Regulation of transcription can be a complex process in which many cis-and trans-interactions determine the final pattern of expression. Among these interactions are trans-interactions mediated by the pairing of homologous chromosomes. These transeffects are wide ranging, affecting gene regulation in many species and creating complex possibilities in gene regulation. Here we describe a novel case of trans-interaction between alleles of the Malic enzyme (Men) locus in Drosophila melanogaster that results in allele-specific, non-additive gene expression. Using both empirical biochemical and predictive bioinformatic approaches, we show that the regulatory elements of one allele are capable of interacting in trans with, and modifying the expression of, the second allele. Furthermore, we show that nonlocal factors-different genetic backgrounds-are capable of significant interactions with individual Men alleles, suggesting that these trans-effects can be modified by both locally and distantly acting elements. In sum, these results emphasize the complexity of gene regulation and the need to understand both small-and large-scale interactions as more complete models of the role of trans-interactions in gene regulation are developed.T HE regulation of gene expression is a complex process often involving many levels of organization. In a simple model, gene expression is determined by intragenic interactions (e.g., enhancer-promoter interactions occurring in cis on the same chromosome). In more complex models of regulation, expression is also influenced by the threedimensional genomic structure and organization of chromosomes. In the latter, more realistic models, nuclear organization governs interactions between neighboring genetic elements, such as transcription factories, heterochromatin, homologous chromosomes, and genes that are capable of acting in trans to modulate gene expression (reviewed in Henikoff and Comai 1998;Wu and Morris 1999;Lanctot et al. 2007;Xu and Cook 2008). These transinteractions create levels of complexity in gene regulation involving interphase chromatin structuring, its impact on pairing of homologs, and the potential exchange of transcriptional or regulatory proteins between homologs. One such trans-interaction, transvection, is the modification of gene activity through interactions between the regulatory elements of one allele and its homolog on the homologous chromosome (reviewed by Pirrotta 1999;Wu and Morris 1999;Duncan 2002). Here we describe a case of trans-interaction at the Malic enzyme locus (Men) (Merritt et al. 2005), potentially transvection, and examine interactions between putative regulatory elements on homologous chromosomes.The term "transvection" was first coined by E. B. Lewis (1954) to describe complementation and trans-interactions between two Ultrabithorax (Ubx) alleles in Drosophila. Lewis found that certain Ubx alleles were able to complement each other and that this complementation could be interrupted by chromosomal rearrangements that disrupted local homolog p...

The evolutionary significance of molecular variation is still contentious, with much current interest focusing on the relative contribution of structural changes in proteins versus regulatory variation in gene expression. We present a population genetic and biochemical study of molecular variation at the malic enzyme locus (Men) in Drosophila melanogaster. Two amino acid polymorphisms appear to affect substrate-binding kinetics, while only one appears to affect thermal stability. Interestingly, we find that enzyme activity differences previously assigned to one of the polymorphisms may, instead, be a function of linked regulatory differences. These results suggest that both regulatory and structural changes contribute to differences in protein function. Our examination of the Men coding sequences reveals no evidence for selection acting on the polymorphisms, but earlier work on this enzyme indicates that the biochemical variation observed has physiological repercussions and therefore could potentially be under natural selection.