ArticleNature genetics2016
A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation.
Article in Nature genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
63 citing papers in PubMed.
- Topological mixing and irreversibility in animal chromosome evolution.Science advances · 2026Article
- Article
- Epigenomics and transcriptomics profiles of developing zebrafish heart cells.Scientific data · 2025Article
- The application of irreversible genomic states to define and trace ancient cell type homologies.EvoDevo · 2025Article
- A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence.Nature communications · 2024Article
- A Recql5 mutant facilitates complex CRISPR/Cas9-mediated chromosomal engineering in mouse zygotes.Genetics · 2024Article
- Rewiring of the epigenome and chromatin architecture by exogenously induced retinoic acid signaling during zebrafish embryonic development.Nucleic acids research · 2024Article
- Targeting the chromatin structural changes of antitumor immunity.Journal of pharmaceutical analysis · 2024Review
- Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences.Nature ecology & evolution · 2024Article
- A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes.BMC biology · 2024Article
- Article
- Emergence of novel genomic regulatory regions associated with light-organ development in the bobtail squid.iScience · 2023Article
- Three-dimensional genome rewiring in loci with human accelerated regions.Science (New York, N.Y.) · 2023Article
- Article
- Chromatin Remodeling Enzyme Snf2h Is Essential for Retinal Cell Proliferation and Photoreceptor Maintenance.Cells · 2023Article
- Article
- Three amphioxus reference genomes reveal gene and chromosome evolution of chordates.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Hox genes in development and beyond.Development (Cambridge, England) · 2023Article
- The complete chloroplast genome of two Firmiana species and comparative analysis with other related species.Genetica · 2022Article
- Comparative chloroplast genome analyses of Amomum: insights into evolutionary history and species identification.BMC plant biology · 2022Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The HoxA and HoxD gene clusters of jawed vertebrates are organized into bipartite three-dimensional chromatin structures that separate long-range regulatory inputs coming from the anterior and posterior Hox-neighboring regions. This architecture is instrumental in allowing vertebrate Hox genes to pattern disparate parts of the body, including limbs. Almost nothing is known about how these three-dimensional topologies originated. Here we perform extensive 4C-seq profiling of the Hox cluster in embryos of amphioxus, an invertebrate chordate. We find that, in contrast to the architecture in vertebrates, the amphioxus Hox cluster is organized into a single chromatin interaction domain that includes long-range contacts mostly from the anterior side, bringing distant cis-regulatory elements into contact with Hox genes. We infer that the vertebrate Hox bipartite regulatory system is an evolutionary novelty generated by combining ancient long-range regulatory contacts from DNA in the anterior Hox neighborhood with new regulatory inputs from the posterior side.
Indexed as
Identifiers
26829752What OpenQuestion holds
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.