ArticleBMC biology2022
Comparative 3D genome architecture in vertebrates.
Article in BMC biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 56 citations in OpenAlex.
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- Multi-Layer Transcriptomic Comparison Across Human, Pig, and Mouse Informs Tissue- and Trait-Specific Animal Model Selection.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- The 3D genome of Gigaspora margarita unveils stable chromatin and nucleolar organization and symbiont-dependent genome dynamics.The New phytologist · 2026Article
- Non-coding DNA dynamics and its roles as a physical barrier in genome safeguarding across early development and evolution.Heredity · 2026Review
- Bony fish genomes: Status and gaps.Journal of fish biology · 2026Review
- Condensin IDC has a functional ATPase that is required for X-Chromosome dosage compensation in C. elegans.Genetics · 2026Article
- Integrated Symbiotic Pleiotropy: Long Non-Coding RNAs and Disordered Proteins Interweaving the Functional Layers of the Eukaryotic Cell.International journal of molecular sciences · 2026Review
- The 3D genomics of lampbrush chromosomes highlights the role of active transcription in chromatin organization.Nucleic acids research · 2026Article
- A compendium of chromatin interaction maps in the Giant Panda genome.Communications biology · 2026Article
- LncRNA CISTR-ACT regulates cell size in human and mouse by guiding FOSL2.Nature communications · 2025Article
- Evolution of chromosomes and nuclear architectures of amniotes.Nature communications · 2025Article
- Haplotype-Resolved Chromatin Conformation Data Reveals Relationship Between Transposable Elements and Chromosomal Pairing.Genome biology and evolution · 2025Article
- Integrating Hi-C data and RNA-seq data to reveal the 3D genome in sheep.BMC genomics · 2025Article
- 3D Genome Constrains Breakpoints of Inversions That Can Act as Barriers to Gene Flow in the Stickleback.Molecular ecology · 2025Article
- Article
- Mapping the regulatory genetic landscape of complex traits using a chicken advanced intercross line.Nature communications · 2025Article
- An integrative 3D-genome database for plants.Plant communications · 2025Article
- The 3D genome of plasma cells in multiple myeloma.Scientific reports · 2025Article
- Topologically associating domains and the evolution of three-dimensional genome architecture in rice.The Plant journal : for cell and molecular biology · 2025Article
- 3D Genome Engineering: Current Advances and Therapeutic Opportunities in Human Diseases.Research (Washington, D.C.) · 2025Review
Corrections and comments
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Authors and funding
16 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe three-dimensional (3D) architecture of the genome has a highly ordered and hierarchical nature, which influences the regulation of essential nuclear processes at the basis of gene expression, such as gene transcription. While the hierarchical organization of heterochromatin and euchromatin can underlie differences in gene expression that determine evolutionary differences among species, the way 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species.
resultsThis analysis shows a correlation between genome size and chromosome length that affects chromosome territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through the evolution of vertebrates. Furthermore, conservation of topologically associating domains (TADs) appears strongly associated with the modularity of expression profiles across species. Additionally, LINE and SINE transposable elements likely contribute to heterochromatin and euchromatin organization, respectively, during the evolution of genome architecture.
conclusionsOur analysis uncovers organizational features that appear to determine the conservation and transcriptional regulation of functional genes across species. These findings can guide ongoing investigations of genome evolution by extending our understanding of the mechanisms shaping genome architecture.
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Registered trials
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.