Regulation and Evolution of Genes in Ascidians

Abstract

Understanding how the interaction between transcription factors and cis -regulatory systems has evolved and controls gene expression is a key to uncover mechanisms of evolution and development of organisms. As a model system to study gene regulation in development, we have been using a group of primitive chordates, ascidians. Ascidians are also favorable for evolutionary research because of their phylogenetic position near the vertebrates and of the existence of closely-related species with different modes of development. Our recent research focuses on development and function of nervous systems in ascidians. The ascidian larva has a simple central nervous system (CNS) derived from the dorsal neural tube. Here we present two topics in our studies on development and evolution of chordate features in ascidians. Computational and experimental analyses of cis -regulatory DNAs Genes regulated by the same transcription factors are expected to share cis -regulatory elements in their flanking and/or intronic noncoding regions. DNA motifs over-represented in 5’ flanking regions of potentially co-regulated genes were identified by computational analyses of 5’ flanking regions of tissue-specific genes of Ciona intestinalis and Ciona savignyi . Comparative genomics analysis between C. intestinalis and C. savignyi can efficiently predict cis -regulatory sequences important for tissue-specific gene expression. In vivo functional analysis demonstrated the validity of computational prediction of cis -regulatory elements. The sequences and distribution patterns of potential cis -regulatory DNAs can be incorporated into a model promoter structure, and the model can then be used for genome-wide prediction of co-regulated promoters.