ArticleGenome biology and evolution2009
A universal nonmonotonic relationship between gene compactness and expression levels in multicellular eukaryotes.
Article in Genome biology and evolution, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
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Who cites it
29 citing papers in PubMed, 1 synthesis or guideline pooled it, 45 citations in OpenAlex.
- The transcriptional trajectories of pluripotency and differentiation comprise genes with antithetical architecture and repetitive-element content.BMC biology · 2021Pooled it
- Identification of Human Global, Tissue and Within-Tissue Cell-Specific Stably Expressed Genes at Single-Cell Resolution.International journal of molecular sciences · 2022Article
- Interplay between gene expression and gene architecture as a consequence of gene and genome duplications: evidence from metabolic genes ofPhysiology and molecular biology of plants : an international journal of functional plant biology · 2022Article
- Epigenomic signatures on paralogous genes reveal underappreciated universality of active histone codes adopted across animals.Computational and structural biotechnology journal · 2022Article
- Genome-Wide Identification and Evaluation of New Reference Genes for Gene Expression Analysis Under Temperature and Salinity Stresses inFrontiers in genetics · 2019Article
- Variation of gene expression in plants is influenced by gene architecture and structural properties of promoters.PloS one · 2019Article
- Comparative analysis of housekeeping and tissue-selective genes in human based on network topologies and biological properties.Molecular genetics and genomics : MGG · 2016Article
- A model for competition for ribosomes in the cell.Journal of the Royal Society, Interface · 2016Article
- Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome.Genome biology · 2015Article
- Computer analysis of protein functional sites projection on exon structure of genes in Metazoa.BMC genomics · 2015Article
- Length and GC content variability of introns among teleostean genomes in the light of the metabolic rate hypothesis.PloS one · 2014Article
- Article
- A simple model to explain evolutionary trends of eukaryotic gene architecture and expression: how competition between splicing and cleavage/polyadenylation factors may affect gene expression and splice-site recognition in eukaryotes.BioEssays : news and reviews in molecular, cellular and developmental biology · 2013Review
- Frequency of intron loss correlates with processed pseudogene abundance: a novel strategy to test the reverse transcriptase model of intron loss.BMC biology · 2013Article
- Three independent determinants of protein evolutionary rate.Journal of molecular evolution · 2013Review
- Association of intron loss with high mutation rate in Arabidopsis: implications for genome size evolution.Genome biology and evolution · 2013Article
- Evolution of the correlation between expression divergence and protein divergence in mammals.Genome biology and evolution · 2013Article
- Gene expression levels are correlated with synonymous codon usage, amino acid composition, and gene architecture in the red flour beetle, Tribolium castaneum.Molecular biology and evolution · 2012Article
- Origin and evolution of spliceosomal introns.Biology direct · 2012Review
- Persisting viral sequences shape microbial CRISPR-based immunity.PLoS computational biology · 2012Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
Analysis of gene architecture and expression levels of four organisms, Homo sapiens, Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis thaliana, reveals a surprising, nonmonotonic, universal relationship between expression level and gene compactness. With increasing expression level, the genes tend at first to become longer but, from a certain level of expression, they become more and more compact, resulting in an approximate bell-shaped dependence. There are two leading hypotheses to explain the compactness of highly expressed genes. The selection hypothesis predicts that gene compactness is predominantly driven by the level of expression, whereas the genomic design hypothesis predicts that expression breadth across tissues is the driving force. We observed the connection between gene expression breadth in humans and gene compactness to be significantly weaker than the connection between expression level and compactness, a result that is compatible with the selection hypothesis but not the genome design hypothesis. The initial gene elongation with increasing expression level could be explained, at least in part, by accumulation of regulatory elements enhancing expression, in particular, in introns. This explanation is compatible with the observed positive correlation between intron density and expression level of a gene. Conversely, the trend toward increasing compactness for highly expressed genes could be caused by selection for minimization of energy and time expenditure during transcription and splicing and for increased fidelity of transcription, splicing, and/or translation that is likely to be particularly critical for highly expressed genes. Regardless of the exact nature of the forces that shape the gene architecture, we present evidence that, at least, in animals, coding and noncoding parts of genes show similar architectonic trends.
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