article
- RNA Biogenesis Instructs Functional Inter-Chromosomal Genome Architecture.Frontiers in genetics · 2021Article
- IsoXpressor: A Tool to Assess Transcriptional Activity within Isochores.Genome biology and evolution · 2020Article
Corrections and comments
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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
In this study, by exploring chromatin conformation capture data, we show that the nuclear segregation of Topologically Associated Domains (TADs) is contributed by DNA sequence composition. GC-peaks and valleys of TADs strongly influence interchromosomal interactions and chromatin 3D structure. To gain insight on the compositional and functional constraints associated with chromatin interactions and TADs formation, we analysed intra-TAD and intra-loop GC variations. This led to the identification of clear GC-gradients, along which, the density of genes, super-enhancers, transcriptional activity, and CTCF binding sites occupancy co-vary non-randomly. Further, the analysis of DNA base composition of nucleolar aggregates and nuclear speckles showed strong sequence-dependant effects. We conjecture that dynamic DNA binding affinity and flexibility underlay the emergence of chromatin condensates, their growth is likely promoted in mechanically soft regions (GC-rich) of the lowest chromatin and nucleosome densities. As a practical perspective, the strong linear association between sequence composition and interchromosomal contacts can help define consensus chromatin interactions, which in turn may be used to study alternative states of chromatin architecture.
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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.