An Examination of the Mechanism and Conservation of Adjacent Gene Co-regulation in S. Cerevisae and Higher Eukaryotes

<p>Coordinated cell growth and development largely depends on the appropriate regulation of ribosome production. In budding yeast, ribosome production is primarily regulated at the level of transcription. This process involves the coordinated expression of three independently co-regulated gene sets that are necessary to produce the 79 ribosomal proteins (RPs), the 4 heavily processed and modified rRNAs, and the rRNA and ribosome biosynthesis (RRB) genes. Interestingly, in a variety of yeast species, a significant fraction of the RRB and RP genes exist throughout the genome as immediately adjacent gene pairs. Further analysis revealed that the set of paired genes in both regulons are much more tightly co-regulated than the unpaired genes are during changing cellular conditions. Here, we extend this initial observation and provide evidence for adjacent gene pairing in a variety of other functionally related gene sets in yeast. Moreover, we discovered adjacent gene pairing in the ribosome production pathways of higher eukaryotes, including humans. Previous genetic analysis of the yeast <em>MPP10-YJR003C</em> RRB gene pair has shown that the transcriptional response of both genes is controlled from the <em>MPP10</em> promoter. Our results show that the ability of the <em>MPP10</em> promoter to control the transcription of its neighboring gene is specific to <em>YJR003C</em>. Finally, we find that the co-regulation of this gene pair is not mediated by nucleosome remodeling events at either promoter.</p>