A sensitive genetic system for assaying RIP in regions of interspersed homology.

<p>(a) Tester constructs comprise pairs of closely-positioned DNA repeats: the base-pair sequence of the “left” repeat (“Reference”) is held constant and corresponds to an arbitrarily chosen segment of the Neurospora genome, the base-pair sequence of the “right” repeat (“Test”) can be varied as desired. (b) Patterns of interspersed homology (relative to the reference sequence) are defined by the three distances: <b>X</b>—the length of the homologous unit, <b>Y</b>—the separation between homologous units, and <b>Z</b>—the sequence position of the first homologous unit relative to the reference sequence. The sum of <b>X</b> and <b>Y</b> defines the periodicity of interspersed homology. (c) Alignment of a reference sequence and three different test sequences. A minimally effective pattern of interspersed homology is "3H-8N" [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006015#pgen.1006015.ref014" target="_blank">14</a>]. One such pattern, with the sequence position parameter set to 1 (<b>Z</b> = 1), is shown as 3H-8N_1. Two homology patterns examined in this study are 4H-7N_1 and 4H-7N_7.