Nucleosome patterning evolution: steady aim despite moving targets

Mol Syst Biol. 6: 376Molecular systems are the scaffolding on which natural selection builds. Comparing the tendency of different molecular mechanisms to generate tolerable and useful raw genetic variation is a challenging interdisciplinary problem. Modulation of gene expression is thought to be an important source of interspecific phenotypic divergence, and as new mechanisms are revealed, their potential roles must be considered. In this issue of Molecular Systems Biology , Tirosh et al (2010) use an interspecies hybrid approach to examine the genetic basis of variation in nucleosome arrangement and its potential to explain differences in gene expression. They find that most nucleosome occupancy and position differences are explained by changes in nearby DNA, and these differences prove to be surprisingly poor predictors of gene expression differences between species.If a gene differs in expression between two species, the causal genetic locus of variation could either be linked to the gene itself ( cis ) or located somewhere else ( trans ). With a few assumptions, whether the locus of change is in cis or trans can often be determined by examining gene expression in a hybrid of the two species (Wittkopp et al , 2004; Tirosh et al , 2009). In purely trans cases, the alleles of both species will be expressed identically in the hybrid, whereas alleles will …