ArticleNucleic acids research2018
From 1D sequence to 3D chromatin dynamics and cellular functions: a phase separation perspective.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 74 citations in OpenAlex.
- GenoME: a MoE-based generative model for individualized, multimodal prediction and perturbation of genomic profiles.Nucleic acids research · 2026Article
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Polycomb repressive-deubiquitinase complex safeguards oocyte epigenome and female fertility by restraining Polycomb activity.Nature communications · 2026Article
- Analysis of long-range contacts across cell types outlines a core sequence determinant of 3D genome organization.NAR genomics and bioinformatics · 2025Article
- Hierarchical Prediction and Perturbation of Chromatin Organization Reveal How Loop Domains Mediate Higher-Order Architectures.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- The emerging sequence grammar of 3D genome organisation.Human genetics · 2025Review
- On correlative and causal links of replicative epimutations.Trends in genetics : TIG · 2025Review
- Unraveling the key role of chromatin structure in cancer development through epigenetic landscape characterization of oral cancer.Molecular cancer · 2024Article
- Article
- From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization.Annual review of biophysics · 2024Review
- Tet-mediated DNA methylation dynamics affect chromosome organization.Nucleic acids research · 2024Article
- Spatiotemporal DNA methylation dynamics shape megabase-scale methylome landscapes.Life science alliance · 2024Article
- OpenNucleome for high resolution nuclear structural and dynamical modeling.bioRxiv : the preprint server for biology · 2024Article
- A novel approach to risk exposure and epigenetics-the use of multidimensional context to gain insights into the early origins of cardiometabolic and neurocognitive health.BMC medicine · 2023Article
- Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction.Biophysical journal · 2023Article
- Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome.Genome research · 2023Article
- Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction.bioRxiv : the preprint server for biology · 2023Article
- Plant Tolerance to Drought Stress with Emphasis on Wheat.Plants (Basel, Switzerland) · 2023Review
- PML and PML-like exonucleases restrict retrotransposons in jawed vertebrates.Nucleic acids research · 2023Article
- Phase Separation: Direct and Indirect Driving Force for High-Order Chromatin Organization.Genes · 2023Review
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The high-order chromatin structure plays a non-negligible role in gene regulation. However, the mechanism, especially the sequence dependence for the formation of varied chromatin structures in different cells remains to be elucidated. As the nucleotide distributions in human and mouse genomes are highly uneven, we identified CGI (CpG island) forest and prairie genomic domains based on CGI densities of a species, dividing the genome into two sequentially, epigenetically, and transcriptionally distinct regions. These two megabase-sized domains also spatially segregate to different extents in different cell types. Forests and prairies show enhanced segregation from each other in development, differentiation, and senescence, meanwhile the multi-scale forest-prairie spatial intermingling is cell-type specific and increases in differentiation, helping to define cell identity. We propose that the phase separation of the 1D mosaic sequence in space serves as a potential driving force, and together with cell type specific epigenetic marks and transcription factors, shapes the chromatin structure in different cell types. The mosaicity in genome of different species in terms of forests and prairies could relate to observations in their biological processes like development and aging. In this way, we provide a bottoms-up theory to explain the chromatin structural and epigenetic changes in different processes.
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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.