ArticleBMC genomics2004
Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes.
Article in BMC genomics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 158 papers.
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Who cites it
158 citing papers in PubMed, 335 citations in OpenAlex.
- Regulatory Evolution and the Genetic Basis of Human Brain Expansion.Journal of molecular evolution · 2026Review
- Characterizing highly conserved fragments in 3'UTRs via statistical and transfer learning approaches.NAR genomics and bioinformatics · 2026Article
- Non-Random Association of Ultraconserved Genomic Elements (UCE) with Human Genes.International journal of molecular sciences · 2026Article
- CNEwrap: a scalable toolkit with a novel algorithm for large-scale genome-wide accelerated conserved non-coding elements detection.Nucleic acids research · 2026Article
- Functional genomics analysis of developing zebrafish and human endoderm reveals highly conservedGenome research · 2026Article
- Evaluating Probe Design for Phylogenomics Across Taxonomic Scales: First Steps for Applying Ultraconserved Elements in an Understudied Class (Mollusca: Polyplacophora).Molecular ecology resources · 2026Article
- Characterizing and decoding ultraconserved regions uncovers their regulatory significance in human brain development and disorders.Communications biology · 2025Article
- Two deeply conserved non-coding sequences control PLETHORA1/2 expression and coordinate embryo and root development.Plant communications · 2025Article
- Article
- The transcriptome of the olm provides insights into its evolution and gene expression.Scientific reports · 2025Article
- Functional associations of evolutionarily recent human genes exhibit sensitivity to the 3D genome landscape and disease.bioRxiv : the preprint server for biology · 2024Article
- The Evolution of Ultraconserved Elements in Vertebrates.Molecular biology and evolution · 2024Article
- Patterns of Genetic Diversity and Gene Flow Associated With an Aridity Gradient in Populations of Common Mole-rats, Cryptomys hottentotus hottentotus.Genome biology and evolution · 2024Article
- Conserved Noncoding Elements Evolve Around the Same Genes Throughout Metazoan Evolution.Genome biology and evolution · 2024Article
- Developmental and evolutionary comparative analysis of a regulatory landscape in mouse and chicken.Development (Cambridge, England) · 2022Article
- Perfect and imperfect views of ultraconserved sequences.Nature reviews. Genetics · 2022Review
- B Chromosomes' Sequences in Yellow-Necked MiceLife (Basel, Switzerland) · 2021Article
- Functional and structural basis of extreme conservation in vertebrate 5' untranslated regions.Nature genetics · 2021Article
- Fish-Ing for Enhancers in the Heart.International journal of molecular sciences · 2021Review
- Sox2-Development (Cambridge, England) · 2021Article
98 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundEvolutionarily conserved sequences within or adjoining orthologous genes often serve as critical cis-regulatory regions. Recent studies have identified long, non-coding genomic regions that are perfectly conserved between human and mouse, termed ultra-conserved regions (UCRs). Here, we focus on UCRs that cluster around genes involved in early vertebrate development; genes conserved over 450 million years of vertebrate evolution.
resultsBased on a high resolution detection procedure, our UCR set enables novel insights into vertebrate genome organization and regulation of developmentally important genes. We find that the genomic positions of deeply conserved UCRs are strongly associated with the locations of genes encoding key regulators of development, with particularly strong positional correlation to transcription factor-encoding genes. Of particular importance is the observation that most UCRs are clustered into arrays that span hundreds of kilobases around their presumptive target genes. Such a hallmark signature is present around several uncharacterized human genes predicted to encode developmentally important DNA-binding proteins.
conclusionThe genomic organization of UCRs, combined with previous findings, suggests that UCRs act as essential long-range modulators of gene expression. The exceptional sequence conservation and clustered structure suggests that UCR-mediated molecular events involve greater complexity than traditional DNA binding by transcription factors. The high-resolution UCR collection presented here provides a wealth of target sequences for future experimental studies to determine the nature of the biochemical mechanisms involved in the preservation of arrays of nearly identical non-coding sequences over the course of vertebrate evolution.
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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.