The effects of development on gene expression in L4 Caenorhabditis elegans larvae

Organismal development is the most dynamic period of the life cycle yet we have only a rough understanding of the dynamics of gene expression during this period. We explore how development affects gene expression, by a detailed map of the C. elegans transcriptome. We found that over 10,000 genes display changes in expression and explored the properties of genes with different dynamics. A time series experiment was conducted on synchronized populations of C. elegans Bristol N2. The worms were grown in three batches, covering the time points from 42-64 hours post bleaching leading to a dense time series with 1 hour intervals on average. A follow up experiment was conducted using N2 and seven wild-isolates, CB4856, JU1581, JU1921, JU1930, JU1932, JU1944 and JU 1949. These were grown on two different food sources to show the applicability of the generated data as a transcriptional determinant of age. It was found that more than 10,000 genes have a dynamic expression pattern during the L4 stage. We found up- and down-regulated genes and also genes with more specific patterns. One noticeable pattern was a group of genes that is specifically up-regulated around 50 hours. Signs of purifying selection in non-coding regions of string up-regulated genes were found. This is an indication that highly up-regulated genes during development are constrained on their regulatory properties. Using the time-series we show that genotype and environment affect the development and the applicability of transcriptomics data to measure age. Our data help in understanding the transition from larvae to adult worms and can be used te eliminate experimental artefacts due to differences in developmental timing between experiments.