ArticleGenome biology2011
Support for multiple classes of local expression clusters in Drosophila melanogaster, but no evidence for gene order conservation.
Article in Genome biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed, 53 citations in OpenAlex.
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- Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks.BMC genomics · 2019Article
- Large-scale mammalian genome rearrangements coincide with chromatin interactions.Bioinformatics (Oxford, England) · 2019Article
- Gene Repositioning Is Under Constraints After Evolutionary Conserved Gene Neighborhood Separate.Frontiers in genetics · 2019Article
- Pervasive coexpression of spatially proximal genes is buffered at the protein level.Molecular systems biology · 2017Article
- Evolutionary origin and function of NOX4-art, an arthropod specific NADPH oxidase.BMC evolutionary biology · 2017Article
- A benchmark of gene expression tissue-specificity metrics.Briefings in bioinformatics · 2017Article
- Shared regulatory sites are abundant in the human genome and shed light on genome evolution and disease pleiotropy.PLoS genetics · 2017Article
- Transcriptional Interference Promotes Rapid Expression Divergence of Drosophila Nested Genes.Genome biology and evolution · 2016Article
- The Role of Transcription Factors at Antisense-Expressing Gene Pairs in Yeast.Genome biology and evolution · 2016Article
- Article
- Putative synaptic genes defined from a Drosophila whole body developmental transcriptome by a machine learning approach.BMC genomics · 2015Article
- Neighboring Genes Show Correlated Evolution in Gene Expression.Molecular biology and evolution · 2015Article
- The clustering of functionally related genes contributes to CNV-mediated disease.Genome research · 2015Article
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2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGene order in eukaryotic genomes is not random, with genes with similar expression profiles tending to cluster. In yeasts, the model taxon for gene order analysis, such syntenic clusters of non-homologous genes tend to be conserved over evolutionary time. Whether similar clusters show gene order conservation in other lineages is, however, undecided. Here, we examine this issue in Drosophila melanogaster using high-resolution chromosome rearrangement data.
resultsWe show that D. melanogaster has at least three classes of expression clusters: first, as observed in mammals, large clusters of functionally unrelated housekeeping genes; second, small clusters of functionally related highly co-expressed genes; and finally, as previously defined by Spellman and Rubin, larger domains of co-expressed but functionally unrelated genes. The latter are, however, not independent of the small co-expression clusters and likely reflect a methodological artifact. While the small co-expression and housekeeping/essential gene clusters resemble those observed in yeast, in contrast to yeast, we see no evidence that any of the three cluster types are preserved as synteny blocks. If anything, adjacent co-expressed genes are more likely to become rearranged than expected. Again in contrast to yeast, in D. melanogaster, gene pairs with short intergene distance or in divergent orientations tend to have higher rearrangement rates. These findings are consistent with co-expression being partly due to shared chromatin environment.
conclusionsWe conclude that, while similar in terms of cluster types, gene order evolution has strikingly different patterns in yeasts and in D. melanogaster, although recombination is associated with gene order rearrangement in both.
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