Another main research interest is the epigenetic effects of maternal behavior and how epigenetic variation emerge in response to variation in mother-infant interactions experienced during development. She also researches prenatal programming of offspring development and the impact of prenatal exposure to stress, toxins, or nutritional variation on placental and offspring brain gene expression. Paternal-maternal interplay and offspring development is another research main interest of Champagne and is the impact of fathers on mothers and offspring and the epigenetic mechanisms through which this interplay occurs.