Specific cell types or tissues adjust their gene expression programs in response to sensory stimuli to help an organism cope with its environment. However, transcriptome-wide analyses are often limited by a lack of spatial resolution when studying whole-animal samples. This difficulty makes it challenging to identify the extent of broader gene expression differences in individual tissues or in specific cell types in vivo.
To tackle this problem, we adapted the Translating Ribosome Affinity Purification method (TRAP) (Heiman et al. 2008) in C. elegans. In TRAP, cell-type specific promoters drive expression of eGFP-tagged Ribosomal Protein L10a of the Large subunit to tag sets of genetically defined cell types in vivo. These GFP-tagged ribosomes can be subsequently affinity purified to obtain enriched populations of ribosome-associated mRNAs from cells of interest. We have recently coupled TRAP to deep sequencing and computational analyses to identify tissue- and neuron-specific patterns of gene and isoform abundance.
By using TRAP, we globally surveyed the repertoire of mRNAs in the nervous system and specific neuronal classes expressing the neurotransmitters dopamine and serotonin. Comparative analyses between these samples and non-neuronal tissues revealed hundreds of tissue- and neuron-biased mRNA isoforms, and neuronal-enriched mRNAs encoding conserved proteins whose functions have not been characterized. Among these we found elc-2/ElonginC/TCEB1, a regulatory subunit of the transcription elongation factor complex Elongin/SIII. Using a GFP-tagged fosmid we found that ELC-2 protein is selectively expressed in a pair of sensory neurons that we confirmed to be the serotonergic ADFs.
ADF neurons are a hub for integrating several stress responses that ultimately lead to the release of serotonin to alter animal physiology. We unexpectedly found that upon heat shock ELC-2 redistributes in the ADF soma, becoming more nuclear enriched. Concomitantly, a backcrossed natural variant containing an elc-2 deletion fails to increase pharyngeal pumping rates upon heat shock, a phenotype of increased serotonin release. We are investigating whether other stresses also induce ELC-2 redistribution, and what the role of its nuclear accumulation is for coordinating heat shock-dependent gene regulation in ADF.
We hypothesize that redistribution of this transcription elongation factor subunit ELC-2 may act as a modulator of sensory-dependent transcriptional programs that induce longer lasting neural effects that help the organism successfully respond and adapt to its environment. .
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