Quantitative epigenetics: DNA sequence variation need not apply

Abstract

Two recent reports, including one by Reinders and colleagues (pp. 939-950) in the April 15, 2009, issue of Genes & Development, describe the construction of Arabidopsis recombinant inbred populations that maximize epigenetic rather than genetic variation. The distribution and behavior of phenotypic variation in these populations suggest that stable epialleles can control complex quantitative traits. However, stochastic epimutation and transposon movement in these populations present some unexpected technical hurdles to implementing quantitative epigenetic analysis.

Figure 1.

Construction of epiRILs. The scheme for construction of conventional recombinant inbred lines is shown in the left column. A single chromosome pair in a diploid is illustrated. Two different strains (A and B) are intercrossed, and strain-specific polymorphisms (symbolized by yellow vs. blue) will segregate into the F₂ (or backcrossed progeny). Propagation through single-seed descent generates lines that are fixed—homozygous at most loci. The center column of the figure depicts a model for the generation of epiRILs assuming stable inheritance of parental epigenetic states. The underlying genome sequence is the same in the wild-type and epimutator parents with the exception of the met1 or ddm1 mutation (red). The filled boxes that overlay the genome sequence illustrate the epigenetic states of the two parents. The black boxes indicate regions of epigenetic silencing marks, many of which are lost in the mutant parent. In addition, ectopic silencing marks (green boxes) are found in the mutant parent. Assuming faithful epigenetic inheritance of parental epigenetic marks, the resulting epiRIL lines will be composed of epigenetic haplotypes representing blocks derived from the parent chromosomes. The right column describes the sources of additional genetic and epigenetic variation observed in epiRILs, and the single chromosome pair in the inset illustrates the resulting deviations from the idealized scheme shown in the center column.