Abstract
BackgroundGC content varies greatly between different genomic regions in many eukaryotes. In order to determine whether this organization named isochore organization influences gene expression patterns, the relationship between GC content and gene expression has been investigated in man and mouse. However, to date, this question is still a matter for debate. Among the avian species, chicken (Gallus gallus) is the best studied representative with a complete genome sequence. The distinctive features and organization of its sequence make it a good model to explore important issues in genome structure and evolution.MethodsOnly nuclear genes with complete information on protein-coding sequence with no evidence of multiple-splicing forms were included in this study. Chicken protein coding sequences, complete mRNA sequences (or full length cDNA sequences), and 5′ untranslated region sequences (5′ UTR) were downloaded from Ensembl and chicken expression data originated from a previous work. Three indices i.e. expression level, expression breadth and maximum expression level were used to measure the expression pattern of a given gene. CpG islands were identified using hgTables of the UCSC Genome Browser. Correlation analysis between variables was performed by SAS Proprietary Software Release 8.1.ResultsIn chicken, the GC content of 5′ UTR is significantly and positively correlated with expression level, expression breadth, and maximum expression level, whereas that of coding sequences and introns and at the third coding position are negatively correlated with expression level and expression breadth, and not correlated with maximum expression level. These significant trends are independent of recombination rate, chromosome size and gene density. Furthermore, multiple linear regression analysis indicated that GC content in genes could explain approximately 10% of the variation in gene expression.ConclusionsGC content is significantly associated with gene expression pattern and could be one of the important regulation factors in the chicken genome.
Highlights
GC content varies greatly between different genomic regions in many eukaryotes
In a study on the human genome, Vinogradov [8] showed that a correlation existed between the GC content in genes and the maximum level of gene expression among tissues but that the promoter CpG island and gene CpG levels were more strongly related to expression breadth, which suggests that the variations of GC content and CpG level could determine the characteristics of gene expression in a synergistic interplay with transcription-factor-binding sites
The sequence collection contained 8631 coding DNA sequences (CDS), each corresponding to a unique gene in the Gallus gallus genome
Summary
In order to determine whether this organization named isochore organization influences gene expression patterns, the relationship between GC content and gene expression has been investigated in man and mouse. To date, this question is still a matter for debate. In order to investigate whether the isochore structure of a genome influences gene expression patterns, several studies have analyzed the relationship between GC content and gene expression in man and mouse. Based on different measures of gene expression (EST, SAGE and microarray) and GC content in human and mouse genomes, Sémon et al [11] showed that the correlations (either positive or negative) between GC content and gene expression were very weak. This question is still a matter for debate
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