Enhancer-like Elements and Evolutionary Age of Dictyostelium discoideum Genes: Association with Stage Activity

Abstract The development of the social amoeba Dictyostelium discoideum provides a convenient model for studying the transition from a unicellular to a multicellular state and the accompanying changes in gene expression regulation. The evolutionary age of genes and the activity of enhancer-like elements (ELEs) were comparatively analyzed at four stages of the amoeba life cycle: vegetative, streaming, mound, and fruiting. Calculation of the transcriptomic age index (TAI) showed that the relative contribution of evolutionarily young genes increases during the transition to multicellularity, while ancient genes maintain a high level of expression throughout the entire developmental cycle. Genes associated with ELEs were found to be evolutionarily more ancient and, on average, longer due to the greater length of the coding sequence, with a lower density of introns per gene. Changes in ELE accessibility were most often accompanied by a decrease in expression of neighbor genes, especially within 10 kb, while the total number of identified elements strongly depended on the sequencing depth. The results indicate a combination of a conservative set of ancient enhancer-associated genes with selective activation of young, stage-dependent transcripts at the late stages of D. discoideum development.