ArticleGenome research2009
Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved.
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 32 papers.
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Who cites it
32 citing papers in PubMed.
- Widespread changes in gene expression accompany body size evolution in nematodes.G3 (Bethesda, Md.) · 2024Article
- Widespread changes in gene expression accompany body size evolution in nematodes.bioRxiv : the preprint server for biology · 2023Article
- Systems-level transcriptional regulation of Caenorhabditis elegans metabolism.Molecular systems biology · 2023Article
- Evolution of miRNA-Binding Sites and Regulatory Networks in Cichlids.Molecular biology and evolution · 2022Article
- Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase.Biomolecules · 2021Article
- Evolution of regulatory networks associated with traits under selection in cichlids.Genome biology · 2021Article
- Independent evolution of transcript abundance and gene regulatory dynamics.Genome research · 2020Article
- Night science.Genome biology · 2019Article
- CeNDR, the Caenorhabditis elegans natural diversity resource.Nucleic acids research · 2017Article
- Divergence of ectodermal and mesodermal gene regulatory network linkages in early development of sea urchins.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Article
- Membrane-associated collagens with interrupted triple-helices (MACITs): evolution from a bilaterian common ancestor and functional conservation in C. elegans.BMC evolutionary biology · 2015Article
- The Homeobox Genes of Caenorhabditis elegans and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis.PloS one · 2015Article
- Natural RNA interference directs a heritable response to the environment.Scientific reports · 2014Article
- Evolutionary Dynamics of GLD-1-mRNA complexes in Caenorhabditis nematodes.Genome biology and evolution · 2014Article
- Molecular hyperdiversity defines populations of the nematode Caenorhabditis brenneri.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Nonlinear fitness consequences of variation in expression level of a eukaryotic gene.Molecular biology and evolution · 2013Article
- From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome.PloS one · 2013Article
- Article
- A comparative analysis of transcription factor expression during metazoan embryonic development.PloS one · 2013Article
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2 authors.
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Abstract
Genomic analyses have shown that adjacent genes are often coexpressed. However, it remains unclear whether the observed coexpression is a result of functional organization or a consequence of adjacent active chromatin or transcriptional read-through, which may be free of selective biases. Here, we compare temporal expression profiles of one-to-one orthologs in conserved or divergent genomic positions in two genetically distant nematode species-Caenorhabditis elegans and C. briggsae-that share a near-identical developmental program. We find, for all major patterns of temporal expression, a substantive amount of gene expression divergence. However, this divergence is not random: Genes that function in essential developmental processes show less divergence than genes whose functions are not required for viability. Coexpression of gene neighbors in either species is highly divergent in the other, in particular when the neighborhood is not conserved. Interestingly, essential genes appear to maintain their expression profiles despite changes in neighborhoods suggesting exposure to stronger selection. Our results suggest that a significant fraction of the coexpression observed among gene neighbors may be accounted for by neutral processes, and further that these may be distinguished by comparative gene expression analyses.
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