ArticleGenome research2006
Ancient duplicated conserved noncoding elements in vertebrates: a genomic and functional analysis.
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 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
53 citing papers in PubMed, 105 citations in OpenAlex.
- Review
- Mechanisms of enhancer action: the known and the unknown.Genome biology · 2021Review
- Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications.Molecular biology and evolution · 2020Article
- Ancestrally Duplicated Conserved Noncoding Element Suggests Dual Regulatory Roles of HOTAIR in cis and trans.iScience · 2020Article
- Conserved non-coding elements: developmental gene regulation meets genome organization.Nucleic acids research · 2017Review
- Role of the LF-SINE-Derived DistalJournal of pediatric genetics · 2017Article
- Evaluation of IRX Genes and Conserved Noncoding Elements in a Region on 5p13.3 Linked to Families with Familial Idiopathic Scoliosis and Kyphosis.G3 (Bethesda, Md.) · 2016Article
- Molecular evolution and functional divergence of the metallothionein gene family in vertebrates.Journal of molecular evolution · 2014Article
- A reporter assay in lamprey embryos reveals both functional conservation and elaboration of vertebrate enhancers.PloS one · 2014Article
- Purifying selection in deeply conserved human enhancers is more consistent than in coding sequences.PloS one · 2014Article
- The mystery of extreme non-coding conservation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Review
- Chromatin and epigenetic features of long-range gene regulation.Nucleic acids research · 2013Review
- Article
- Vertebrate paralogous conserved noncoding sequences may be related to gene expressions in brain.Genome biology and evolution · 2013Article
- UCNEbase--a database of ultraconserved non-coding elements and genomic regulatory blocks.Nucleic acids research · 2013Article
- Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints.Genome research · 2012Article
- Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements.Bioinformatics (Oxford, England) · 2012Article
- Article
- Origin and evolution of spliceosomal introns.Biology direct · 2012Review
- An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement.Genome research · 2012Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Fish-mammal genomic comparisons have proved powerful in identifying conserved noncoding elements likely to be cis-regulatory in nature, and the majority of those tested in vivo have been shown to act as tissue-specific enhancers associated with genes involved in transcriptional regulation of development. Although most of these elements share little sequence identity to each other, a small number are remarkably similar and appear to be the product of duplication events. Here, we searched for duplicated conserved noncoding elements in the human genome, using comparisons with Fugu to select putative cis-regulatory sequences. We identified 124 families of duplicated elements, each containing between two and five members, that are highly conserved within and between vertebrate genomes. In 74% of cases, we were able to assign a specific set of paralogous genes with annotation relating to transcriptional regulation and/or development to each family, thus removing much of the ambiguity in identifying associated genes. We find that duplicate elements have the potential to up-regulate reporter gene expression in a tissue-specific manner and that expression domains often overlap, but are not necessarily identical, between family members. Over two thirds of the families are conserved in duplicate in fish and appear to predate the large-scale duplication events thought to have occurred at the origin of vertebrates. We propose a model whereby gene duplication and the evolution of cis-regulatory elements can be considered in the context of increased morphological diversity and the emergence of the modern vertebrate body plan.
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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.