Selection for short introns in highly expressed genes

@article{CastilloDavis2002SelectionFS,
  title={Selection for short introns in highly expressed genes},
  author={Cristian I. Castillo-Davis and Sergei L. Mekhedov and Daniel L. Hartl and Eugene V. Koonin and Fyodor A. Kondrashov},
  journal={Nature Genetics},
  year={2002},
  volume={31},
  pages={415-418}
}
Transcription is a slow and expensive process: in eukaryotes, approximately 20 nucleotides can be transcribed per second at the expense of at least two ATP molecules per nucleotide. Thus, at least for highly expressed genes, transcription of long introns, which are particularly common in mammals, is costly. Using data on the expression of genes that encode proteins in Caenorhabditis elegans and Homo sapiens, we show that introns in highly expressed genes are substantially shorter than those in… 
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479 Citations
Highly Influential Citations
27
Background Citations
247
Methods Citations
12
Results Citations
16

479 Citations

Evidence against the energetic cost hypothesis for the short introns in highly expressed genes
TLDR
Qualitative estimation shows that the deleterious effect of long introns in highly expressed genes is too negligible to be efficiently selected against in mammals and should not be attributed to energy constraint.
Higher frequency of intron loss from the promoter proximally paused genes of Drosophila melanogaster
TLDR
It is suggested that transcription delay is comparable to splicing delay only when the intron is 28.5 kb or larger, which is greater in size than 95% of vertebrate introns, 99.5% of Drosophila introns and all the annotated introns of Saccharomyces cerevisiae and Arabidopsis thaliana.
Gametophytic Selection in Arabidopsis thaliana Supports the Selective Model of Intron Length Reduction
TLDR
Observations support the view that selection for efficiency contributes to the reduction in intron length and provide the first report of a molecular signature of strong gametophytic selection.
The Small Introns of Antisense Genes Are Better Explained by Selection for Rapid Transcription Than by “Genomic Design”
TLDR
It is shown that the effects of the economy model arguing that the time that expression takes is more important than the energetic cost, such that some weakly but rapidly expressed genes might also have small introns are not specific to noncoding RNAs and that the predictions of the “genomic design” model for the most part are not upheld.
Intron Length Coevolution across Mammalian Genomes
TLDR
The results reveal a novel aspect of gene coevolution and provide a means to identify genes, protein complexes and biological processes that may be particularly sensitive to changes in transcriptional dynamics.
Relationship between Gene Compactness and Base Composition in Rice and Human Genome
TLDR
It is suggested that in GC-rich rice genes long introns are under selection for enhancing transcriptional efficiency by modulating pre-mRNA secondary structural stability and evolutionary mechanisms behind genome organization are different between these two genomes.
Analysis of intronless genes involved in oscillation and differentiation
TLDR
This research set out to elucidate the functions of intronless genes in humans by studying their involvement in the expression pattern of oscillatory gene that occurs in the pre-somitic mesoderm of developing embryo.
Selection for the miniaturization of highly expressed genes.
Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes
TLDR
A model whereby codon use in highly expressed genes, including optimal, wobble, and non-optimal codons, and their tRNA abundances, as well as amino acid use, have been influenced by adaptation for various functional roles in translation within this cricket is suggested.
Abundance of dinucleotide repeats and gene expression are inversely correlated: a role for gene function in addition to intron length.
TLDR
It is observed that even after controlling for the effects of GC and average intron lengths, the effect of repeats albeit somewhat weaker was persistent and definite, and suggest that negative selection of (TG/CA)(n>or=12) microsatellites in the evolution of the highly expressed genes was also controlled by gene function in addition to intron length.
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