ArticleNature ecology & evolution2022
Recent reconfiguration of an ancient developmental gene regulatory network in Heliocidaris sea urchins.
Article in Nature ecology & evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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
18 citing papers in PubMed, 34 citations in OpenAlex.
- A stage and anatomy ontology for embryogenesis in indirect-developing echinoderms.Development (Cambridge, England) · 2026Article
- Evolutionary innovation within conserved gene regulatory networks underlying biomineralized skeletons in Bilateria.Molecular biology and evolution · 2026Article
- Microbial communities experienced during early development shape the host immune system and epigenome.iScience · 2025Article
- Article
- Single-Cell Transcriptomics Reveals Evolutionary Reconfiguration of Embryonic Cell Fate Specification in the Sea Urchin Heliocidaris erythrogramma.Genome biology and evolution · 2025Article
- Developmental regulatory genes in recalcitrant forest trees: advances in somatic regeneration and genetic transformation.Frontiers in plant science · 2025Review
- Evolution of Maternal Provisioning and Development in the Ophiuroidea: Egg Size, Larval Form, and Parental Care.Integrative and comparative biology · 2024Article
- A chromosome-level genome assembly of tropical purple sea urchin Heliocidaris crassispina.Scientific data · 2024Article
- Contrasting the development of larval and adult body plans during the evolution of biphasic lifecycles in sea urchins.Development (Cambridge, England) · 2024Article
- Leveraging explainable deep learning methodologies to elucidate the biological underpinnings of Huntington's disease using single-cell RNA sequencing data.BMC genomics · 2024Article
- The brittle star genome illuminates the genetic basis of animal appendage regeneration.Nature ecology & evolution · 2024Article
- Single-cell transcriptomics reveals evolutionary reconfiguration of embryonic cell fate specification in the sea urchinbioRxiv : the preprint server for biology · 2024Article
- Chromosomal-level genome assembly of the long-spined sea urchinGigaByte (Hong Kong, China) · 2024Article
- Marine Invertebrates One Cell at A Time: Insights from Single-Cell Analysis.Integrative and comparative biology · 2023Review
- Comparative Analysis of Bivalve and Sea Urchin Genetics and Development: Investigating the Dichotomy in Bilateria.International journal of molecular sciences · 2023Review
- Near-Chromosomal-Level Genome Assembly of the Sea Urchin Echinometra lucunter, a Model for Speciation in the Sea.Genome biology and evolution · 2023Article
- High level of novelty under the hood of convergent evolution.Science (New York, N.Y.) · 2023Article
- Evolutionary Changes in the Chromatin Landscape Contribute to Reorganization of a Developmental Gene Network During Rapid Life History Evolution in Sea Urchins.Molecular biology and evolution · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Changes in developmental gene regulatory networks (dGRNs) underlie much of the diversity of life, but the evolutionary mechanisms that operate on regulatory interactions remain poorly understood. Closely related species with extreme phenotypic divergence provide a valuable window into the genetic and molecular basis for changes in dGRNs and their relationship to adaptive changes in organismal traits. Here we analyse genomes, epigenomes and transcriptomes during early development in two Heliocidaris sea urchin species that exhibit highly divergent life histories and in an outgroup species. Positive selection and chromatin accessibility modifications within putative regulatory elements are enriched on the branch leading to the derived life history, particularly near dGRN genes. Single-cell transcriptomes reveal a dramatic delay in cell fate specification in the derived state, which also has far fewer open chromatin regions, especially near conserved cell fate specification genes. Experimentally perturbing key transcription factors reveals profound evolutionary changes to early embryonic patterning events, disrupting regulatory interactions previously conserved for ~225 million years. These results demonstrate that natural selection can rapidly reshape developmental gene expression on a broad scale when selective regimes abruptly change. More broadly, even highly conserved dGRNs and patterning mechanisms in the early embryo remain evolvable under appropriate ecological circumstances.
Indexed as
Identifiers
What 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.