ArticleGenome biology2007
Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed, 138 citations in OpenAlex.
- Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes.Nature ecology & evolution · 2026Article
- Conserved Noncoding Elements Evolve Around the Same Genes Throughout Metazoan Evolution.Genome biology and evolution · 2024Article
- Cis-regulatory control of mammalian Trps1 gene expression.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2024Article
- PlantPAN 4.0: updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters.Nucleic acids research · 2024Article
- DNA Conserved in Diverse Animals Since the Precambrian Controls Genes for Embryonic Development.Molecular biology and evolution · 2023Article
- Conserved noncoding sequences and de novo Mutator insertion alleles are imprinted in maize.Plant physiology · 2023Article
- tiRNAs: Insights into Their Biogenesis, Functions, and Future Applications in Livestock Research.Non-coding RNA · 2022Review
- High-quality reference genomes of swallowtail butterflies provide insights into their coloration evolution.Zoological research · 2022Article
- Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction.Systematic biology · 2021Article
- The Developmental Gene Hypothesis for Punctuated Equilibrium: Combined Roles of Developmental Regulatory Genes and Transposable Elements.BioEssays : news and reviews in molecular, cellular and developmental biology · 2020Review
- Genomic Insights into the Adaptive Convergent Evolution.Current genomics · 2019Review
- Ultraconserved Elements Occupy Specific Arenas of Three-Dimensional Mammalian Genome Organization.Cell reports · 2018Article
- Conserved non-coding elements: developmental gene regulation meets genome organization.Nucleic acids research · 2017Review
- Chromatin accessibility dynamics reveal novel functional enhancers inGenome research · 2017Article
- Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom.The New phytologist · 2017Article
- Article
- GC Content Heterogeneity Transition of Conserved Noncoding Sequences Occurred at the Emergence of Vertebrates.Genome biology and evolution · 2016Article
- Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle.Genome biology and evolution · 2016Article
- A Simple Predictive Enhancer Syntax for Hindbrain Patterning Is Conserved in Vertebrate Genomes.PloS one · 2015Article
- Lineage-specific conserved noncoding sequences of plant genomes: their possible role in nucleosome positioning.Genome biology and evolution · 2014Article
3 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundThe human genome contains thousands of non-coding sequences that are often more conserved between vertebrate species than protein-coding exons. These highly conserved non-coding elements (CNEs) are associated with genes that coordinate development, and have been proposed to act as transcriptional enhancers. Despite their extreme sequence conservation in vertebrates, sequences homologous to CNEs have not been identified in invertebrates.
resultsHere we report that nematode genomes contain an alternative set of CNEs that share sequence characteristics, but not identity, with their vertebrate counterparts. CNEs thus represent a very unusual class of sequences that are extremely conserved within specific animal lineages yet are highly divergent between lineages. Nematode CNEs are also associated with developmental regulatory genes, and include well-characterized enhancers and transcription factor binding sites, supporting the proposed function of CNEs as cis-regulatory elements. Most remarkably, 40 of 156 human CNE-associated genes with invertebrate orthologs are also associated with CNEs in both worms and flies.
conclusionA core set of genes that regulate development is associated with CNEs across three animal groups (worms, flies and vertebrates). We propose that these CNEs reflect the parallel evolution of alternative enhancers for a common set of developmental regulatory genes in different animal groups. This 're-wiring' of gene regulatory networks containing key developmental coordinators was probably a driving force during the evolution of animal body plans. CNEs may, therefore, represent the genomic traces of these 'hard-wired' core gene regulatory networks that specify the development of each alternative animal body plan.
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