Widespread Differential Expression of Coding Region and 3' UTR Sequences in Neurons and Other Tissues.

Mature messenger RNAs (mRNAs) consist of coding sequence (CDS) and 5' and typically expected to show similar abundance within a given neuron. Examining mRNA from defined neurons, we unexpectedly show extremely common unbalanced expression of cognate and CDS sequences; many genes show high duanyu3 relative to CDS, others show high CDS to In situ hybridization (19 of 19 genes) shows a broad range of expression ratios across neurons and tissues. Ratios may be spatially graded or change with developmental age but are consistent across animals. Further, for two genes examined, a duanyu3-to-CDS ratio above a particular threshold in any given neuron correlated with reduced or undetectable protein expression. Our findings raise questions about the role of isolated duanyu3 sequences in regulation of protein expression and highlight the importance of separately examining duanyu3 and CDS sequences in gene expression analyses.

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