cis versus trans effects

Wang H-Y, Fu Y, McPeek MS, Lu X, Nuzhdin S, Xu A, Lu J, Wu M-L, Wu C-I 2008 Complex genetic interactions underlying expression differences between Drosophila races: analysis of chromosome substitutions. PNAS 105:6362-6367.

• regulation of gene expression is usually separated into cis and trans components
• the separation may become artificial if much of the variation in expression is under multigenic and epistatic (e.g., cis-by-trans) control

• seemingly incongruent results from different studies of expression regulation may be resolvable if the distinction between cis and inclusive cis effects is made
• the analysis of expression in the F1 progeny [both between and within species (Wittkopp et al. 2004, 2008)] may be primarily about the inclusive cis effect

• the contribution of interactive terms to expression variation between populations is > 30% and can be as large as 50%
• cis and trans factors can interact in opposition to each other
• we have observed substantial counterbalancing effects in gene expression between Z and M races (H.-Y.W., unpublished results)