Gene expression in 3D: Hidden genomic functionality is revealed in the maturing yeast colony (#168)
Human development is a clear example of how multicellular communities of genetically identical cells can generate an astounding level of complexity. We recently showed that the individual cells of the simple model eukaryote, Saccharomyces cerevisiae, display different gene-expression patterns depending on their position within a mature colony. Whereas cells of the colony exterior are metabolically active, the cells of the colony interior are starving. To our surprise, a disproportionately large number of genes that were differentially expressed between the inner and outer layers of the colony have no known function, encoding either uncharacterized proteins or being non-coding RNAs. To better understand how the growth environment of yeast shapes gene-expression, we used a custom RNA-seq approach to transcriptionally profile yeast cells growing in either the standard laboratory conditions (liquid culture with high glucose and high aeration) and compared these to maturing (2, 3 and 4 day) yeast colonies grown on nutritionally identical solid media. These experiments reveal that the mature yeast colony expresses a large proportion of its genome that is silent under standard conditions. Among genes specifically unregulated in the colony are, non-coding RNA, transcription factors, regulatory RNA-binding proteins, and a suite of enzymes with catabolic functions that are normally expressed at low levels or in only a few cells in the liquid culture population. Of particular interest to us is Ngl3, a poorly characterized deadenylase whose expression is unregulated ~50 fold in cells growing as colonies and whose expression is limited to the colony interior. We will present data showing that Ngl3 is a homolog of the metazoan protein Nocturnin, a deadenylase essential for normal fat metabolism. We will report on our current work in search of the targets of deadenylation by Ngl3 in the mature yeast colony.