ArticleBioinformatics (Oxford, England)2012
Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context.Frontiers in molecular biosciences · 2022Review
- The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research.Insects · 2021Article
- Functional and structural basis of extreme conservation in vertebrate 5' untranslated regions.Nature genetics · 2021Article
- 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
- Dark-matter matters: Discriminating subtle blood cancers using the darkest DNA.PLoS computational biology · 2019Article
- Introduction of 'Generalized Genomic Signatures' for the quantification of neighbour preferences leads to taxonomy- and functionality-based distinction among sequences.Scientific reports · 2019Article
- Evolutionary stability of topologically associating domains is associated with conserved gene regulation.BMC biology · 2018Article
- Ultraconserved Elements Occupy Specific Arenas of Three-Dimensional Mammalian Genome Organization.Cell reports · 2018Article
- Differential Gene Expression in the Human Brain Is Associated with Conserved, but Not Accelerated, Noncoding Sequences.Molecular biology and evolution · 2017Article
- SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles.Bioinformatics (Oxford, England) · 2016Article
- Allele frequencies of variants in ultra conserved elements identify selective pressure on transcription factor binding.PloS one · 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
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2 authors.
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Abstract
motivationGenomic context analysis, also known as phylogenetic profiling, is widely used to infer functional interactions between proteins but rarely applied to non-coding cis-regulatory DNA elements. We were wondering whether this approach could provide insights about utlraconserved non-coding elements (UCNEs). These elements are organized as large clusters, so-called gene regulatory blocks (GRBs) around key developmental genes. Their molecular functions and the reasons for their high degree of conservation remain enigmatic.
resultsIn a special setting of genomic context analysis, we analyzed the fate of GRBs after a whole-genome duplication event in five fish genomes. We found that in most cases all UCNEs were retained together as a single block, whereas the corresponding target genes were often retained in two copies, one completely devoid of UCNEs. This 'winner-takes-all' pattern suggests that UCNEs of a GRB function in a highly cooperative manner. We propose that the multitude of interactions between UCNEs is the reason for their extreme sequence conservation. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online and at http://ccg.vital-it.ch/ucne/
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