BackgroundCoordinated cell growth and development requires that cells regulate the expression of large sets of genes in an appropriate manner, and one of the most complex and metabolically demanding pathways that cells must manage is that of ribosome biogenesis. Ribosome biosynthesis depends upon the activity of hundreds of gene products, and it is subject to extensive regulation in response to changing cellular conditions. We previously described an unusual property of the genes that are involved in ribosome biogenesis in yeast; a significant fraction of the genes exist on the chromosomes as immediately adjacent gene pairs. The incidence of gene pairing can be as high as 24% in some species, and the gene pairs are found in all of the possible tandem, divergent, and convergent orientations.ResultsWe investigated co-regulated gene sets in S. cerevisiae beyond those related to ribosome biogenesis, and found that a number of these regulons, including those involved in DNA metabolism, heat shock, and the response to cellular stressors were also significantly enriched for adjacent gene pairs. We found that as a whole, adjacent gene pairs were more tightly co-regulated than unpaired genes, and that the specific gene pairing relationships that were most widely conserved across divergent fungal lineages were correlated with those genes that exhibited the highest levels of transcription. Finally, we investigated the gene positions of ribosome related genes across a widely divergent set of eukaryotes, and found a significant level of adjacent gene pairing well beyond yeast species.ConclusionWhile it has long been understood that there are connections between genomic organization and transcriptional regulation, this study reveals that the strategy of organizing genes from related, co-regulated pathways into pairs of immediately adjacent genes is widespread, evolutionarily conserved, and functionally significant.

The relative positions that genes occupy on their respective chromosomes can play a critical role in determining how they are regulated at the transcriptional level. For example, a significant fraction of the genes from a variety of coregulated gene sets, including the ribosomal protein (RP) and the rRNA and ribosome biogenesis (RRB) regulons, exist as immediate, adjacent gene pairs. These gene pairs occur in all possible divergent, tandem, and convergent orientations. Adjacent-gene pairing in these regulons is associated with a tighter transcriptional coregulation than is observed for nonpaired genes of the same regulons. In order to define the cis and trans factors that regulate adjacent-gene coregulation (AGC), we conducted a mutational analysis of the convergently oriented RRB gene pair MPP10-YJR003C. We observed that coupled corepression of the gene pair under heat shock was abrogated when the two genes were separated by an actively expressed RNA polymerase (Pol) II transcription unit (the LEU2 gene) but not when the inserted LEU2 gene was repressed. In contrast, the insertion of an RNA Pol III-transcribed tRNA (Thr) gene did not disrupt the coregulated repression of MPP10 and YJR003C. A targeted screen of mutants defective in regulating chromosome architecture revealed that the Spt20, Snf2, and Chd1 proteins were required for coupling the repression of YJR003C to that of MPP10. Nucleosome occupancy assays performed across the MPP10 and YJR003C promoter regions revealed that the mechanism of corepression of the gene pair was not related to the repositioning of nucleosomes across the respective gene promoters.

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 MPP10-YJR003C RRB gene pair has shown that the transcriptional response of both genes is controlled from the MPP10 promoter. Our results show that the ability of the MPP10 promoter to control the transcription of its neighboring gene is specific to YJR003C. Finally, we find that the co-regulation of this gene pair is not mediated by nucleosome remodeling events at either promoter.