Biochemical and Biophysical Research Communications
Selection for the miniaturization of highly expressed genes
Section snippets
Materials and methods
The gene characters were parsed from the annotated genomes downloaded from NCBI (ftp://ftp.ncbi.nih.gov/genomes/): Homo sapiens (build 36 version 1), Mus musculus (build 35 version 1), and A. thaliana (updated Nov. 04, 2005). The protein characters were estimated using the SwissPfam version 20 (ftp://ftp.genetics.wustl.edu/pub/Pfam/). In the case of alternative splicing variants, we retained the longest mRNA for analysis.
We determined the gene expression breadth, level and tissue specificity
Highly expressed genes are compact, but widely expressed genes are not
HK genes are ubiquitously expressed in all tissues, so their size evolution is not related to expression breadth. We found that the compactness of HK genes is correlated with their expression levels except that highly expressed Arabidopsis HK genes have longer introns (Table 1).
Besides ubiquitous expression, some researchers used other additional criteria (e.g. basic cellular functions) to define HK genes more stringently [13]. In well-compiled sets of human housekeeping genes, we got stronger
Discussion
In A. thaliana, the highly expressed genes tend to have longer introns (Table 1, [35]), while the genes with complex expression pattern do not have longer introns (Table 2). Thus, the majority of introns in plants may not play important roles in expression complexity other than increasing expression level [36].
We successively find evidence against genome design hypothesis [14] as well as the transcription-associated mutational bias hypothesis [5], [6], and support the energetic cost hypothesis
Acknowledgments
We thank the anonymous referee for useful comments. This research was supported by NSFC (30270695) and BNU.
References (39)
Low-level illegitimate transcription of genes may be to silence the genes
Biochem. Biophys. Res. Commun.
(2005)- et al.
Human housekeeping genes are compact
Trends Genet.
(2003) Compactness of human housekeeping genes: selection for economy or genomic design?
Trends Genet.
(2004)- et al.
The Drosophila homologue of the dystrophin gene—introns containing promoters are the major contributors to the large size of the gene
FEBS Lett.
(2005) - et al.
Human antisense genes have unusually short introns: evidence for selection for rapid transcription
Trends Genet.
(2005) - et al.
Intron size in mammals: complexity comes to terms with economy
Trends Genet.
(2007) Pseudogenes in yeast?
Cell
(1987)- et al.
In plants, highly expressed genes are the least compact
Trends Genet.
(2006) - et al.
How introns influence and enhance eukaryotic gene expression
Trends Biochem. Sci.
(2003) - et al.
Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: A multiple regression to identify sources of variations
Biochem. Biophys. Res. Commun.
(2006)
Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae
Yeast
Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins
Nucleic Acids Res.
Selection for short introns in highly expressed genes
Nat. Genet.
Translational selection and yeast proteome evolution
Genetics
The signature of selection mediated by expression on human genes
Genome Res.
Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence
Genetics
Evolutionary constraints on yeast protein size
BMC Evol. Biol.
Imprinted genes have few and small introns
Nat. Genet.
Access to a messenger RNA sequence or its protein product is not limited by tissue or species specificity
Science
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