ArticleGenome research2006
Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans.
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 30 papers.
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Who cites it
30 citing papers in PubMed, 49 citations in OpenAlex.
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- Pervasive Conservation of Intron Number and Other Genetic Elements Revealed by a Chromosome-level Genome Assembly of the Hyper-polymorphic Nematode Caenorhabditis brenneri.Genome biology and evolution · 2025Article
- Pervasive conservation of intron number and other genetic elements revealed by a chromosome-level genomic assembly of the hyper-polymorphic nematodebioRxiv : the preprint server for biology · 2024Article
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- 3' Untranslated regions mediate transcriptional interference between convergent genes both locally and ectopically in Saccharomyces cerevisiae.PLoS genetics · 2014Article
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- The evolution and functional significance of nested gene structures in Drosophila melanogaster.Genome biology and evolution · 2013Article
- Long noncoding RNAs in C. elegans.Genome research · 2012Article
- RNA-seq analysis of the C. briggsae transcriptome.Genome research · 2012Article
- Family size and turnover rates among several classes of small non-protein-coding RNA genes in Caenorhabditis nematodes.Genome biology and evolution · 2012Article
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- Neighbourhood continuity is not required for correct testis gene expression in Drosophila.PLoS biology · 2010Article
- Positive correlation between gene coexpression and positional clustering in the zebrafish genome.BMC genomics · 2009Article
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Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have systematically examined the correlation between transcriptional expression pattern and the physical layout of gene pairs in the genome of Caenorhabditis elegans using a public tissue-specific SAGE library data set. We find a strong positive correlation in the expression patterns of neighboring gene pairs that are close together and transcribed in the same direction as well as for neighboring pairs that are located on opposing strands and transcribed in divergent directions. Coupling between members of nonoverlapping neighboring gene pairs is independent of operons and decreases to background levels as the distance increases beyond 10 kb. These findings suggest the existence of regional transcriptional domains in the C. elegans genome. In contrast, genes that are on opposing strands and transcribed in convergent directions are less transcriptionally coupled than the genome-wide background, suggesting a mutual inhibition mechanism. We have also examined the conservation and functional consequences of extreme cases of topological entanglement in the C. elegans genome, in which two or more genes physically overlap in their UTRs or coding regions. We have found that overlapping gene pairs are more conserved and are enriched in essential genes and genes that cause various defined phenotypes revealed by RNAi trials. SAGE analysis indicates that genes that are on the same strand, physically overlap, and transcript at the same directions are very highly correlated in gene expression, while overlapping gene pairs in which one member of the pair resides within an intron of the other are weakly, if at all, coupled, similar to convergent overlapping genes.
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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.