ArticleNucleic acids research2012
Hundreds of conserved non-coding genomic regions are independently lost in mammals.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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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
29 citing papers in PubMed, 49 citations in OpenAlex.
- Comparative analysis of conserved non-coding elements identifies gene regulatory networks rewired during the water-to-land transition in vertebrates.Biologia futura · 2026Article
- Experimental evidence for cancer resistance in a bat species.Nature communications · 2024Article
- Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages.Molecular biology and evolution · 2023Article
- Whole-genome comparisons identify repeated regulatory changes underlying convergent appendage evolution in diverse fish lineages.bioRxiv : the preprint server for biology · 2023Article
- Article
- Pleiotropic Enhancers are Ubiquitous Regulatory Elements in the Human Genome.Genome biology and evolution · 2022Article
- The Dynamics, Causes, and Impacts of Mammalian Evolutionary Rates Revealed by the Analyses of Capybara Draft Genome Sequences.Genome biology and evolution · 2020Article
- Losses of human disease-associated genes in placental mammals.NAR genomics and bioinformatics · 2020Article
- A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers.GigaScience · 2020Article
- Identification and Conservation Analysis ofGenes · 2019Article
- Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution.Nature communications · 2018Article
- Article
- Conserved non-coding elements: developmental gene regulation meets genome organization.Nucleic acids research · 2017Review
- Differential Gene Expression in the Human Brain Is Associated with Conserved, but Not Accelerated, Noncoding Sequences.Molecular biology and evolution · 2017Article
- Dynamics of genome size evolution in birds and mammals.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Evolution ofFrontiers in physiology · 2017Article
- Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle.Genome biology and evolution · 2016Article
- Controlling for Phylogenetic Relatedness and Evolutionary Rates Improves the Discovery of Associations Between Species' Phenotypic and Genomic Differences.Molecular biology and evolution · 2016Article
- Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences.Genome biology and evolution · 2016Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Conserved non-protein-coding DNA elements (CNEs) often encode cis-regulatory elements and are rarely lost during evolution. However, CNE losses that do occur can be associated with phenotypic changes, exemplified by pelvic spine loss in sticklebacks. Using a computational strategy to detect complete loss of CNEs in mammalian genomes while strictly controlling for artifacts, we find >600 CNEs that are independently lost in at least two mammalian lineages, including a spinal cord enhancer near GDF11. We observed several genomic regions where multiple independent CNE loss events happened; the most extreme is the DIAPH2 locus. We show that CNE losses often involve deletions and that CNE loss frequencies are non-uniform. Similar to less pleiotropic enhancers, we find that independently lost CNEs are shorter, slightly less constrained and evolutionarily younger than CNEs without detected losses. This suggests that independently lost CNEs are less pleiotropic and that pleiotropic constraints contribute to non-uniform CNE loss frequencies. We also detected 35 CNEs that are independently lost in the human lineage and in other mammals. Our study uncovers an interesting aspect of the evolution of functional DNA in mammalian genomes. Experiments are necessary to test if these independently lost CNEs are associated with parallel phenotype changes in mammals.
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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.