cis versus trans effects

Zhang X & Borevitz JO 2009 Global analysis of allele-specific expression in Arabidopsis thaliana. Genetics 182:943-954.

  • in a single hybrid pair, cis variation is not tested across segregating trans backgrounds
  • thus, the cis × trans effect cannot be dissected
  • a recent study in Drosophila suggests however that cis × trans dependent regulation may not be common (Wittkopp et al. 2008a)
  • the approach of dissecting cis- and trans-regulatory variation using F1 hybrid system, however, has potential drawbacks
  • the detection of cis effect relies on the subtraction of hybrid cis effect from parental expression difference
  • in the hybrid both additive trans effect and nonadditive trans × trans and cis × trans interaction could occur
  • the interpretation of the detected trans effect could be complicated when epistatic interaction is common
  • another drawback of this approach is that epigenetic regulation could potentially interfere with the detection of cis-genetic variation