title: Impact of GC content on gene expression pattern in chicken.
abstract: BACKGROUND
  GC 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.
  
  
  METHODS
  Only 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.
  
  
  RESULTS
  In 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.
  
  
  CONCLUSIONS
  GC content is significantly associated with gene expression pattern and could be one of the important regulation factors in the chicken genome.
authors.affiliation: Department of Biological Technology, Jiangxi Educational Institute, Jiangxi, Nanchang 330029, China.
authors.forename: You Sheng
authors.initials: YS
authors.lastname: Rao
authors.forename: Xue Wen
authors.initials: XW
authors.lastname: Chai
authors.forename: Zhang Feng
authors.initials: ZF
authors.lastname: Wang
authors.forename: Qing Hua
authors.initials: QH
authors.lastname: Nie
authors.forename: Xi Quan
authors.initials: XQ
authors.lastname: Zhang
mesh_terms: D020121:5' Untranslated Regions; D000818:Animals; D001482:Base Composition; D002645:Chickens; D016678:Genome; D016366:Open Reading Frames; D014158:Transcription, Genetic
chemical_list: D020121:5' Untranslated Regions
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