ArticleGenome biology2021
SPIN reveals genome-wide landscape of nuclear compartmentalization.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.
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Who cites it
80 citing papers in PubMed.
- Controlling for DNA dosage with whole-genome sequencing improves ATAC-seq peak calling.NAR genomics and bioinformatics · 2026Article
- Nuclear speckle-associated perispeckle networks partition active chromatin into gene expression niches.Cell reports · 2026Article
- Genome folding and nuclear speckles converge to orchestrate fibroblast activation.Science advances · 2026Article
- Pan-cell type continuous chromatin state annotation of 1,698 epigenomes from the International Human Epigenome Consortium.Genome biology · 2026Article
- Jointly-hic: joint decomposition of contact frequency maps captures salient features of genome architecture across tissues and development.Genome biology · 2026Article
- Relationship between the distribution of LEDGF along genes and positions of HIV-1 DNA integration.mBio · 2026Article
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- Transcription elongation can be sufficient, but is not necessary, to advance replication timing.EMBO reports · 2026Article
- Replication timing uncovers a two-compartment nuclear architecture of interphase euchromatin.The Plant cell · 2026Article
- Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm.Nature cell biology · 2026Article
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- Evolution of chromosomes and nuclear architectures of amniotes.Nature communications · 2025Article
- Generating three-dimensional genome structures with a variational quantum algorithm.Briefings in bioinformatics · 2025Article
- From Rabl-like Architecture to Chromosome Territories: A Conserved Developmental Transition in Animal Genomes.Molecular biology and evolution · 2025Article
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- CDACHIE: chromatin domain annotation by integrating chromatin interaction and epigenomic data with contrastive learning.Bioinformatics (Oxford, England) · 2025Article
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- Regulatory roles of three-dimensional structures of chromatin domains.Genome biology · 2025Article
- CTCF/RAD21 organize the ground state of chromatin-nuclear speckle association.Nature structural & molecular biology · 2025Article
- Timed chromatin invasion during mitosis governs prototype foamy virus integration site selection and infectivity.Nucleic acids research · 2025Article
20 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
Funding
Abstract
We report SPIN, an integrative computational method to reveal genome-wide intranuclear chromosome positioning and nuclear compartmentalization relative to multiple nuclear structures, which are pivotal for modulating genome function. As a proof-of-principle, we use SPIN to integrate nuclear compartment mapping (TSA-seq and DamID) and chromatin interaction data (Hi-C) from K562 cells to identify 10 spatial compartmentalization states genome-wide relative to nuclear speckles, lamina, and putative associations with nucleoli. These SPIN states show novel patterns of genome spatial organization and their relation to other 3D genome features and genome function (transcription and replication timing). SPIN provides critical insights into nuclear spatial and functional compartmentalization.
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