A genomic study of the inter-ORF distances in Saccharomyces cerevisiae

The genome of eukaryotic microbes is usually quite compacted. The yeast Saccharomyces cerevisiae is one of the best-known examples. Open reading frames (ORFs) occupy about 75% of the total DNA sequence. The existence of other, non-protein coding genes and other genetic elements leaves very little space for gene promoters and terminators. We have performed an in silico study of inter-ORF distances that shows that there is a minimum distance between two adjacent ORFs that depends on the relative orientation between them. Our analyses suggest that different kinds of promoters and terminators exist with regard to their length and ability to overlap each other. The experimental testing of some putative exceptions to the minimum length model in tandemly orientated ORF pairs suggests that, in those cases, defects in promoter or terminator functionality exist that provoke transcription of polycistronic mRNAs.