Post-genomics and the neutral theory: variation and conservation in the tumor necrosis factor-alpha promoter

In the post-genomics era, molecular evolutionary geneticists have come to p ossess the molecular, statistical, and computational tools for estimating t he relative importance of selection and random genetic drift in virtually a ny gene in almost any organism. We have examined single-nucleotide polymorp hisms (SNPs) and nucleotide divergence across a region of approximately 1 k b in the promoter of the human tumor necrosis factor alpha (TNF-alpha) gene . TNF-alpha, which plays an important role in lymphocyte biology and in the pathogenesis of infectious and autoimmune diseases, is tightly regulated a t the level of transcription through sequence-specific binding of transcrip tion factors to cognate binding sites in a relatively small region of the 5 ' non-coding region of the gene. Analysis of the promoter region in 207 hum an chromosomes revealed nine SNPs, none of which were located in regions kn own to be important in transcriptional activation. Comparison with one prom oter sequence in each of seven species of primates revealed 162 nucleotide sites occupied by a monomorphic nucleotide in the human sample but occupied by a different nucleotide in at least one of the primate sequences (a 'fix ed human difference'). The fixed human differences were found outside the r egions known to be important in transcriptional activation, and their large number suggests that they might be effectively neutral (\Ns\ <<1). With re gard to the human SNPs, although the hypothesis Ns similar to 0 cannot be r ejected, the sample configurations suggest that the substitutions might be mildly deleterious. We emphasize the analytical insight to be gained from i nterspecific comparisons: through the interspecific comparisons, 3.1% of th e total sequence information yielded 94.7% of the variable nucleotides. Thi s combined approach, using interspecific comparisons and human polymorphism together with data from functional analyses, provides valuable insights in to the evolutionary history and regulation of a key gene in the human immun e response. (C) 2000 Elsevier Science B.V. All rights reserved.