ArticleProceedings of the National Academy of Sciences of the United States of America2016
Topologically associated domains enriched for lineage-specific genes reveal expression-dependent nuclear topologies during myogenesis.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 60 citations in OpenAlex.
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- Genes that are Used Together are More Likely to be Fused Together in Evolution by Mutational Mechanisms: A Bioinformatic Test of the Used-Fused Hypothesis.Evolutionary biology · 2023Article
- Multiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in Drosophila.Nature communications · 2022Article
- The Impact of Space and Time on the Functional Output of the Genome.Cold Spring Harbor perspectives in biology · 2022Review
- Making sense of the linear genome, gene function and TADs.Epigenetics & chromatin · 2022Article
- Hierarchical chromatin features reveal the toxin production in Bungarus multicinctus.Chinese medicine · 2021Article
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- Histone variants in skeletal myogenesis.Epigenetics · 2021Review
- TGFβ promotes widespread enhancer chromatin opening and operates on genomic regulatory domains.Nature communications · 2020Article
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- Biased visibility in Hi-C datasets marks dynamically regulated condensed and decondensed chromatin states genome-wide.BMC genomics · 2020Article
- Cohesin controls intestinal stem cell identity by maintaining association of Escargot with target promoters.eLife · 2020Article
- MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome.Genome research · 2020Article
- Varying levels of X chromosome coalescence in female somatic cells alters the balance of X-linked dosage compensation and is implicated in female-dominant systemic lupus erythematosus.Scientific reports · 2019Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The linear distribution of genes across chromosomes and the spatial localization of genes within the nucleus are related to their transcriptional regulation. The mechanistic consequences of linear gene order, and how it may relate to the functional output of genome organization, remain to be fully resolved, however. Here we tested the relationship between linear and 3D organization of gene regulation during myogenesis. Our analysis has identified a subset of topologically associated domains (TADs) that are significantly enriched for muscle-specific genes. These lineage-enriched TADs demonstrate an expression-dependent pattern of nuclear organization that influences the positioning of adjacent nonenriched TADs. Therefore, lineage-enriched TADs inform cell-specific genome organization during myogenesis. The reduction of allelic spatial distance of one of these domains, which contains Myogenin, correlates with reduced transcriptional variability, identifying a potential role for lineage-specific nuclear topology. Using a fusion-based strategy to decouple mitosis and myotube formation, we demonstrate that the cell-specific topology of syncytial nuclei is dependent on cell division. We propose that the effects of linear and spatial organization of gene loci on gene regulation are linked through TAD architecture, and that mitosis is critical for establishing nuclear topologies during cellular differentiation.
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