Genomics-driven insights into gene regulation and aging in C. elegans [electronic resource]
Keywords: Genetics

Although the development of high-throughput techniques to quantify gene expression have enabled us to characterize genes that change in various conditions, identifying the regulators that drive these changes remains a challenging problem. Recent efforts to identify direct transcription factor targets provide a foothold to addressing the identification of regulators, by allowing inference of critical factors based on the expression patterns of their targets. However, success in this approach requires an improved ability to infer factor-responsive targets (those regulated by the transcription factor) from direct targets (those bound by the factor). By identifying factor-specific binding sites (i.e., those regions bound by the factor of interest but not by many additional random transcription factors), we found that the link between direct and functional targets was significantly improved -- e.g., although only 26% of significant HLH-1 binding sites correlated with altered expression when HLH-1 was over-expressed, over 40% of factor-specific significant binding sites did so. In the course of this work, we identified HOT (Highly Occupied Target) regions that were bound by more than 65% of factors assayed. Surprisingly, our analysis indicated that these regions were not artifacts of the target identification methodology. Rather, they instead indicate a potentially novel regulatory mechanism for expression of housekeeping genes, as genes associated with HOT regions were highly and ubiquitously expressed and essential for development. Next, we applied this approach to the study of aging. Although genome-wide microarray experiments in C. elegans have identified over a thousand genes with age-dependent expression, only a handful of transcriptional regulators are known to link altered lifespan with modulation of genes that change during wild-type aging. We describe an approach to infer potential regulators of aging and longevity by interrogating direct transcription factor targets generated by the modENCODE project. We identify nine factors with targets significantly enriched for altered expression with age, including three previously shown to modulate lifespan. We further show that for two additional factors, NHR-28 and NHR-76, strains in which these factors are over-expressed show increased lifespan, suggesting that these factors may represent additional links between age-dependent gene expression changes with longevity. This approach identified HOX co-factor unc-62 (Homothorax) as a developmental regulator that binds age-regulated transcripts and modulates lifespan. In the intestine (in which UNC-62 knockdown increases lifespan) we identify multiple activities: UNC-62 binds to and activates both intestine-expressed yolk protein genes that decline with age as well as neuronal-enriched genes that increase in intestinal expression with age. An alternatively spliced, tissue-specific isoform of unc-62 is expressed exclusively in the intestine and declines with age, providing a potential mechanism for distinct activities of UNC-62 between tissues and stages. Thus, UNC-62 provides a proof of principle for uncovering unexplored transcription factors effecting aging and longevity through integrated analysis of developmental regulatory targets.