Minisymposium 19: Mechanisms of Gene Regulation
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M1903: EVOLUTIONARY and Functional Diversification of Chromatin and the Epigenome
Chromatin is comprised of >100 families of proteins with diverse molecular functions, ranging from structural components and histone modifying enzymes to RNAi machinery and nucleosome remodeling complexes, which collectively comprise the "epigenome", control and integrate patterns of gene expression, and mediate chromosome condensation, genetic recombination and DNA repair. By molecular phylogenetic analyses of more than 60 protein families we estimated the number of clades of chromatin proteins that existed prior to divergence of plants and animals, monocots and dicots, fission and budding yeasts, and insects and vertebrates, and identified new clades representing ancient gene duplications that arose prior to each divergence. In plants histone methyltransferases diversified at 5x the rate of duplication of histone acetylases/deacetylases, whereas these families expanded at similar rates in animals. RNAi interference-directed chromatin modification factors have expanded dramatically in plants as compared to animals, consistent with a much greater role for RNAi-mediated control in plants, possibly involving systemic RNA signals that act on chromatin and transmit epigenetic information throughout the plant. The evolution of new RNAi-mediated functions was often associated with positive selection on branches leading to new clades. During the evolution of dicotyledous plants, duplications of multiple polycomb proteins contributed to the evolution of vernalization and imprinting, with positive selection acting in newly arisen clades which contain genes known to be involved in these functions in Arabidopsis. Dicot-specific duplications also arose in the AP1, SOC1, FLC, and SVP clades of MADS box genes that control flowering in Arabidopsis, several of which were also subject to positive selection. In each case, positive selection appears to have acted in the time interval following the dicot-specific duplication and preceeding the divergence of ancestors of Arabidopsis and poplar (eurosids I and eurosids II). One conclusion of our observations on MADS genes involved in flowering control is that the system for control of flowering by vernalization did not necessarily arise independently in monocots and dicots, contrary to previously published interpretations.
