ArticleGenome research2012
Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
94 citing papers in PubMed, 158 citations in OpenAlex.
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- Gene clustering drives the transcriptional coherence of disparate biological processes in eukaryotes.iScience · 2026Article
- Topological mixing and irreversibility in animal chromosome evolution.Science advances · 2026Article
- An ancient anthozoan protein reveals an alternative evolutionary path of antiviral signalling.Nature ecology & evolution · 2026Article
- Evolutionary trajectories, early diversification, and species-specific amplification of the metazoan inhibitor of apoptosis (IAP) repertoire.Molecular biology and evolution · 2026Article
- Insights into cephalochordate genome and gene evolution from the early-diverging amphioxusProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes.Nature ecology & evolution · 2026Article
- Tunicates have a complex, highly dynamic TNF superfamily.PloS one · 2026Article
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- The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity.Genome biology and evolution · 2025Review
- Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods.bioRxiv : the preprint server for biology · 2025Article
- Evolutionarily diverse caveolins share a common structural framework built around amphipathic disks.The Journal of cell biology · 2025Article
- Genome synteny reveals hidden enhancer conservation.Nature genetics · 2025Article
- The application of irreversible genomic states to define and trace ancient cell type homologies.EvoDevo · 2025Article
- Morphogenesis of Fractofusus andersoni and the nature of early animal development.Nature communications · 2025Article
- Alternative splicing controls pan-neuronal homeobox gene expression.Genes & development · 2025Article
- Hemichordate cis-regulatory genomics and the gene expression dynamics of deuterostomes.Nature ecology & evolution · 2024Article
- Phylogenomic and synteny analysis of BAHD and SCP/SCPL gene families reveal their evolutionary histories in plant specialized metabolism.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Article
34 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 3 institutions in 3 countries.
Funding
Abstract
The order of genes in eukaryotic genomes has generally been assumed to be neutral, since gene order is largely scrambled over evolutionary time. Only a handful of exceptional examples are known, typically involving deeply conserved clusters of tandemly duplicated genes (e.g., Hox genes and histones). Here we report the first systematic survey of microsynteny conservation across metazoans, utilizing 17 genome sequences. We identified nearly 600 pairs of unrelated genes that have remained tightly physically linked in diverse lineages across over 600 million years of evolution. Integrating sequence conservation, gene expression data, gene function, epigenetic marks, and other genomic features, we provide extensive evidence that many conserved ancient linkages involve (1) the coordinated transcription of neighboring genes, or (2) genomic regulatory blocks (GRBs) in which transcriptional enhancers controlling developmental genes are contained within nearby bystander genes. In addition, we generated ChIP-seq data for key histone modifications in zebrafish embryos, which provided further evidence of putative GRBs in embryonic development. Finally, using chromosome conformation capture (3C) assays and stable transgenic experiments, we demonstrate that enhancers within bystander genes drive the expression of genes such as Otx and Islet, critical regulators of central nervous system development across bilaterians. These results suggest that ancient genomic functional associations are far more common than previously thought-involving ∼12% of the ancestral bilaterian genome-and that cis-regulatory constraints are crucial in determining metazoan 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.