Genetic and epigenetic dissection of cis regulatory variation

Divergence in gene expression is of interest because it generates molecular markers for phenotypic variation, potentially including the causes underlying this variation. Alteration of gene expression patterns can have a direct genetic (or epigenetic) basis in cis regulatory polymorphism or can be indirectly regulated by trans-acting factors. Expression mapping studies have begun to reveal the local (suggesting cis) and distant (usually trans) patterns of inheritance of genetic variation that underlies transcriptional polymorphism. The molecular basis that contributes to transcriptional divergence is, however, largely unknown especially for genes under selection that might influence phenotype. Additional genome-wide empirical data from many related organisms are required to dissect cis-, trans-, and cis x trans- dependent sources of variation in gene expression to provide a better understanding of the evolution of transcriptional regulatory networks.