ArticleGenome research2009
Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 48 citations in OpenAlex.
- Article
- MicroRNAs as Indicators into the Causes and Consequences of Whole-Genome Duplication Events.Molecular biology and evolution · 2022Article
- Conserved noncoding sequences conserve biological networks and influence genome evolution.Heredity · 2018Article
- A screen for deeply conserved non-coding GWAS SNPs uncovers a MIR-9-2 functional mutation associated to retinal vasculature defects in human.Nucleic acids research · 2018Article
- Integrated gene mapping and synteny studies give insights into the evolution of a sex proto-chromosome in Solea senegalensis.Chromosoma · 2017Article
- Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle.Genome biology and evolution · 2016Article
- ORegAnno 3.0: a community-driven resource for curated regulatory annotation.Nucleic acids research · 2016Article
- Tunicates: exploring the sea shores and roaming the open ocean. A tribute to Thomas Huxley.Open biology · 2015Review
- Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes.Nature communications · 2014Article
- Whole-genome duplication in teleost fishes and its evolutionary consequences.Molecular genetics and genomics : MGG · 2014Review
- Underreplicated regions in Drosophila melanogaster are enriched with fast-evolving genes and highly conserved noncoding sequences.Genome biology and evolution · 2014Article
- The most deeply conserved noncoding sequences in plants serve similar functions to those in vertebrates despite large differences in evolutionary rates.The Plant cell · 2014Article
- Conserved noncoding elements follow power-law-like distributions in several genomes as a result of genome dynamics.PloS one · 2014Article
- The mystery of extreme non-coding conservation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Review
- Deep conservation of cis-regulatory elements in metazoans.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Review
- Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development.Nucleic acids research · 2013Article
- Study of Cis-regulatory Elements in the Ascidian Ciona intestinalis.Current genomics · 2013Article
- Vertebrate paralogous conserved noncoding sequences may be related to gene expressions in brain.Genome biology and evolution · 2013Article
- How much does the amphioxus genome represent the ancestor of chordates?Briefings in functional genomics · 2012Review
- Evaluation of the role of functional constraints on the integrity of an ultraconserved region in the genus Drosophila.PLoS genetics · 2012Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Animal genomes possess highly conserved cis-regulatory sequences that are often found near genes that regulate transcription and development. Researchers have proposed that the strong conservation of these sequences may affect the evolution of the surrounding genome, both by repressing rearrangement, and possibly by promoting duplicate gene retention. Conflicting data, however, have made the validity of these propositions unclear. Here, we use a new computational method to identify phylogenetically conserved noncoding elements (PCNEs) in a manner that is not biased by rearrangement and duplication. This method is powerful enough to identify more than a thousand PCNEs that have been conserved between vertebrates and the basal chordate amphioxus. We test 42 of our PCNEs in transgenic zebrafish assays--including examples from vertebrates and amphioxus--and find that the majority are functional enhancers. We find that PCNEs are enriched around genes with ancient synteny conservation, and that this association is strongest for extragenic PCNEs, suggesting that cis-regulatory interdigitation plays a key role in repressing genome rearrangement. Next, we classify mouse and zebrafish genes according to association with PCNEs, synteny conservation, duplication history, and presence in bidirectional promoter pairs, and use these data to cluster gene functions into a series of distinct evolutionary patterns. These results demonstrate that subfunctionalization of conserved cis-regulation has not been the primary determinate of gene duplicate retention in vertebrates. Instead, the data support the gene balance hypothesis, which proposes that duplicate retention has been driven by selection against dosage imbalances in genes with many protein connections.
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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.