Just had a great talk by Mike McAlear who was visiting us on his way to Poland. He gave a talk about co-regulation of adjustment genes, specifically ribosomal proteins and ribosomal assembly enzymes. I know what you are thinking about now, transcriptional read-through and the like. But it seems to be much more fun than that!
Genes can be on the opposite strands, they can face in opposite directions, but still, there is co-regulation which can not be contributed simply to a shared regulatory system. Something with chromatin structure, probably. Being positioned next to each other was shown to be an important factor for noise in protein expression. Becsei at al. showed in yeast that noise in protein expression is sensitive to gene position in the chromosome, and, consequently, genes positioned next to each other show somewhat correlated behavior. I think it is all different sides of one story...
Adjacent gene pairing plays a role in the coordinated expression of ribosome biogenesis genes MPP10 and YJR003C in Saccharomyces cerevisiae. Arnone JT, McAlear MA. Eukaryot Cell. 2011 Jan;10(1):43-53. PIMD: 21115740
Prime movers of noisy gene expression. Paulsson J. Nat Genet. 2005 Sep;37(9):925-6. PIMD: 16132049
Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Becskei A, Kaufmann BB, van Oudenaarden A. Nat Genet. 2005 Sep;37(9):937-44. PIMD: 16086016
Co-expression of adjacent genes in yeast cannot be simply attributed to shared regulatory system. Tsai HK, Su CP, Lu MY, Shih CH, Wang D. BMC Genomics. 2007 Oct 3;8:352. PIMD: 17910772