The present invention provides methods and compositions that allow for the modulation of the level of at least two polynucleotides or the polypeptides encoded thereby in a plant or plant part. Specifically, the present invention relates to recombinant polynucleotides that are designed to allow for the overexpression of a polynucleotide of interest and also elicits a specific silencing effect on a second polynucleotide of interest. In specific embodiments, the level of at least two agronomically important sequences is modulated. Recombinant polynucleotides capable of eliciting these effects, as well as, plants, plant parts, seeds and grain having the recombinant polynucleotides are also provided.