Two human gene families display preferences for different nucleotides and have distinct codon usage patterns

Analysis of base composition has proven important for functional gene analysis. By comparing base composition and codon usage between two specific human gene families we were able to show a highly conserved nucleotide distribution among the members of one gene family and a significant difference between the two families. The two groups selected for analysis were the human factor H gene family, which represents six secreted human plasma proteins with functions in immune defense, and a class of four human zinc finger proteins, termed early growth response (EGR) proteins, which represent DNA-binding transcription factors. The nucleotide distribution of each gene family is distinct: members of the factor H gene family represent AT-rich genes, displaying an overall AT nucleotide content of 62.8% and a particular preference for A nucleotides (33.9%). In contrast, the EGR genes are GC-rich (55.9%) and C nucleotides are used in 31.2%. This nucleotide difference affects codon usage among synonymous codons and is considered of biological significance, as it affects DNA stability. The codon preference is particularly high at codon position 3, where each family selects for codons which have the preferred nucleotide at this silent third position. At position 3, A nucleotides are preferred by factor H genes in 36.3% of the 2, 503 codons analyzed, compared to 10% of the 1,876 codons analyzed for the EGR family. In contrast, C nucleotides are used by the EGR family in 48.1%, compared to 16% of the triplets used by the factor H gene family. This comparison of two human gene families shows that nucleotide distribution and codon usage is not uniform within the human organism and the described differences most likely represent selection constraints between the polymorphic factor H and highly conserved EGR genes.